Identification and characterization of the DNA replication origin recognition complex gene family in the silkworm Bombyx mori.

PubMed

Yang, Hui-Peng; Luo, Su-Juan; Li, Yi-Nü; Zhang, Yao-Zhou; Zhang, Zhi-Fang

2011-10-01

The ORC (origin recognition complex) binds to the DNA replication origin and recruits other replication factors to form the pre-replication complex. The cDNA and genomic sequences of all six subunits of ORC in Bombyx mori (BmORC1-6) were determined by RACE (rapid amplification of cDNA ends) and bioinformatic analysis. The conserved domains were identified in BmOrc1p-6p and the C-terminal of BmOrc6p features a short sequence that may be specific for Lepidoptera. As in other organisms, each of the six BmORC subunits had evolved individually from ancestral genes in early eukaryotes. During embryo development, the six genes were co-regulated, but different ratios of the abundance of mRNAs were observed in 13 tissues of the fifth instar day-6 larvae. Infection by BmNPV (B. mori nucleopolyhedrovirus) initially decreased and then increased the abundance of BmORC. We suggest that some of the BmOrc proteins may have additional functions and that BmOrc proteins participate in the replication of BmNPV.

Co-localization of polar replication fork barriers and rRNA transcription terminators in mouse rDNA.

PubMed

López-estraño, C; Schvartzman, J B; Krimer, D B; Hernández, P

1998-03-27

We investigated the replication of the region where transcription terminates in mouse rDNA. It contains a replication fork barrier (RFB) that behaves in a polar manner, arresting only replication forks moving in the direction opposite to transcription. This RFB consists of several closely spaced fork arrest sites that co-localize with the transcription terminator elements, known as Sal boxes. Sal boxes are the target for mTTF-I (murine transcription termination factor I). These results suggest that both termination of rRNA transcription and replication fork arrest may share cis-acting as well as trans-acting factors. Copyright 1998 Academic Press Limited.

Transcriptional regulation of human papillomavirus type 18 P105 promoter by the co-activator CBP.

PubMed

Valencia-Hernández, Armando; Cuevas-Bennett, Christian; Garrido, Efraín

2007-01-01

Human papillomaviruses (HPVs) are the etiological agents of cervical cancer, with HPV-16 and 18 being the representative types of the higher risk group. The expression of the viral genes with transforming activity (E6 and E7) is controlled by the upstream regulatory region (URR), a segment of the viral genome that contains elements recognized by several transcription factors. We have analyzed the participation of the cellular co-activator CBP on the transcriptional regulation of the HPV-18 URR. We generated mutants and 5' end deletion constructs derived from the HPV-18 URR and evaluated their transcriptional activity performing transient co-transfection assays on C-33A cells with a plasmid that over-expresses the co-activator CBP. We also performed quantitative chromatin immunoprecipitation assays to analyze the participation of the co-activator CBP on the HPV-18 P105 promoter. Our results demonstrate that in C-33A cells CBP acts as a strong activator of the HPV-18 P105 promoter by a mechanism that depends on the integrity of the SP1-binding site, directly correlating with the acetylation of the histone H3 that is involved in nucleosomal stability. We propose a mechanism of regulation of the HPV-18 P105 promoter by the cellular co-activator CBP, recruited by the transcription factor SP1. (c) 2008 S. Karger AG, Basel

Serine 192 in the tiny RS repeat of the adenoviral L4-33K splicing enhancer protein is essential for function and reorganization of the protein to the periphery of viral replication centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oestberg, Sara, E-mail: sara.ostberg@imbim.uu.se; Toermaenen Persson, Heidi, E-mail: heidi.tormanen.persson@imbim.uu.se; Akusjaervi, Goeran, E-mail: goran.akusjarvi@imbim.uu.se

2012-11-25

The adenovirus L4-33K protein is a key regulator involved in the temporal shift from early to late pattern of mRNA expression from the adenovirus major late transcription unit. L4-33K is a virus-encoded alternative splicing factor, which enhances processing of 3 Prime splice sites with a weak sequence context. Here we show that L4-33K expressed from a plasmid is localized at the nuclear margin of uninfected cells. During an infection L4-33K is relocalized to the periphery of E2A-72K containing viral replication centers. We also show that serine 192 in the tiny RS repeat of the conserved carboxy-terminus of L4-33K, which ismore » critical for the splicing enhancer function of L4-33K, is necessary for the nuclear localization and redistribution of the protein to viral replication sites. Collectively, our results show a good correlation between the activity of L4-33K as a splicing enhancer protein and its localization to the periphery of viral replication centers.« less

The role of co-opted ESCRT proteins and lipid factors in protection of tombusviral double-stranded RNA replication intermediate against reconstituted RNAi in yeast

PubMed Central

Nagy, Peter D.

2017-01-01

Reconstituted antiviral defense pathway in surrogate host yeast is used as an intracellular probe to further our understanding of virus-host interactions and the role of co-opted host factors in formation of membrane-bound viral replicase complexes in protection of the viral RNA against ribonucleases. The inhibitory effect of the RNA interference (RNAi) machinery of S. castellii, which only consists of the two-component DCR1 and AGO1 genes, was measured against tomato bushy stunt virus (TBSV) in wild type and mutant yeasts. We show that deletion of the co-opted ESCRT-I (endosomal sorting complexes required for transport I) or ESCRT-III factors makes TBSV replication more sensitive to the RNAi machinery in yeast. Moreover, the lack of these pro-viral cellular factors in cell-free extracts (CFEs) used for in vitro assembly of the TBSV replicase results in destruction of dsRNA replication intermediate by a ribonuclease at the 60 min time point when the CFE from wt yeast has provided protection for dsRNA. In addition, we demonstrate that co-opted oxysterol-binding proteins and membrane contact sites, which are involved in enrichment of sterols within the tombusvirus replication compartment, are required for protection of viral dsRNA. We also show that phosphatidylethanolamine level influences the formation of RNAi-resistant replication compartment. In the absence of peroxisomes in pex3Δ yeast, TBSV subverts the ER membranes, which provide as good protection for TBSV dsRNA against RNAi or ribonucleases as the peroxisomal membranes in wt yeast. Altogether, these results demonstrate that co-opted protein factors and usurped lipids are exploited by tombusviruses to build protective subcellular environment against the RNAi machinery and possibly other cellular ribonucleases. PMID:28759634

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, Jong; Phelan, Paul J.; Chhum, Panharith

2014-11-15

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCVmore » DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.« less

Identification of novel host factors via conserved domain search: Cns1 cochaperone is a novel restriction factor of tombusvirus replication in yeast.

PubMed

Lin, Jing-Yi; Nagy, Peter D

2013-12-01

A large number of host-encoded proteins affect the replication of plus-stranded RNA viruses by acting as susceptibility factors. Many other cellular proteins are known to function as restriction factors of viral infections. Previous studies with tomato bushy stunt tombusvirus (TBSV) in a yeast model host have revealed the inhibitory function of TPR (tetratricopeptide repeat) domain-containing cyclophilins, which are members of the large family of host prolyl isomerases, in TBSV replication. In this paper, we tested additional TPR-containing yeast proteins in a cell-free TBSV replication assay and identified the Cns1p cochaperone for heat shock protein 70 (Hsp70) and Hsp90 chaperones as a strong inhibitor of TBSV replication. Cns1p interacted with the viral replication proteins and inhibited the assembly of the viral replicase complex and viral RNA synthesis in vitro. Overexpression of Cns1p inhibited TBSV replication in yeast. The use of a temperature-sensitive (TS) mutant of Cns1p in yeast revealed that at a semipermissive temperature, TS Cns1p could not inhibit TBSV replication. Interestingly, Cns1p and the TPR-containing Cpr7p cyclophilin have similar inhibitory functions during TBSV replication, although some of the details of their viral restriction mechanisms are different. Our observations indicate that TPR-containing cellular proteins could act as virus restriction factors.

RPA Interacts with HIRA and Regulates H3.3 Deposition at Gene Regulatory Elements in Mammalian Cells.

PubMed

Zhang, Honglian; Gan, Haiyun; Wang, Zhiquan; Lee, Jeong-Heon; Zhou, Hui; Ordog, Tamas; Wold, Marc S; Ljungman, Mats; Zhang, Zhiguo

2017-01-19

The histone chaperone HIRA is involved in depositing histone variant H3.3 into distinct genic regions, including promoters, enhancers, and gene bodies. However, how HIRA deposits H3.3 to these regions remains elusive. Through a short hairpin RNA (shRNA) screening, we identified single-stranded DNA binding protein replication protein A (RPA) as a regulator of the deposition of newly synthesized H3.3 into chromatin. We show that RPA physically interacts with HIRA to form RPA-HIRA-H3.3 complexes, and it co-localizes with HIRA and H3.3 at gene promoters and enhancers. Depletion of RPA1, the largest subunit of the RPA complex, dramatically reduces both HIRA association with chromatin and the deposition of newly synthesized H3.3 at promoters and enhancers and leads to altered transcription at gene promoters. These results support a model whereby RPA, best known for its role in DNA replication and repair, recruits HIRA to promoters and enhancers and regulates deposition of newly synthesized H3.3 to these regulatory elements for gene regulation. Copyright © 2017 Elsevier Inc. All rights reserved.

Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn disease susceptibility

PubMed Central

Parkes, Miles; Barrett, Jeffrey C; Prescott, Natalie; Tremelling, Mark; Anderson, Carl A; Fisher, Sheila A; Roberts, Roland G; Nimmo, Elaine R; Cummings, Fraser R; Soars, Dianne; Drummond, Hazel; Lees, Charlie W; Khawaja, Saud A; Bagnall, Richard; Burke, Denis A; Todhunter, Catherine E; Ahmad, Tariq; Onnie, Clive M; McArdle, Wendy; Strachan, David; Bethel, Graeme; Bryan, Claire; Deloukas, Panos; Forbes, Alastair; Sanderson, Jeremy; Jewell, Derek P; Satsangi, Jack; Mansfield, John C; Cardon, Lon; Mathew, Christopher G

2008-01-01

A genome-wide association scan in Crohn disease by the Wellcome Trust Case Control Consortium1 detected strong association at 6 novel loci. We tested 37 SNPs from these and other loci for association in an independent case control sample. Replication was obtained for the IRGM gene on chromosome 5q33.1 which induces autophagy (replication P = 6.6 × 10−4, combined P = 2.1 × 10−10), and for 9 other loci including NKX2-3 and gene deserts on chromosomes 1q and 5p13. PMID:17554261

Co-administration of plasmid-encoded granulocyte-macrophage colony-stimulating factor increases human immunodeficiency virus-1 DNA vaccine-induced polyfunctional CD4+ T-cell responses

PubMed Central

Santana, Vinicius Canato; Almeida, Rafael Ribeiro; Ribeiro, Susan Pereira; Ferreira, Luís Carlos de Souza; Kalil, Jorge; Rosa, Daniela Santoro; Cunha-Neto, Edecio

2015-01-01

T-cell based vaccines against human immunodeficiency virus (HIV) generate specific responses that may limit both transmission and disease progression by controlling viral load. Broad, polyfunctional, and cytotoxic CD4+T-cell responses have been associated with control of simian immunodeficiency virus/HIV-1 replication, supporting the inclusion of CD4+ T-cell epitopes in vaccine formulations. Plasmid-encoded granulocyte-macrophage colony-stimulating factor (pGM-CSF) co-administration has been shown to induce potent CD4+ T-cell responses and to promote accelerated priming and increased migration of antigen-specific CD4+ T-cells. However, no study has shown whether co-immunisation with pGM-CSF enhances the number of vaccine-induced polyfunctional CD4+ T-cells. Our group has previously developed a DNA vaccine encoding conserved, multiple human leukocyte antigen (HLA)-DR binding HIV-1 subtype B peptides, which elicited broad, polyfunctional and long-lived CD4+ T-cell responses. Here, we show that pGM-CSF co-immunisation improved both magnitude and quality of vaccine-induced T-cell responses, particularly by increasing proliferating CD4+ T-cells that produce simultaneously interferon-γ, tumour necrosis factor-α and interleukin-2. Thus, we believe that the use of pGM-CSF may be helpful for vaccine strategies focused on the activation of anti-HIV CD4+ T-cell immunity. PMID:26602876

An ADAM33 polymorphism associates with progression of preschool wheeze into childhood asthma: a prospective case-control study with replication in a birth cohort study.

PubMed

Klaassen, Ester M M; Penders, John; Jöbsis, Quirijn; van de Kant, Kim D G; Thijs, Carel; Mommers, Monique; van Schayck, Constant P; van Eys, Guillaume; Koppelman, Gerard H; Dompeling, Edward

2015-01-01

The influence of asthma candidate genes on the development from wheeze to asthma in young children still needs to be defined. To link genetic variants in asthma candidate genes to progression of wheeze to persistent wheeze into childhood asthma. In a prospective study, children with recurrent wheeze from the ADEM (Asthma DEtection and Monitoring) study were followed until the age of six. At that age a classification (transient wheeze or asthma) was based on symptoms, lung function and medication use. In 198 children the relationship between this classification and 30 polymorphisms in 16 asthma candidate genes was assessed by logistic regression. In case of an association based on a p<0.10, replication analysis was performed in an independent birth cohort study (KOALA study, n = 248 included for the present analysis). In the ADEM study, the minor alleles of ADAM33 rs511898 and rs528557 and the ORMDL3/GSDMB rs7216389 polymorphisms were negatively associated, whereas the minor alleles of IL4 rs2243250 and rs2070874 polymorphisms were positively associated with childhood asthma. When replicated in the KOALA study, ADAM33 rs528557 showed a negative association of the CG/GG-genotype with progression of recurrent wheeze into childhood asthma (0.50 (0.26-0.97) p = 0.04) and no association with preschool wheeze. Polymorphisms in ADAM33, ORMDL3/GSDMB and IL4 were associated with childhood asthma in a group of children with recurrent wheeze. The replication of the negative association of the CG/GG-genotype of rs528557 ADAM33 with childhood asthma in an independent birth cohort study confirms that a compromised ADAM33 gene may be implicated in the progression of wheeze into childhood asthma.

Targeting GLI by GANT61 involves mechanisms dependent on inhibition of both transcription and DNA licensing.

PubMed

Zhang, Ruowen; Wu, Jiahui; Ferrandon, Sylvain; Glowacki, Katie J; Houghton, Janet A

2016-12-06

The GLI genes are transcription factors and in cancers are oncogenes, aberrantly and constitutively activated. GANT61, a specific GLI inhibitor, has induced extensive cytotoxicity in human models of colon cancer. The FOXM1 promoter was determined to be a transcriptional target of GLI1. In HT29 cells, inhibition of GLI1 binding at the GLI consensus sequence by GANT61 led to inhibited binding of Pol II, the pause-release factors DSIF, NELF and p-TEFb. The formation of R-loops (RNA:DNA hybrids, ssDNA), were reduced by GANT61 at the FOXM1 promoter. Pretreatment of HT29 cells with α-amanitin reduced GANT61-induced γH2AX foci. Co-localization of GLI1 and BrdU foci, inhibited by GANT61, indicated GLI1 and DNA replication to be linked. By co-immunoprecipitation and confocal microscopy, GLI1 co-localized with the DNA licensing factors ORC4, CDT1, and MCM2. Significant co-localization of GLI1 and ORC4 was inhibited by GANT61, and enrichment of ORC4 occurred at the GLI binding site in the FOXM1 promoter. CDT1 was found to be a transcription target of GLI1. Overexpression of CDT1 in HT29 and SW480 cells reduced GANT61-induced cell death, gH2AX foci, and cleavage of caspase-3. Data demonstrate involvement of transcription and of DNA replication licensing factors by non-transcriptional and transcriptional mechanisms in the GLI-dependent mechanism of action of GANT61.

Phosphorus mitigation during springtime runoff by amendments applied to grassed soil.

PubMed

Uusi-Kämppä, J; Turtola, E; Närvänen, A; Jauhiainen, L; Uusitalo, R

2012-01-01

Permanent grass vegetation on sloping soils is an option to protect fields from erosion, but decaying grass may liberate considerable amounts of dissolved reactive P (DRP) in springtime runoff. We studied the effects of freezing and thawing of grassed soil on surface runoff P concentrations by indoor rainfall simulations and tested whether the peak P concentrations could be reduced by amending the soil with P-binding materials containing Ca or Fe. Forty grass-vegetated soil blocks (surface area 0.045 m, depth 0.07 m) were retrieved from two permanent buffer zones on a clay and loam soil in southwest Finland. Four replicates were amended with either: (i) gypsum from phosphoric acid processing (CaSO × 2HO, 6 t ha), (ii) chalk powder (CaCO, 3.3 t ha), (iii) Fe-gypsum (6 t ha) from TiO processing, or (iv) granulated ferric sulfate (Fe[SO], 0.7 t ha), with four replicates serving as untreated controls. Rainfall (3.3 h × 5 mm h) was applied on presaturated samples set at a slope of 5% and the surface runoff was analyzed for DRP, total dissolved P (TDP), total P (TP), and suspended solids. Rainfall simulation was repeated twice after the samples were frozen. Freezing and thawing of the samples increased the surface runoff DRP concentration of the control treatment from 0.19 to 0.46 mg L, up to 2.6-3.7 mg L, with DRP being the main P form in surface runoff. Compared with the controls, surface runoff from soils amended with Fe compounds had 57 to 80% and 47 to 72% lower concentrations of DRP and TP, respectively, but the gypsum and chalk powder did not affect the P concentrations. Thus, amendments containing Fe might be an option to improve DRP retention in, e.g., buffer zones. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Replication of a rare protective allele in the noradrenaline transporter gene and ADHD

PubMed Central

Xu, X; Hawi, Z; Brookes, KJ; Anney, R; Bellgrove, M; Franke, B; Barry, E; Chen, W; Kuntsi, J; Banaschewski, T; Buitelaar, J; Ebstein, R; Fitzgerald, M; Miranda, A; Oades, RD; Roeyers, H; Rothenberger, A; Sergeant, J; Sonuga-Barke, E; Steinhausen, H-C; Faraone, SV; Gill, M

2008-01-01

Objective Replication is a key to resolving whether a reported genetic association represents a false positive finding or an actual genetic risk factor. In a previous study screening 51 candidate genes for association with ADHD in a multi-centre European sample (the IMAGE project), two single nucleotide polymorphisms (SNPs) within the norepinephrine transporter (SLC6A2) gene were found to be associated with attention deficit hyperactivity disorder (ADHD). The same SNP alleles were also reported to be associated with ADHD in a separate study from the Massachusetts General Hospital in the US. Method Using two independent samples of ADHD DSM-IV combined subtype trios we attempted to replicate the reported associations with SNPs rs11568324 and rs3785143 in SLC6A2. Results Significant association of the two markers was not observed in the two independent replication samples. However, across all four datasets the overall evidence of association with ADHD was significant (for SNP rs11568324 P=0.0001; average odds ratio=0.33; for SNP rs3785143 P=0.008; average odds ratio=1.3). Conclusions The data were consistent for rs11568324, suggesting the existence of a rare allele conferring protection for ADHD within the SLC6A2 gene. Further investigations should focus on identifying the mechanisms underlying the protective effect. PMID:18937296

Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children?

PubMed

Cebey-López, Miriam; Herberg, Jethro; Pardo-Seco, Jacobo; Gómez-Carballa, Alberto; Martinón-Torres, Nazareth; Salas, Antonio; Martinón-Sánchez, José María; Justicia, Antonio; Rivero-Calle, Irene; Sumner, Edward; Fink, Colin; Martinón-Torres, Federico

2016-01-01

Multiple viruses are often detected in children with respiratory infection but the significance of co-infection in pathogenesis, severity and outcome is unclear. To correlate the presence of viral co-infection with clinical phenotype in children admitted with acute respiratory infections (ARI). We collected detailed clinical information on severity for children admitted with ARI as part of a Spanish prospective multicenter study (GENDRES network) between 2011-2013. A nested polymerase chain reaction (PCR) approach was used to detect respiratory viruses in respiratory secretions. Findings were compared to an independent cohort collected in the UK. 204 children were recruited in the main cohort and 97 in the replication cohort. The number of detected viruses did not correlate with any markers of severity. However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). In addition, pneumococcal vaccination was found to be a protective factor in terms of degree of respiratory distress (OR: 2.917; P-value = 0.035), PICU admission (OR: 0.301; P-value = 0.011), lower clinical score (-1.499; P-value = 0.021) respiratory support requirement (OR: 0.324; P-value = 0.016) and oxygen necessity (OR: 0.328; P-value = 0.001). All these findings were replicated in the UK cohort. The presence of more than one virus in hospitalized children with ARI is very frequent but it does not seem to have a major clinical impact in terms of severity. However bacterial superinfection increases the severity of the disease course. On the contrary, pneumococcal vaccination plays a protective role.

Developmental Neurogenetics and Multimodal Neuroimaging of Sex Differences in Autism

PubMed Central

Chen, Christina; Van Horn, John Darrell

2016-01-01

Examining sex differences in the brain has been contentious but is nonetheless important for advancing mental health for both girls and boys. Unfortunately, females in biomedical research remain underrepresented in most mental health conditions including autism spectrum disorders (ASD), even though equal inclusion of females would improve treatment for girls and yield benefits to boys. This review examines sex differences in the relationship between neuroanatomy and neurogenetics of ASD. Recent findings reveal that girls diagnosed with ASD exhibit more intellectual and behavioral problems compared to their male counterparts, suggesting that girls may be less likely diagnosed in the absence of such problems or that they require a higher mutational load to meet the diagnostic criteria. Thus far, the female biased effect of chromosome 4, 5p15.33, 8p, 9p24.1, 11p12-13, 15q, and Xp22.3 and the male biased effect of 1p31.3, 5q12.3, 7q, 9q33.3, 11q13.4, 13q33.3, 16p11.2, 17q11-21, Xp22.33/Yp11.31, DRD1, NLGN3, MAOA, and SHANK1 deletion have been discovered in ASD. The SNPs of genes such as RYR2, UPP2, and the androgen receptor gene have been shown to have sex-biasing factors in both girls and boys diagnosed with ASD. These sex-related genetic factors may drive sex differences in the neuroanatomy of these girls and boys, including abnormal enlargement in temporal gray and white matter volumes, and atypical reduction in cerebellar gray matter volumes and corpus callosum fibers projecting to the anterior frontal cortex in ASD girls relative to boys. Such factors may also be responsible for the attenuation of brain sexual differentiation in adult men and women with ASD; however, much remains to be uncovered or replicated. Future research should leverage further the association between neuroanatomy and genetics in girls for an integrated and interdisciplinary understanding of ASD. PMID:26781567

Developmental neurogenetics and multimodal neuroimaging of sex differences in autism.

PubMed

Chen, Christina; Van Horn, John Darrell

2017-02-01

Examining sex differences in the brain has been historically contentious but is nonetheless important for advancing mental health for both girls and boys. Unfortunately, females in biomedical research remain underrepresented in most mental health conditions including autism spectrum disorders (ASD), even though equal inclusion of females would improve treatment for girls and yield benefits to boys. This review examines sex differences in the relationship between neuroanatomy and neurogenetics of ASD. Recent findings reveal that girls diagnosed with ASD exhibit more intellectual and behavioral problems compared to their male counterparts, suggesting that girls may be less likely diagnosed in the absence of such problems or that they require a higher mutational load to meet the diagnostic criteria. Thus far, the female biased effect of chromosome 4, 5p15.33, 8p, 9p24.1, 11p12-13, 15q, and Xp22.3 and the male biased effect of 1p31.3, 5q12.3, 7q, 9q33.3, 11q13.4, 13q33.3, 16p11.2, 17q11-21, Xp22.33/Yp11.31, DRD1, NLGN3, MAOA, and SHANK1 deletion have been discovered in ASD. The SNPs of genes such as RYR2, UPP2, and the androgen receptor gene have been shown to have sex-biasing factors in both girls and boys diagnosed with ASD. These sex-related genetic factors may drive sex differences in the neuroanatomy of these girls and boys, including abnormal enlargement in temporal gray and white matter volumes, and atypical reduction in cerebellar gray matter volumes and corpus callosum fibers projecting to the anterior frontal cortex in ASD girls relative to boys. Such factors may also be responsible for the attenuation of brain sexual differentiation in adult men and women with ASD; however, much remains to be uncovered or replicated. Future research should leverage further the association between neuroanatomy and genetics in girls for an integrated and interdisciplinary understanding of ASD.

The structure of the nucleoprotein binding domain of lyssavirus phosphoprotein reveals a structural relationship between the N-RNA binding domains of Rhabdoviridae and Paramyxoviridae.

PubMed

Delmas, Olivier; Assenberg, Rene; Grimes, Jonathan M; Bourhy, Hervé

2010-01-01

The phosphoprotein P of non-segmented negative-sense RNA viruses is an essential component of the replication and transcription complex and acts as a co-factor for the viral RNA-dependent RNA polymerase. P recruits the viral polymerase to the nucleoprotein-bound viral RNA (N-RNA) via an interaction between its C-terminal domain and the N-RNA complex. We have obtained the structure of the C-terminal domain of P of Mokola virus (MOKV), a lyssavirus that belongs to the Rhabdoviridae family and mapped at the amino acid level the crucial positions involved in interaction with N and in the formation of the viral replication complex. Comparison of the N-RNA binding domains of P solved to date suggests that the N-RNA binding domains are structurally conserved among paramyxoviruses and rhabdoviruses in spite of low sequence conservation. We also review the numerous other functions of this domain and more generally of the phosphoprotein.

Nuclear Proteins Hijacked by Mammalian Cytoplasmic Plus Strand RNA Viruses

PubMed Central

Lloyd, Richard E.

2015-01-01

Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. PMID:25818028

Vectors for co-expression of an unrestricted number of proteins

PubMed Central

Scheich, Christoph; Kümmel, Daniel; Soumailakakis, Dimitri; Heinemann, Udo; Büssow, Konrad

2007-01-01

A vector system is presented that allows generation of E. coli co-expression clones by a standardized, robust cloning procedure. The number of co-expressed proteins is not limited. Five ‘pQLink’ vectors for expression of His-tag and GST-tag fusion proteins as well as untagged proteins and for cloning by restriction enzymes or Gateway cloning were generated. The vectors allow proteins to be expressed individually; to achieve co-expression, two pQLink plasmids are combined by ligation-independent cloning. pQLink co-expression plasmids can accept an unrestricted number of genes. As an example, the co-expression of a heterotetrameric human transport protein particle (TRAPP) complex from a single plasmid, its isolation and analysis of its stoichiometry are shown. pQLink clones can be used directly for pull-down experiments if the proteins are expressed with different tags. We demonstrate pull-down experiments of human valosin-containing protein (VCP) with fragments of the autocrine motility factor receptor (AMFR). The cloning method avoids PCR or gel isolation of restriction fragments, and a single resistance marker and origin of replication are used, allowing over-expression of rare tRNAs from a second plasmid. It is expected that applications are not restricted to bacteria, but could include co-expression in other hosts such as Bacluovirus/insect cells. PMID:17311810

Urinary p-cresol is elevated in young French children with autism spectrum disorder: a replication study.

PubMed

Gabriele, Stefano; Sacco, Roberto; Cerullo, Sonia; Neri, Cristina; Urbani, Andrea; Tripi, Gabriele; Malvy, Joëlle; Barthelemy, Catherine; Bonnet-Brihault, Frédérique; Persico, Antonio M

2014-09-01

The aromatic compound p-cresol (4-methylphenol) has been found elevated in the urines of Italian autistic children up to 8 years of age. The present study aims at replicating these initial findings in an ethnically distinct sample and at extending them by measuring also the three components of urinary p-cresol, namely p-cresylsulfate, p-cresylglucuronate and free p-cresol. Total urinary p-cresol, p-cresylsulfate and p-cresylglucuronate were significantly elevated in 33 French autism spectrum disorder (ASD) cases compared with 33 sex- and age-matched controls (p < 0.05). This increase was limited to ASD children aged ≤8 years (p < 0.01), and not older (p = 0.17). Urinary levels of p-cresol and p-cresylsulfate were associated with stereotypic, compulsive/repetitive behaviors (p < 0.05), although not with overall autism severity. These results confirm the elevation of urinary p-cresol in a sizable set of small autistic children and spur interest into biomarker roles for p-cresol and p-cresylsulfate in autism.

Inhibition of polyomavirus ori-dependent DNA replication by mSin3B.

PubMed

Xie, An-Yong; Folk, William R

2002-12-01

When tethered in cis to DNA, the transcriptional corepressor mSin3B inhibits polyomavirus (Py) ori-dependent DNA replication in vivo. Histone deacetylases (HDACs) appear not to be involved, since tethering class I and class II HDACs in cis does not inhibit replication and treating the cells with trichostatin A does not specifically relieve inhibition by mSin3B. However, the mSin3B L59P mutation that impairs mSin3B interaction with N-CoR/SMRT abrogates inhibition of replication, suggesting the involvement of N-CoR/SMRT. Py large T antigen interacts with mSin3B, suggesting an HDAC-independent mechanism by which mSin3B inhibits DNA replication.

Co-generating synthetic parts toward a self-replicating system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jun; Haas, Wilhelm; Jackson, Kirsten

To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE, might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when co-expressed in batchmore » format PURE system. By optimizing DNA template concentrations and adapting a miniaturized Fluid Array Device with optimized feeding solution, we were able to cogenerate and detect at least 29 of the 33 50S and all of the 21 30S subunit r-proteins in one pot. The boost on yield of a single r-protein in co-expression pool varied from ~1.5 to 5-fold compared to the batch mode, with up to ~ 2.4 µM yield for a single r-protein. Reconstituted ribosomes under physiological condition from PURE system synthesized 30S r-proteins and native 16S rRNA showed ~13% activity of native 70S ribosomes, which increased to 21% when supplemented with GroEL/ES. As a result, this work also points to what is still needed to obtain self-replicating synthetic ribosomes in-situ in the PURE system.« less

Co-generating synthetic parts toward a self-replicating system

DOE PAGES

Li, Jun; Haas, Wilhelm; Jackson, Kirsten; ...

2017-03-23

To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE, might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when co-expressed in batchmore » format PURE system. By optimizing DNA template concentrations and adapting a miniaturized Fluid Array Device with optimized feeding solution, we were able to cogenerate and detect at least 29 of the 33 50S and all of the 21 30S subunit r-proteins in one pot. The boost on yield of a single r-protein in co-expression pool varied from ~1.5 to 5-fold compared to the batch mode, with up to ~ 2.4 µM yield for a single r-protein. Reconstituted ribosomes under physiological condition from PURE system synthesized 30S r-proteins and native 16S rRNA showed ~13% activity of native 70S ribosomes, which increased to 21% when supplemented with GroEL/ES. As a result, this work also points to what is still needed to obtain self-replicating synthetic ribosomes in-situ in the PURE system.« less

Functional characterization of replication and stability factors of an incompatibility group P-1 plasmid from Xylella fastidiosa.

PubMed

Lee, Min Woo; Rogers, Elizabeth E; Stenger, Drake C

2010-12-01

Xylella fastidiosa strain riv11 harbors a 25-kbp plasmid (pXF-RIV11) belonging to the IncP-1 incompatibility group. Replication and stability factors of pXF-RIV11 were identified and used to construct plasmids able to replicate in X. fastidiosa and Escherichia coli. Replication in X. fastidiosa required a 1.4-kbp region from pXF-RIV11 containing a replication initiation gene (trfA) and the adjacent origin of DNA replication (oriV). Constructs containing trfA and oriV from pVEIS01, a related IncP-1 plasmid of the earthworm symbiont Verminephrobacter eiseniae, also were competent for replication in X. fastidiosa. Constructs derived from pXF-RIV11 but not pVEIS01 replicated in Agrobacterium tumefaciens, Xanthomonas campestris, and Pseudomonas syringae. Although plasmids bearing replication elements from pXF-RIV11 or pVEIS01 could be maintained in X. fastidiosa under antibiotic selection, removal of selection resulted in plasmid extinction after 3 weekly passages. Addition of a toxin-antitoxin addiction system (pemI/pemK) from pXF-RIV11 improved plasmid stability such that >80 to 90% of X. fastidiosa cells retained plasmid after 5 weekly passages in the absence of antibiotic selection. Expression of PemK in E. coli was toxic for cell growth, but toxicity was nullified by coexpression of PemI antitoxin. Deletion of N-terminal sequences of PemK containing the conserved motif RGD abolished toxicity. In vitro assays revealed a direct interaction of PemI with PemK, suggesting that antitoxin activity of PemI is mediated by toxin sequestration. IncP-1 plasmid replication and stability factors were added to an E. coli cloning vector to constitute a stable 6.0-kbp shuttle vector (pXF20-PEMIK) suitable for use in X. fastidiosa.

The eukaryotic translation initiation factor 3 subunit E binds to classical swine fever virus NS5A and facilitates viral replication.

PubMed

Liu, Xiaofeng; Wang, Xiaoyu; Wang, Qian; Luo, Mingyang; Guo, Huancheng; Gong, Wenjie; Tu, Changchun; Sun, Jinfu

2018-02-01

Classical swine fever virus (CSFV) NS5A protein is a multifunctional protein, playing critical roles in viral RNA replication, translation and assembly. To further explore its functions in viral replication, interaction of NS5A with host factors was assayed using a his-tag "pull down" assay coupled with shotgun LC-MS/MS. Host protein translation initiation factor 3 subunit E was identified as a binding partner of NS5A, and confirmed by co-immunoprecipitation and co-localization analysis. Overexpression of eIF3E markedly enhanced CSFV genomic replication, viral protein expression and production of progeny virus, and downregulation of eIF3E by siRNA significantly decreased viral proliferation in PK-15 cells. Luciferase reporter assay showed an enhancement of translational activity of the internal ribosome entry site of CSFV by eIF3E and a decrease in cellular translation by NS5A. These data indicate that eIF3E plays an important role in CSFV replication, thereby identifying it as a potential target for inhibition of the virus. Copyright © 2017 Elsevier Inc. All rights reserved.

Acetyl-coenzyme A synthetase 2 is a nuclear protein required for replicative longevity in Saccharomyces cerevisiae

PubMed Central

Falcón, Alaric A.; Chen, Shaoping; Wood, Michael S.

2013-01-01

Acs2p is one of two acetyl-coenzyme A synthetases in Saccharomyces cerevisiae. We have prepared and characterized a monoclonal antibody specific for Acs2p and find that Acs2p is localized primarily to the nucleus, including the nucleolus, with a minor amount in the cytosol. We find that Acs2p is required for replicative longevity: an acs2Δ strain has a reduced replicative life span compared to wild-type and acs1Δ strains. Furthermore, replicatively aged acs2Δ cells contain elevated levels of extrachromosomal rDNA circles, and silencing at the rDNA locus is impaired in an acs2Δ strain. These findings indicate that Acs2p-mediated synthesis of acetyl-CoA in the nucleus functions to promote rDNA silencing and replicative longevity in yeast. PMID:19618123

RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs.

PubMed

Huang, Feng; Zhang, Junsong; Zhang, Yijun; Geng, Guannan; Liang, Juanran; Li, Yingniang; Chen, Jingliang; Liu, Chao; Zhang, Hui

2015-12-01

Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-box of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle. Copyright © 2015 Elsevier Inc. All rights reserved.

An ADAM33 Polymorphism Associates with Progression of Preschool Wheeze into Childhood Asthma: A Prospective Case-Control Study with Replication in a Birth Cohort Study

PubMed Central

Klaassen, Ester M. M.; Penders, John; Jöbsis, Quirijn; van de Kant, Kim D. G.; Thijs, Carel; Mommers, Monique; van Schayck, Constant P.; van Eys, Guillaume; Koppelman, Gerard H.; Dompeling, Edward

2015-01-01

Background The influence of asthma candidate genes on the development from wheeze to asthma in young children still needs to be defined. Objective To link genetic variants in asthma candidate genes to progression of wheeze to persistent wheeze into childhood asthma. Materials and Methods In a prospective study, children with recurrent wheeze from the ADEM (Asthma DEtection and Monitoring) study were followed until the age of six. At that age a classification (transient wheeze or asthma) was based on symptoms, lung function and medication use. In 198 children the relationship between this classification and 30 polymorphisms in 16 asthma candidate genes was assessed by logistic regression. In case of an association based on a p<0.10, replication analysis was performed in an independent birth cohort study (KOALA study, n = 248 included for the present analysis). Results In the ADEM study, the minor alleles of ADAM33 rs511898 and rs528557 and the ORMDL3/GSDMB rs7216389 polymorphisms were negatively associated, whereas the minor alleles of IL4 rs2243250 and rs2070874 polymorphisms were positively associated with childhood asthma. When replicated in the KOALA study, ADAM33 rs528557 showed a negative association of the CG/GG-genotype with progression of recurrent wheeze into childhood asthma (0.50 (0.26-0.97) p = 0.04) and no association with preschool wheeze. Conclusion Polymorphisms in ADAM33, ORMDL3/GSDMB and IL4 were associated with childhood asthma in a group of children with recurrent wheeze. The replication of the negative association of the CG/GG-genotype of rs528557 ADAM33 with childhood asthma in an independent birth cohort study confirms that a compromised ADAM33 gene may be implicated in the progression of wheeze into childhood asthma. PMID:25768087

Ocean acidification and viral replication cycles: Frequency of lytically infected and lysogenic cells during a mesocosm experiment in the NW Mediterranean Sea

NASA Astrophysics Data System (ADS)

Tsiola, Anastasia; Pitta, Paraskevi; Giannakourou, Antonia; Bourdin, Guillaume; Marro, Sophie; Maugendre, Laure; Pedrotti, Maria Luiza; Gazeau, Frédéric

2017-02-01

The frequency of lytically infected and lysogenic cells (FLIC and FLC, respectively) was estimated during an in situ mesocosm experiment studying the impact of ocean acidification on the plankton community of a low nutrient low chlorophyll (LNLC) system in the north-western Mediterranean Sea (Bay of Villefranche, France) in February/March 2013. No direct effect of elevated partial pressure of CO2 (pCO2) on viral replication cycles could be detected. FLC variability was negatively correlated to heterotrophic bacterial and net community production as well as the ambient bacterial abundance, confirming that lysogeny is a prevailing life strategy under unfavourable-for-the-hosts conditions. Further, the phytoplankton community, assessed by chlorophyll a concentration and the release of >0.4 μm transparent exopolymeric particles, was correlated with the occurrence of lysogeny, indicating a possible link between photosynthetic processes and bacterial growth. Higher FLC was found occasionally at the highest pCO2-treated mesocosm in parallel to subtle differences in the phytoplankton community. This observation suggests that elevated pCO2 could lead to short-term alterations in lysogenic dynamics coupled to phytoplankton-derived processes. Correlation of FLIC with any environmental parameter could have been obscured by the sampling time or the synchronization of lysis to microbial processes not assessed in this experiment. Furthermore, alterations in microbial and viral assemblage composition and gene expression could be a confounding factor. Viral-induced modifications in organic matter flow affect bacterial growth and could interact with ocean acidification with unpredictable ecological consequences.

Validation of variants in SLC28A3 and UGT1A6 as genetic markers predictive of anthracycline-induced cardiotoxicity in children.

PubMed

Visscher, H; Ross, C J D; Rassekh, S R; Sandor, G S S; Caron, H N; van Dalen, E C; Kremer, L C; van der Pal, H J; Rogers, P C; Rieder, M J; Carleton, B C; Hayden, M R

2013-08-01

The use of anthracyclines as effective antineoplastic drugs is limited by the occurrence of cardiotoxicity. Multiple genetic variants predictive of anthracycline-induced cardiotoxicity (ACT) in children were recently identified. The current study was aimed to assess replication of these findings in an independent cohort of children. . Twenty-three variants were tested for association with ACT in an independent cohort of 218 patients. Predictive models including genetic and clinical risk factors were constructed in the original cohort and assessed in the current replication cohort. . We confirmed the association of rs17863783 in UGT1A6 and ACT in the replication cohort (P = 0.0062, odds ratio (OR) 7.98). Additional evidence for association of rs7853758 (P = 0.058, OR 0.46) and rs885004 (P = 0.058, OR 0.42) in SLC28A3 was found (combined P = 1.6 × 10(-5) and P = 3.0 × 10(-5), respectively). A previously constructed prediction model did not significantly improve risk prediction in the replication cohort over clinical factors alone. However, an improved prediction model constructed using replicated genetic variants as well as clinical factors discriminated significantly better between cases and controls than clinical factors alone in both original (AUC 0.77 vs. 0.68, P = 0.0031) and replication cohort (AUC 0.77 vs. 0.69, P = 0.060). . We validated genetic variants in two genes predictive of ACT in an independent cohort. A prediction model combining replicated genetic variants as well as clinical risk factors might be able to identify high- and low-risk patients who could benefit from alternative treatment options. Copyright © 2013 Wiley Periodicals, Inc.

p53 Is a Host Cell Regulator during Herpes Simplex Encephalitis.

PubMed

Maruzuru, Yuhei; Koyanagi, Naoto; Takemura, Naoki; Uematsu, Satoshi; Matsubara, Daisuke; Suzuki, Yutaka; Arii, Jun; Kato, Akihisa; Kawaguchi, Yasushi

2016-08-01

p53 is a critical host cell factor in the cellular response to a broad range of stress factors. We recently reported that p53 is required for efficient herpes simplex virus 1 (HSV-1) replication in cell culture. However, a defined role for p53 in HSV-1 replication and pathogenesis in vivo remains elusive. In this study, we examined the effects of p53 on HSV-1 infection in vivo using p53-deficient mice. Following intracranial inoculation, p53 knockout reduced viral replication in the brains of mice and led to significantly reduced rates of mortality due to herpes simplex encephalitis. These results suggest that p53 is an important host cell regulator of HSV-1 replication and pathogenesis in the central nervous system (CNS). HSV-1 causes sporadic cases of encephalitis, which, even with antiviral therapy, can result in severe neurological defects and even death. Many host cell factors involved in the regulation of CNS HSV-1 infection have been investigated using genetically modified mice. However, most of these factors are immunological regulators and act via immunological pathways in order to restrict CNS HSV-1 infection. They therefore provide limited information on intrinsic host cell regulators that may be involved in the facilitation of CNS HSV-1 infection. Here we demonstrate that a host cell protein, p53, which has generally been considered a host cell restriction factor for various viral infections, is required for efficient HSV-1 replication and pathogenesis in the CNS of mice. This is the first report showing that p53 positively regulates viral replication and pathogenesis in vivo and provides insights into its molecular mechanism, which may suggest novel clinical treatment options for herpes simplex encephalitis. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Subramanian, T.; Zhao, Ling-jun; Chinnadurai, G., E-mail: chinnag@slu.edu

Adenovirus E1A induces cell proliferation, oncogenic transformation and promotes viral replication through interaction with p300/CBP, TRRAP/p400 multi-protein complex and the retinoblastoma (pRb) family proteins through distinct domains in the E1A N-terminal region. The C-terminal region of E1A suppresses E1A/Ras co-transformation and interacts with FOXK1/K2, DYRK1A/1B/HAN11 and CtBP1/2 (CtBP) protein complexes. To specifically dissect the role of CtBP interaction with E1A, we engineered a mutation (DL→AS) within the CtBP-binding motif, PLDLS, and investigated the effect of the mutation on immortalization and Ras cooperative transformation of primary cells and viral replication. Our results suggest that CtBP–E1A interaction suppresses immortalization and Ras co-operativemore » transformation of primary rodent epithelial cells without significantly influencing the tumorigenic activities of transformed cells in immunodeficient and immunocompetent animals. During productive infection, CtBP–E1A interaction enhances viral replication in human cells. Between the two CtBP family proteins, CtBP2 appears to restrict viral replication more than CtBP1 in human cells. - Highlights: • Adenovirus E1A C-terminal region suppresses E1A/Ras co-transformation. • This E1A region binds with FOXK, DYRK1/HAN11 and CtBP cellular protein complexes. • We found that E1A–CtBP interaction suppresses immortalization and transformation. • The interaction enhances viral replication in human cells.« less

Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lloyd, Richard E., E-mail: rlloyd@bcm.edu

Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizesmore » recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.« less

RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Feng; Zhang, Junsong; Zhang, Yijun

Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-boxmore » of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle. - Highlights: • MOV10 can function as a co-factor of HIV-1 Rev. • MOV10 facilitates Rev/RRE-dependent transport of viral mRNAs. • MOV10 interacts with Rev in an RNA-independent manner. • The DEAG-box of MOV10 is required for the enhancement of Rev/RRE-dependent export.« less

Interaction of the Tumor Suppressor p53 with Replication Protein A.

DTIC Science & Technology

1996-08-01

The DNA replication factor RPA physically associates with the tumor suppressor protein p53, an interaction that could be important for the function...binding single-stranded DNA, this mutant of RPA fails to support DNA replication . Therefore the region of RPA which interacts with p53 is essential for...of p53, p21/WAFl/CIPl, inhibits the cell-cycle by associating with cyclin-cdk kinases. It also inhibits DNA replication by interacting with a

Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression.

PubMed

Franz, André; Pirson, Paul A; Pilger, Domenic; Halder, Swagata; Achuthankutty, Divya; Kashkar, Hamid; Ramadan, Kristijan; Hoppe, Thorsten

2016-02-04

The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin-associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging.

Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression

PubMed Central

Franz, André; Pirson, Paul A.; Pilger, Domenic; Halder, Swagata; Achuthankutty, Divya; Kashkar, Hamid; Ramadan, Kristijan; Hoppe, Thorsten

2016-01-01

The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin-associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging. PMID:26842564

SARS-CoV ORF1b-encoded nonstructural proteins 12-16: replicative enzymes as antiviral targets.

PubMed

Subissi, Lorenzo; Imbert, Isabelle; Ferron, François; Collet, Axelle; Coutard, Bruno; Decroly, Etienne; Canard, Bruno

2014-01-01

The SARS (severe acute respiratory syndrome) pandemic caused ten years ago by the SARS-coronavirus (SARS-CoV) has stimulated a number of studies on the molecular biology of coronaviruses. This research has provided significant new insight into many mechanisms used by the coronavirus replication-transcription complex (RTC). The RTC directs and coordinates processes in order to replicate and transcribe the coronavirus genome, a single-stranded, positive-sense RNA of outstanding length (∼27-32kilobases). Here, we review the up-to-date knowledge on SARS-CoV replicative enzymes encoded in the ORF1b, i.e., the main RNA-dependent RNA polymerase (nsp12), the helicase/triphosphatase (nsp13), two unusual ribonucleases (nsp14, nsp15) and RNA-cap methyltransferases (nsp14, nsp16). We also review how these enzymes co-operate with other viral co-factors (nsp7, nsp8, and nsp10) to regulate their activity. These last ten years of research on SARS-CoV have considerably contributed to unravel structural and functional details of one of the most fascinating replication/transcription machineries of the RNA virus world. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses". Copyright © 2013 Elsevier B.V. All rights reserved.

ATAD2 is an epigenetic reader of newly synthesized histone marks during DNA replication.

PubMed

Koo, Seong Joo; Fernández-Montalván, Amaury E; Badock, Volker; Ott, Christopher J; Holton, Simon J; von Ahsen, Oliver; Toedling, Joern; Vittori, Sarah; Bradner, James E; Gorjánácz, Mátyás

2016-10-25

ATAD2 (ATPase family AAA domain-containing protein 2) is a chromatin regulator harboring an AAA+ ATPase domain and a bromodomain, previously proposed to function as an oncogenic transcription co-factor. Here we suggest that ATAD2 is also required for DNA replication. ATAD2 is co-expressed with genes involved in DNA replication in various cancer types and predominantly expressed in S phase cells where it localized on nascent chromatin (replication sites). Our extensive biochemical and cellular analyses revealed that ATAD2 is recruited to replication sites through a direct interaction with di-acetylated histone H4 at K5 and K12, indicative of newly synthesized histones during replication-coupled chromatin reassembly. Similar to ATAD2-depletion, ectopic expression of ATAD2 mutants that are deficient in binding to these di-acetylation marks resulted in reduced DNA replication and impaired loading of PCNA onto chromatin, suggesting relevance of ATAD2 in DNA replication. Taken together, our data show a novel function of ATAD2 in cancer and for the first time identify a reader of newly synthesized histone di-acetylation-marks during replication.

Effects of ocean acidification on primary production in a coastal North Sea phytoplankton community

PubMed Central

Eberlein, Tim; Wohlrab, Sylke; Rost, Björn; John, Uwe; Bach, Lennart T.; Riebesell, Ulf; Van de Waal, Dedmer B.

2017-01-01

We studied the effect of ocean acidification (OA) on a coastal North Sea plankton community in a long-term mesocosm CO2-enrichment experiment (BIOACID II long-term mesocosm study). From March to July 2013, 10 mesocosms of 19 m length with a volume of 47.5 to 55.9 m3 were deployed in the Gullmar Fjord, Sweden. CO2 concentrations were enriched in five mesocosms to reach average CO2 partial pressures (pCO2) of 760 μatm. The remaining five mesocosms were used as control at ambient pCO2 of 380 μatm. Our paper is part of a PLOS collection on this long-term mesocosm experiment. Here, we here tested the effect of OA on total primary production (PPT) by performing 14C-based bottle incubations for 24 h. Furthermore, photoacclimation was assessed by conducting 14C-based photosynthesis-irradiance response (P/I) curves. Changes in chlorophyll a concentrations over time were reflected in the development of PPT, and showed higher phytoplankton biomass build-up under OA. We observed two subsequent phytoplankton blooms in all mesocosms, with peaks in PPT around day 33 and day 56. OA had no significant effect on PPT, except for a marginal increase during the second phytoplankton bloom when inorganic nutrients were already depleted. Maximum light use efficiencies and light saturation indices calculated from the P/I curves changed simultaneously in all mesocosms, and suggest that OA did not alter phytoplankton photoacclimation. Despite large variability in time-integrated productivity estimates among replicates, our overall results indicate that coastal phytoplankton communities can be affected by OA at certain times of the seasonal succession with potential consequences for ecosystem functioning. PMID:28273107

Fish Viruses: Buffers and Methods for Plaquing Eight Agents Under Normal Atmosphere

PubMed Central

Wolf, Ken; Quimby, M. C.

1973-01-01

A universal procedure was sought for plaque assay of eight fish viruses (bluegill myxovirus, channel catfish virus, eel virus, Egtved virus, infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus, lymphocystis virus, and the agent of spring viremia of carp (Rhabdovirus carpio), in dish cultures of various fish cells. Eagle minimal essential medium with sodium bicarbonate-CO2 buffer (Earle’s salt solution) was compared with minimal essential medium buffered principally with tris (hydroxymethyl)aminomethane or N-2-hydroxyethylpiperazine-N′-2′-ethanesulfonic acid at a pH or in the range of 7.6 to 8.0 depending upon temperature. Five fish cell lines collectively capable of replicating all fish viruses thus far isolated were tested and quantitatively found to grow comparably well in the three media. Two-phase (gel-liquid) media incorporating the various buffer systems allowed plaquing at 15 to 33 C either in partial pressures of CO2 or in normal atmosphere, but greater efficiency and sensitivity were obtained with the organic buffers, and, overall, the best results were obtained with tris(hydroxymethyl)aminomethane. Epizootiological data, specific fish cell line response, and plaque morphology permit presumptive identification of most of the agents. At proper pH, use of organic buffers obviates the need for CO2 incubators. Images PMID:4349252

NorWood: a gene expression resource for evo-devo studies of conifer wood development.

PubMed

Jokipii-Lukkari, Soile; Sundell, David; Nilsson, Ove; Hvidsten, Torgeir R; Street, Nathaniel R; Tuominen, Hannele

2017-10-01

The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children?

PubMed Central

Pardo-Seco, Jacobo; Gómez-Carballa, Alberto; Martinón-Torres, Nazareth; Salas, Antonio; Martinón-Sánchez, José María; Justicia, Antonio; Rivero-Calle, Irene; Sumner, Edward; Fink, Colin

2016-01-01

Background Multiple viruses are often detected in children with respiratory infection but the significance of co-infection in pathogenesis, severity and outcome is unclear. Objectives To correlate the presence of viral co-infection with clinical phenotype in children admitted with acute respiratory infections (ARI). Methods We collected detailed clinical information on severity for children admitted with ARI as part of a Spanish prospective multicenter study (GENDRES network) between 2011–2013. A nested polymerase chain reaction (PCR) approach was used to detect respiratory viruses in respiratory secretions. Findings were compared to an independent cohort collected in the UK. Results 204 children were recruited in the main cohort and 97 in the replication cohort. The number of detected viruses did not correlate with any markers of severity. However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). In addition, pneumococcal vaccination was found to be a protective factor in terms of degree of respiratory distress (OR: 2.917; P-value = 0.035), PICU admission (OR: 0.301; P-value = 0.011), lower clinical score (-1.499; P-value = 0.021) respiratory support requirement (OR: 0.324; P-value = 0.016) and oxygen necessity (OR: 0.328; P-value = 0.001). All these findings were replicated in the UK cohort. Conclusion The presence of more than one virus in hospitalized children with ARI is very frequent but it does not seem to have a major clinical impact in terms of severity. However bacterial superinfection increases the severity of the disease course. On the contrary, pneumococcal vaccination plays a protective role. PMID:27096199

Regulated Eukaryotic DNA Replication Origin Firing with Purified Proteins

PubMed Central

Yeeles, Joseph T.P.; Deegan, Tom D.; Janska, Agnieszka; Early, Anne; Diffley, John F. X.

2016-01-01

Eukaryotic cells initiate DNA replication from multiple origins, which must be tightly regulated to promote precise genome duplication in every cell cycle. To accomplish this, initiation is partitioned into two temporally discrete steps: a double hexameric MCM complex is first loaded at replication origins during G1 phase, and then converted to the active CMG (Cdc45, MCM, GINS) helicase during S phase. Here we describe the reconstitution of budding yeast DNA replication initiation with 16 purified replication factors, made from 42 polypeptides. Origin-dependent initiation recapitulates regulation seen in vivo. Cyclin dependent kinase (CDK) inhibits MCM loading by phosphorylating the origin recognition complex (ORC) and promotes CMG formation by phosphorylating Sld2 and Sld3. Dbf4 dependent kinase (DDK) promotes replication by phosphorylating MCM, and can act either before or after CDK. These experiments define the minimum complement of proteins, protein kinase substrates and co-factors required for regulated eukaryotic DNA replication. PMID:25739503

Regulated eukaryotic DNA replication origin firing with purified proteins.

PubMed

Yeeles, Joseph T P; Deegan, Tom D; Janska, Agnieszka; Early, Anne; Diffley, John F X

2015-03-26

Eukaryotic cells initiate DNA replication from multiple origins, which must be tightly regulated to promote precise genome duplication in every cell cycle. To accomplish this, initiation is partitioned into two temporally discrete steps: a double hexameric minichromosome maintenance (MCM) complex is first loaded at replication origins during G1 phase, and then converted to the active CMG (Cdc45-MCM-GINS) helicase during S phase. Here we describe the reconstitution of budding yeast DNA replication initiation with 16 purified replication factors, made from 42 polypeptides. Origin-dependent initiation recapitulates regulation seen in vivo. Cyclin-dependent kinase (CDK) inhibits MCM loading by phosphorylating the origin recognition complex (ORC) and promotes CMG formation by phosphorylating Sld2 and Sld3. Dbf4-dependent kinase (DDK) promotes replication by phosphorylating MCM, and can act either before or after CDK. These experiments define the minimum complement of proteins, protein kinase substrates and co-factors required for regulated eukaryotic DNA replication.

Interaction of CtBP with adenovirus E1A suppresses immortalization of primary epithelial cells and enhances virus replication during productive infection.

PubMed

Subramanian, T; Zhao, Ling-Jun; Chinnadurai, G

2013-09-01

Adenovirus E1A induces cell proliferation, oncogenic transformation and promotes viral replication through interaction with p300/CBP, TRRAP/p400 multi-protein complex and the retinoblastoma (pRb) family proteins through distinct domains in the E1A N-terminal region. The C-terminal region of E1A suppresses E1A/Ras co-transformation and interacts with FOXK1/K2, DYRK1A/1B/HAN11 and CtBP1/2 (CtBP) protein complexes. To specifically dissect the role of CtBP interaction with E1A, we engineered a mutation (DL→AS) within the CtBP-binding motif, PLDLS, and investigated the effect of the mutation on immortalization and Ras cooperative transformation of primary cells and viral replication. Our results suggest that CtBP-E1A interaction suppresses immortalization and Ras co-operative transformation of primary rodent epithelial cells without significantly influencing the tumorigenic activities of transformed cells in immunodeficient and immunocompetent animals. During productive infection, CtBP-E1A interaction enhances viral replication in human cells. Between the two CtBP family proteins, CtBP2 appears to restrict viral replication more than CtBP1 in human cells. Copyright © 2013 Elsevier Inc. All rights reserved.

Interaction of CtBP with adenovirus E1A suppresses immortalization of primary epithelial cells and enhances virus replication during productive infection

PubMed Central

Subramanian, T.; Zhao, Ling-jun; Chinnadurai, G.

2013-01-01

Adenovirus E1A induces cell proliferation, oncogenic transformation and promotes viral replication through interaction with p300/CBP, TRRAP/p400 multi-protein complex and the retinoblastoma (pRb) family proteins through distinct domains in the E1A N-terminal region. The C-terminal region of E1A suppresses E1A/Ras co-transformation and interacts with FOXK1/K2, DYRK1A/1B/HAN11 and CtBP1/2 (CtBP) protein complexes. To specifically dissect the role of CtBP interaction with E1A, we engineered a mutation (DL→AS) within the CtBP-binding motif, PLDLS, and investigated the effect of the mutation on immortalization and Ras cooperative transformation of primary cells and viral replication. Our results suggest that CtBP-E1A interaction suppresses immortalization and Ras co-operative transformation of primary rodent epithelial cells without significantly influencing the tumorigenic activities of transformed cells in immunodeficient and immunocompetent animals. During productive infection, CtBP-E1A interaction enhances viral replication in human cells. Between the two CtBP family proteins, CtBP2 appears to restrict viral replication more than CtBP1 in human cells. PMID:23747199

Transcription of INO2 and INO4 is regulated by the state of protein N-myristoylation in Saccharomyces cerevisiae.

PubMed Central

Cok, S J; Martin, C G; Gordon, J I

1998-01-01

Inositol regulates transcription of Saccharomyces cerevisiae genes required for de novo synthesis of acylCoAs and phospholipids. Removal of inositol results in transcriptional activation by heterodimeric complexes of two bHLH proteins, Ino2p and Ino4p. In the presence of inositol, transcription is repressed by Opi1p. MyristoylCoA:protein N-myristoyltransferase (Nmt1p) is an essential enzyme whose activity is influenced by cellular myristoylCoA pool size and availability. nmt451Dp contains a Gly451-->Asp substitution that produces temperature-dependent reductions in affinity for myristoylCoA and associated reductions in acylation of cellular N-myristoylproteins. The conditional lethality produced by nmt1-451D is rescued at temperatures up to 33 degreesC by withdrawal of inositol. We tested the hypothesis that N-myristoylproteins function to regulate INO2, INO4 and/or OPI1 transcription, thereby affecting the expression of inositol-sensitive genes that influence myristoylCoA metabolism. The effect of nmt1-451D on INO2 , INO4 and OPI1 promoter activities was examined by introducing episomes, containing their 5' non-transcribed domains linked to reporters, into isogenic NMT1 and nmt1-451D cells. The activity of INO2 is significantly higher, INO4 significantly lower and OPI1 unaffected in nmt1-451D cells, both in the presence and absence of inositol. These changes are associated with a net increase in expression of some inositol target genes, including FAS1 . FAS1 encodes one of the subunits of the fatty acid synthase complex that catalyzes de novo acylCoA (including myristoylCoA) biosynthesis. Augmented expression of FAS1 overcomes the kinetic defects in nmt451Dp. FAS1 expression is Ino2p-dependent in NMT1 cells at 24-33 degreesC. In contrast, FAS1 expression becomes Ino2p-independent in nmt1-451D cells at temperatures where efficient acylation of cellular N-myristoylproteins is jeopardized. The ability to maintain expression of FAS1 in nmt1-451Dino2 Delta cells suggests the existence of another transcription factor, or factors, whose expression/activity is inversely related to overall levels of cellular protein N-myristoy-lation. This factor is not functionally identical to Ino2p since other inositol-responsive genes (e.g. CHO1 ) maintain INO2 -dependent expression in nmt1-451D cells. PMID:9611229

Function analysis of Ac-PCNA and Sf-PCNA during the Autographa californica multiple nucleopolyhedrovirus infection process.

PubMed

Fu, Yuejun; Wang, Ruisheng; Liang, Aihua

2018-06-01

The baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) possesses a gene, ac-pcna or ac49, which encodes a protein with similarity to proliferating cell nuclear antigen (PCNA). Homologs of this gene code for DNA polymerase processivity factors and are essential in the DNA replication systems. But the function of ac-pcna still remains unclear. To define the function of Ac-pcna in AcMNPV and Sf-pcna in host Sf9 cells, Bac-to-Bac baculovirus expression system was used to generate two recombinant baculoviruses: AcMNPV-Ac-pcna-EGFP and AcMNPV-Sf-pcna-EGFP. Results indicated that AcMNPV-mediated overexpression of Ac-PCNA and Sf-PCNA could stimulate replication of AcMNPV genome in the host Sf9 cells. Meanwhile, either AcMNPV-Ac-pcna-EGFP or AcMNPV-Sf-pcna-EGFP had a significant stimulating effect on Sf9 genome replication during infection. We also found that Ac-PCNA and Sf-PCNA could promote the production of budded virus. Ac-PCNA could improve the transcription level of ie2 gene dramatically and further improved the transcription of late gene, for example 38 K and vp39, at 12 h p.i.. Moreover, insecticidal potency test showed that the larvae of Beet armyworm in the AcMNPV-Ac-pcna-EGFP and AcMNPV-Sf-pcna-EGFP groups had a higher mortality rate (83.33 and 91.67%), a lower pupation rate (16.67 and 8.33%), and a lower emergence rate (6.67 and 3.33%), compared with those in AcMNPV-EGFP group. The function of Ac-PCNA and Sf-PCNA was confirmed in this study, which provided the theoretical foundation for using and modifying AcMNPV.

Milk pH as a function of CO2 concentration, temperature, and pressure in a heat exchanger.

PubMed

Ma, Y; Barbano, D M

2003-12-01

Raw skim milk, with or without added CO2, was heated, held, and cooled in a small pilot-scale tubular heat exchanger (372 ml/min). The experiment was replicated twice, and, for each replication, milk was first carbonated at 0 to 1 degree C to contain 0 (control), 600, 1200, 1800, and 2400 ppm added CO2 using a continuous carbonation unit. After storage at 0 to 1 degree C, portions of milk at each CO2 concentration were heated to 40, 56, 72, and 80 degrees C, held at the desired temperature for 30 s (except 80 degrees C, holding 20 s) and cooled to 0 to 1 degree C. At each temperature, five pressures were applied: 69, 138, 207, 276, and 345 kPa. Pressure was controlled with a needle valve at the heat exchanger exit. Both the pressure gauge and pH probe were inline at the end of the holding section. Milk pH during heating depended on CO2 concentration, temperature, and pressure. During heating of milk without added CO2, pH decreased linearly as a function of increasing temperature but was independent of pressure. In general, the pH of milk with added CO2 decreased with increasing CO2 concentration and pressure. For milk with added CO2, at a fixed CO2 concentration, the effect of pressure on pH decrease was greater at a higher temperature. At a fixed temperature, the effect of pressure on pH decrease was greater for milk with a higher CO2 concentration. Thermal death of bacteria during pasteurization of milk without added CO2 is probably due not only to temperature but also to the decrease in pH that occurs during the process. Increasing milk CO2 concentration and pressure decreases the milk pH even further during heating and may further enhance the microbial killing power of pasteurization.

A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element

PubMed Central

Thomas, Jacob; Lee, Catherine A.; Grossman, Alan D.

2013-01-01

Integrative and conjugative elements (ICEs) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT) by the ICE–encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP), encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability. PMID:23326247

Performance of genetic risk factors in prediction of trichloroethylene induced hypersensitivity syndrome.

PubMed

Dai, Yufei; Chen, Ying; Huang, Hanlin; Zhou, Wei; Niu, Yong; Zhang, Mingrong; Bin, Ping; Dong, Haiyan; Jia, Qiang; Huang, Jianxun; Yi, Juan; Liao, Qijun; Li, Haishan; Teng, Yanxia; Zang, Dan; Zhai, Qingfeng; Duan, Huawei; Shen, Juan; He, Jiaxi; Meng, Tao; Sha, Yan; Shen, Meili; Ye, Meng; Jia, Xiaowei; Xiang, Yingping; Huang, Huiping; Wu, Qifeng; Shi, Mingming; Huang, Xianqing; Yang, Huanming; Luo, Longhai; Li, Sai; Li, Lin; Zhao, Jinyang; Li, Laiyu; Wang, Jun; Zheng, Yuxin

2015-07-20

Trichloroethylene induced hypersensitivity syndrome is dose-independent and potentially life threatening disease, which has become one of the serious occupational health issues and requires intensive treatment. To discover the genetic risk factors and evaluate the performance of risk prediction model for the disease, we conducted genomewide association study and replication study with total of 174 cases and 1761 trichloroethylene-tolerant controls. Fifty seven SNPs that exceeded the threshold for genome-wide significance (P < 5 × 10(-8)) were screened to relate with the disease, among which two independent SNPs were identified, that is rs2857281 at MICA (odds ratio, 11.92; P meta = 1.33 × 10(-37)) and rs2523557 between HLA-B and MICA (odds ratio, 7.33; P meta = 8.79 × 10(-35)). The genetic risk score with these two SNPs explains at least 20.9% of the disease variance and up to 32.5-fold variation in inter-individual risk. Combining of two SNPs as predictors for the disease would have accuracy of 80.73%, the area under receiver operator characteristic curves (AUC) scores was 0.82 with sensitivity of 74% and specificity of 85%, which was considered to have excellent discrimination for the disease, and could be considered for translational application for screening employees before exposure.

Non-structural proteins P17 and P33 are involved in the assembly of the internal membrane-containing virus PRD1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karttunen, Jenni; Mäntynen, Sari; Ihalainen, Teemu O.

2015-08-15

Bacteriophage PRD1, which has been studied intensively at the structural and functional levels, still has some gene products with unknown functions and certain aspects of the PRD1 assembly process have remained unsolved. In this study, we demonstrate that the phage-encoded non-structural proteins P17 and P33, either individually or together, complement the defect in a temperature-sensitive GroES mutant of Escherichia coli for host growth and PRD1 propagation. Confocal microscopy of fluorescent fusion proteins revealed co-localisation between P33 and P17 as well as between P33 and the host chaperonin GroEL. A fluorescence recovery after photobleaching assay demonstrated that the diffusion of themore » P33 fluorescent fusion protein was substantially slower in E. coli than theoretically calculated, presumably resulting from intermolecular interactions. Our results indicate that P33 and P17 function in procapsid assembly, possibly in association with the host chaperonin complex GroEL/GroES. - Highlights: • Two non-structural proteins of PRD1 are involved in the virus assembly. • P17 and P33 complement the defect in GroES of Escherichia coli. • P33 co-localises with GroEL and P17 in the bacterium. • Slow motion of P33 in the bacterium suggests association with cellular components.« less

p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PLpro via E3 ubiquitin ligase RCHY1.

PubMed

Ma-Lauer, Yue; Carbajo-Lozoya, Javier; Hein, Marco Y; Müller, Marcel A; Deng, Wen; Lei, Jian; Meyer, Benjamin; Kusov, Yuri; von Brunn, Brigitte; Bairad, Dev Raj; Hünten, Sabine; Drosten, Christian; Hermeking, Heiko; Leonhardt, Heinrich; Mann, Matthias; Hilgenfeld, Rolf; von Brunn, Albrecht

2016-08-30

Highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) has developed strategies to inhibit host immune recognition. We identify cellular E3 ubiquitin ligase ring-finger and CHY zinc-finger domain-containing 1 (RCHY1) as an interacting partner of the viral SARS-unique domain (SUD) and papain-like protease (PL(pro)), and, as a consequence, the involvement of cellular p53 as antagonist of coronaviral replication. Residues 95-144 of RCHY1 and 389-652 of SUD (SUD-NM) subdomains are crucial for interaction. Association with SUD increases the stability of RCHY1 and augments RCHY1-mediated ubiquitination as well as degradation of p53. The calcium/calmodulin-dependent protein kinase II delta (CAMK2D), which normally influences RCHY1 stability by phosphorylation, also binds to SUD. In vivo phosphorylation shows that SUD does not regulate phosphorylation of RCHY1 via CAMK2D. Similarly to SUD, the PL(pro)s from SARS-CoV, MERS-CoV, and HCoV-NL63 physically interact with and stabilize RCHY1, and thus trigger degradation of endogenous p53. The SARS-CoV papain-like protease is encoded next to SUD within nonstructural protein 3. A SUD-PL(pro) fusion interacts with RCHY1 more intensively and causes stronger p53 degradation than SARS-CoV PL(pro) alone. We show that p53 inhibits replication of infectious SARS-CoV as well as of replicons and human coronavirus NL63. Hence, human coronaviruses antagonize the viral inhibitor p53 via stabilizing RCHY1 and promoting RCHY1-mediated p53 degradation. SUD functions as an enhancer to strengthen interaction between RCHY1 and nonstructural protein 3, leading to a further increase in in p53 degradation. The significance of these findings is that down-regulation of p53 as a major player in antiviral innate immunity provides a long-sought explanation for delayed activities of respective genes.

p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PLpro via E3 ubiquitin ligase RCHY1

PubMed Central

Ma-Lauer, Yue; Carbajo-Lozoya, Javier; Müller, Marcel A.; Deng, Wen; Lei, Jian; Meyer, Benjamin; Kusov, Yuri; von Brunn, Brigitte; Bairad, Dev Raj; Hünten, Sabine; Drosten, Christian; Hermeking, Heiko; Leonhardt, Heinrich; Mann, Matthias; Hilgenfeld, Rolf; von Brunn, Albrecht

2016-01-01

Highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) has developed strategies to inhibit host immune recognition. We identify cellular E3 ubiquitin ligase ring-finger and CHY zinc-finger domain-containing 1 (RCHY1) as an interacting partner of the viral SARS-unique domain (SUD) and papain-like protease (PLpro), and, as a consequence, the involvement of cellular p53 as antagonist of coronaviral replication. Residues 95–144 of RCHY1 and 389–652 of SUD (SUD-NM) subdomains are crucial for interaction. Association with SUD increases the stability of RCHY1 and augments RCHY1-mediated ubiquitination as well as degradation of p53. The calcium/calmodulin-dependent protein kinase II delta (CAMK2D), which normally influences RCHY1 stability by phosphorylation, also binds to SUD. In vivo phosphorylation shows that SUD does not regulate phosphorylation of RCHY1 via CAMK2D. Similarly to SUD, the PLpros from SARS-CoV, MERS-CoV, and HCoV-NL63 physically interact with and stabilize RCHY1, and thus trigger degradation of endogenous p53. The SARS-CoV papain-like protease is encoded next to SUD within nonstructural protein 3. A SUD–PLpro fusion interacts with RCHY1 more intensively and causes stronger p53 degradation than SARS-CoV PLpro alone. We show that p53 inhibits replication of infectious SARS-CoV as well as of replicons and human coronavirus NL63. Hence, human coronaviruses antagonize the viral inhibitor p53 via stabilizing RCHY1 and promoting RCHY1-mediated p53 degradation. SUD functions as an enhancer to strengthen interaction between RCHY1 and nonstructural protein 3, leading to a further increase in in p53 degradation. The significance of these findings is that down-regulation of p53 as a major player in antiviral innate immunity provides a long-sought explanation for delayed activities of respective genes. PMID:27519799

Determination of trace inorganic mercury species in water samples by cloud point extraction and UV-vis spectrophotometry.

PubMed

Ulusoy, Halil Ibrahim

2014-01-01

A new micelle-mediated extraction method was developed for preconcentration of ultratrace Hg(II) ions prior to spectrophotometric determination. 2-(2'-Thiazolylazo)-p-cresol (TAC) and Ponpe 7.5 were used as the chelating agent and nonionic surfactant, respectively. Hg(II) ions form a hydrophobic complex with TAC in a micelle medium. The main factors affecting cloud point extraction efficiency, such as pH of the medium, concentrations of TAC and Ponpe 7.5, and equilibration temperature and time, were investigated in detail. An overall preconcentration factor of 33.3 was obtained upon preconcentration of a 50 mL sample. The LOD obtained under the optimal conditions was 0.86 microg/L, and the RSD for five replicate measurements of 100 microg/L Hg(II) was 3.12%. The method was successfully applied to the determination of Hg in environmental water samples.

HIV infection and hepatitis C virus genotype 1a are associated with phylogenetic clustering among people with recently acquired hepatitis C virus infection.

PubMed

Bartlett, Sofia R; Jacka, Brendan; Bull, Rowena A; Luciani, Fabio; Matthews, Gail V; Lamoury, Francois M J; Hellard, Margaret E; Hajarizadeh, Behzad; Teutsch, Suzy; White, Bethany; Maher, Lisa; Dore, Gregory J; Lloyd, Andrew R; Grebely, Jason; Applegate, Tanya L

2016-01-01

The aim of this study was to identify factors associated with phylogenetic clustering among people with recently acquired hepatitis C virus (HCV) infection. Participants with available sample at time of HCV detection were selected from three studies; the Australian Trial in Acute Hepatitis C, the Hepatitis C Incidence and Transmission Study - Prison and Community. HCV RNA was extracted and Core to E2 region of HCV sequenced. Clusters were identified from maximum likelihood trees with 1000 bootstrap replicates using 90% bootstrap and 5% genetic distance threshold. Among 225 participants with available Core-E2 sequence (ATAHC, n=113; HITS-p, n=90; and HITS-c, n=22), HCV genotype prevalence was: G1a: 38% (n=86), G1b: 5% (n=12), G2a: 1% (n=2), G2b: 5% (n=11), G3a: 48% (n=109), G6a: 1% (n=2) and G6l 1% (n=3). Of participants included in phylogenetic trees, 22% of participants were in a pair/cluster (G1a-35%, 30/85, mean maximum genetic distance=0.031; G3a-11%, 12/106, mean maximum genetic distance=0.021; other genotypes-21%, 6/28, mean maximum genetic distance=0.023). Among HCV/HIV co-infected participants, 50% (18/36) were in a pair/cluster, compared to 16% (30/183) with HCV mono-infection (P=<0.001). Factors independently associated with phylogenetic clustering were HIV co-infection [vs. HCV mono-infection; adjusted odds ratio (AOR) 4.24; 95%CI 1.91, 9.39], and HCV G1a infection (vs. other HCV genotypes; AOR 3.33, 95%CI 0.14, 0.61).HCV treatment and prevention strategies, including enhanced antiviral therapy, should be optimised. The impact of targeting of HCV treatment as prevention to populations with higher phylogenetic clustering, such as those with HIV co-infection, could be explored through mathematical modelling. Copyright © 2015 Elsevier B.V. All rights reserved.

Suitability of human Tenon's fibroblasts as feeder cells for culturing human limbal epithelial stem cells.

PubMed

Scafetta, Gaia; Tricoli, Eleonora; Siciliano, Camilla; Napoletano, Chiara; Puca, Rosa; Vingolo, Enzo Maria; Cavallaro, Giuseppe; Polistena, Andrea; Frati, Giacomo; De Falco, Elena

2013-12-01

Corneal epithelial regeneration through ex vivo expansion of limbal stem cells (LSCs) on 3T3-J2 fibroblasts has revealed some limitations mainly due to the corneal microenvironment not being properly replicated, thus affecting long term results. Insights into the feeder cells that are used to expand LSCs and the mechanisms underlying the effects of human feeder cells have yet to be fully elucidated. We recently developed a standardized methodology to expand human Tenon's fibroblasts (TFs). Here we aimed to investigate whether TFs can be employed as feeder cells for LSCs, characterizing the phenotype of the co-cultures and assessing what human soluble factors are secreted. The hypothesis that TFs could be employed as alternative human feeder layer has not been explored yet. LSCs were isolated from superior limbus biopsies, co-cultured on TFs, 3T3-J2 or dermal fibroblasts (DFs), then analyzed by immunofluorescence (p63α), colony-forming efficiency (CFE) assay and qPCR for a panel of putative stem cell and epithelial corneal differentiation markers (KRT3). Co-cultures supernatants were screened for a set of soluble factors. Results showed that the percentage of p63α(+)LSCs co-cultured onto TFs was significantly higher than those on DFs (p = 0.032) and 3T3-J2 (p = 0.047). Interestingly, LSCs co-cultures on TFs exhibited both significantly higher CFE and mRNA expression levels of ΔNp63α than on 3T3-J2 and DFs (p < 0.0001), showing also significantly greater levels of soluble factors (IL-6, HGF, b-FGF, G-CSF, TGF-β3) than LSCs on DFs. Therefore, TFs could represent an alternative feeder layer to both 3T3-J2 and DFs, potentially providing a suitable microenvironment for LSCs culture.

Inhibition of severe acute respiratory syndrome coronavirus replication in a lethal SARS-CoV BALB/c mouse model by stinging nettle lectin, Urtica dioica agglutinin.

PubMed

Kumaki, Yohichi; Wandersee, Miles K; Smith, Aaron J; Zhou, Yanchen; Simmons, Graham; Nelson, Nathan M; Bailey, Kevin W; Vest, Zachary G; Li, Joseph K-K; Chan, Paul Kay-Sheung; Smee, Donald F; Barnard, Dale L

2011-04-01

Urtica dioica agglutinin (UDA) is a small plant monomeric lectin, 8.7 kDa in size, with an N-acetylglucosamine specificity that inhibits viruses from Nidovirales in vitro. In the current study, we first examined the efficacy of UDA on the replication of different SARS-CoV strains in Vero 76 cells. UDA inhibited virus replication in a dose-dependent manner and reduced virus yields of the Urbani strain by 90% at 1.1 ± 0.4 μg/ml in Vero 76 cells. Then, UDA was tested for efficacy in a lethal SARS-CoV-infected BALB/c mouse model. BALB/c mice were infected with two LD50 (575 PFU) of virus for 4 h before the mice were treated intraperitoneally with UDA at 20, 10, 5 or 0 mg/kg/day for 4 days. Treatment with UDA at 5 mg/kg significantly protected the mice against a lethal infection with mouse-adapted SARS-CoV (p < 0.001), but did not significantly reduce virus lung titers. All virus-infected mice receiving UDA treatments were also significantly protected against weight loss (p < 0.001). UDA also effectively reduced lung pathology scores. At day 6 after virus exposure, all groups of mice receiving UDA had much lower lung weights than did the placebo-treated mice. Thus, our data suggest that UDA treatment of SARS infection in mice leads to a substantial therapeutic effect that protects mice against death and weight loss. Furthermore, the mode of action of UDA in vitro was further investigated using live SARS-CoV Urbani strain virus and retroviral particles pseudotyped with SARS-CoV spike (S). UDA specifically inhibited the replication of live SARS-CoV or SARS-CoV pseudotyped virus when added just before, but not after, adsorption. These data suggested that UDA likely inhibits SARS-CoV infection by targeting early stages of the replication cycle, namely, adsorption or penetration. In addition, we demonstrated that UDA neutralizes the virus infectivity, presumably by binding to the SARS-CoV spike (S) glycoprotein. Finally, the target molecule for the inhibition of virus replication was partially characterized. When UDA was exposed to N-acetylglucosamine and then UDA was added to cells just prior to adsorption, UDA did not inhibit the virus infection. These data support the conclusion that UDA might bind to N-acetylglucosamine-like residues present on the glycosylated envelope glycoproteins, thereby preventing virus attachment to cells. Copyright © 2011 Elsevier B.V. All rights reserved.

Inhibition of severe acute respiratory syndrome coronavirus replication in a lethal SARS-CoV BALB/c mouse model by stinging nettle lectin, Urtica dioica agglutinin

PubMed Central

Kumaki, Yohichi; Wandersee, Miles K.; Smith, Aaron J.; Zhou, Yanchen; Simmons, Graham; Nelson, Nathan M.; Bailey, Kevin W.; Vest, Zachary G.; Li, Joseph K.-K.; Chan, Paul Kay-Sheung; Smee, Donald F.; Barnard, Dale L.

2011-01-01

Urtica dioica agglutinin (UDA) is a small plant monomeric lectin, 8.7 kDa in size, with an N-acetylglucosamine specificity that inhibits viruses from Nidovirales in vitro. In the current study, we first examined the efficacy of UDA on the replication of different SARS-CoV strains in Vero 76 cells. UDA inhibited virus replication in a dose-dependent manner and reduced virus yields of the Urbani strain by 90% at 1.1 ± 0.4 µg/ml in Vero 76 cells. Then, UDA was tested for efficacy in a lethal SARS-CoV-infected BALB/c mouse model. BALB/c mice were infected with two LD50 (575 PFU) of virus for 4 hours before the mice were treated intraperitoneally with UDA at 20, 10, 5 or 0 mg/kg/day for 4 days. Treatment with UDA at 5 mg/kg significantly protected the mice against a lethal infection with mouse-adapted SARS-CoV (p<0.001), but did not significantly reduce virus lung titers. All virus-infected mice receiving UDA treatments were also significantly protected against weight loss (p<0.001). UDA also effectively reduced lung pathology scores. At day 6 after virus exposure, all groups of mice receiving UDA had much lower lung weights than did the placebo-treated mice. Thus, our data suggest that UDA treatment of SARS infection in mice leads to a substantial therapeutic effect that protects mice against death and weight loss. Furthermore, the mode of action of UDA in vitro was further investigated using live SARS-CoV Urbani strain virus and retroviral particles pseudotyped with SARS-CoV spike (S). UDA specifically inhibited the replication of live SARS-CoV or SARS-CoV pseudotyped virus when added just before, but not after, adsorption. These data suggested that UDA likely inhibits SARS-CoV infection by targeting early stages of the replication cycle, namely, adsorption or penetration. In addition, we demonstrated that UDA neutralizes the virus infectivity, presumably by binding to the SARS-CoV spike (S) glycoprotein. Finally, the target molecule for inhibition of virus replication was partially characterized. When UDA was exposed to N-acetylglucosamine and then UDA was added to cells just prior to adsorption, UDA did not inhibit the virus infection. These data support the conclusion that UDA might bind to N-acetylglucosamine-like residues present on the glycosylated envelope glycoproteins, thereby preventing virus attachment to cells. PMID:21338626

Common variants at 12q14 and 12q24 are associated with hippocampal volume.

PubMed

Bis, Joshua C; DeCarli, Charles; Smith, Albert Vernon; van der Lijn, Fedde; Crivello, Fabrice; Fornage, Myriam; Debette, Stephanie; Shulman, Joshua M; Schmidt, Helena; Srikanth, Velandai; Schuur, Maaike; Yu, Lei; Choi, Seung-Hoan; Sigurdsson, Sigurdur; Verhaaren, Benjamin F J; DeStefano, Anita L; Lambert, Jean-Charles; Jack, Clifford R; Struchalin, Maksim; Stankovich, Jim; Ibrahim-Verbaas, Carla A; Fleischman, Debra; Zijdenbos, Alex; den Heijer, Tom; Mazoyer, Bernard; Coker, Laura H; Enzinger, Christian; Danoy, Patrick; Amin, Najaf; Arfanakis, Konstantinos; van Buchem, Mark A; de Bruijn, Renée F A G; Beiser, Alexa; Dufouil, Carole; Huang, Juebin; Cavalieri, Margherita; Thomson, Russell; Niessen, Wiro J; Chibnik, Lori B; Gislason, Gauti K; Hofman, Albert; Pikula, Aleksandra; Amouyel, Philippe; Freeman, Kevin B; Phan, Thanh G; Oostra, Ben A; Stein, Jason L; Medland, Sarah E; Vasquez, Alejandro Arias; Hibar, Derrek P; Wright, Margaret J; Franke, Barbara; Martin, Nicholas G; Thompson, Paul M; Nalls, Michael A; Uitterlinden, Andre G; Au, Rhoda; Elbaz, Alexis; Beare, Richard J; van Swieten, John C; Lopez, Oscar L; Harris, Tamara B; Chouraki, Vincent; Breteler, Monique M B; De Jager, Philip L; Becker, James T; Vernooij, Meike W; Knopman, David; Fazekas, Franz; Wolf, Philip A; van der Lugt, Aad; Gudnason, Vilmundur; Longstreth, W T; Brown, Matthew A; Bennett, David A; van Duijn, Cornelia M; Mosley, Thomas H; Schmidt, Reinhold; Tzourio, Christophe; Launer, Lenore J; Ikram, M Arfan; Seshadri, Sudha

2012-04-15

Aging is associated with reductions in hippocampal volume that are accelerated by Alzheimer's disease and vascular risk factors. Our genome-wide association study (GWAS) of dementia-free persons (n = 9,232) identified 46 SNPs at four loci with P values of <4.0 × 10(-7). In two additional samples (n = 2,318), associations were replicated at 12q14 within MSRB3-WIF1 (discovery and replication; rs17178006; P = 5.3 × 10(-11)) and at 12q24 near HRK-FBXW8 (rs7294919; P = 2.9 × 10(-11)). Remaining associations included one SNP at 2q24 within DPP4 (rs6741949; P = 2.9 × 10(-7)) and nine SNPs at 9p33 within ASTN2 (rs7852872; P = 1.0 × 10(-7)); along with the chromosome 12 associations, these loci were also associated with hippocampal volume (P < 0.05) in a third younger, more heterogeneous sample (n = 7,794). The SNP in ASTN2 also showed suggestive association with decline in cognition in a largely independent sample (n = 1,563). These associations implicate genes related to apoptosis (HRK), development (WIF1), oxidative stress (MSR3B), ubiquitination (FBXW8) and neuronal migration (ASTN2), as well as enzymes targeted by new diabetes medications (DPP4), indicating new genetic influences on hippocampal size and possibly the risk of cognitive decline and dementia.

Magnetic colloidal superparticles of Co, Mn and Ni ferrite featured with comb-type and/or linear amphiphilic polyelectrolytes; NMR and MRI relaxometry.

PubMed

Menelaou, Melita; Iatridi, Zacharoula; Tsougos, Ioannis; Vasiou, Katerina; Dendrinou-Samara, Catherine; Bokias, Georgios

2015-06-28

The ability to encapsulate hydrophobic ferrites in colloidal superparticle structures of an a-telechelic hexadecyl-functionalized poly(methacrylic acid) (C16H33-PMAA) polymer with a linear architecture was investigated and compared with that of two amphiphilic comb-type water-soluble copolymers, namely, P(ANa-co-DAAm) and P(MANa-co-DMA), which are comprised of a poly(sodium acrylate) or poly(sodium methacrylate) backbone and pendent dodecyl acrylamide or dodecyl methacrylate chains, respectively. In the case of C16H33-PMAA, the pH-sensitive self-assembly behavior, which was studied through Nile Red probing and TEM, was related to its encapsulation properties. Hydrophobic MFe2O4 nanoparticles coated with oleylamine (MFe2O4@OAm MNPs, where M = Co, Mn, Ni) with a similar shape and size (∼9 nm) and magnetization values of 87.4, 63.1 and 55.0 emu g(-1) for CoFe2O4@OAm, MnFe2O4@OAm and NiFe2O4@OAm, respectively, were successfully encapsulated into the hydrophobic cores of spherical micellar structures formed by the copolymers in an aqueous solution through a solvent mixing procedure. The synthesized magnetic colloidal superparticles fell in the static dephasing regime (SDR). NMR relaxivity measurements of MFe2O4@P(ANa-co-DAAm), MFe2O4@P(MANa-co-DMA) and MFe2O4@C16H33-PMAA at pH = 4.5 and pH = 7 (where M = Co, Mn, Ni) at 11.7 T were recorded and the transverse relaxivity (r2) (mM(-1) s(-1)) was determined. Among all, the CoFe2O4@polymers demonstrated the highest r2 relaxivity values, ranging from 61.6 for CoFe2O4@C16H33-PMAA (pH = 7) to 316.0 mM(-1) s(-1) for CoFe2O4@P(ANa-co-DAAm). The relaxation efficiency (r1 and r2) of CoFe2O4@P(ANa-co-DAAm) was investigated further by magnetic resonance imaging (MRI) at 1.5 T and 3 T and the r2/r1 ratios were found to be 16.5 and 18.2, respectively, indicating its potential use as a T2 contrast agent.

Chronic Bee Paralysis Virus and Nosema ceranae Experimental Co-Infection of Winter Honey Bee Workers (Apis mellifera L.)

PubMed Central

Toplak, Ivan; Jamnikar Ciglenečki, Urška; Aronstein, Katherine; Gregorc, Aleš

2013-01-01

Chronic bee paralysis virus (CBPV) is an important viral disease of adult bees which induces significant losses in honey bee colonies. Despite comprehensive research, only limited data is available from experimental infection for this virus. In the present study winter worker bees were experimentally infected in three different experiments. Bees were first inoculated per os (p/o) or per cuticle (p/c) with CBPV field strain M92/2010 in order to evaluate the virus replication in individual bees. In addition, potential synergistic effects of co-infection with CBPV and Nosema ceranae (N. ceranae) on bees were investigated. In total 558 individual bees were inoculated in small cages and data were analyzed using quantitative real time RT-PCR (RT-qPCR). Our results revealed successful replication of CBPV after p/o inoculation, while it was less effective when bees were inoculated p/c. Dead bees harbored about 1,000 times higher copy numbers of the virus than live bees. Co-infection of workers with CBPV and N. ceranae using either method of virus inoculation (p/c or p/o) showed increased replication ability for CBPV. In the third experiment the effect of inoculation on bee mortality was evaluated. The highest level of bee mortality was observed in a group of bees inoculated with CBPV p/o, followed by a group of workers simultaneously inoculated with CBPV and N. ceranae p/o, followed by the group inoculated with CBPV p/c and the group with only N. ceranae p/o. The experimental infection with CBPV showed important differences after p/o or p/c inoculation in winter bees, while simultaneous infection with CBPV and N. ceranae suggesting a synergistic effect after inoculation. PMID:24056674

On the causes of trends in the seasonal amplitude of atmospheric CO2.

PubMed

Piao, Shilong; Liu, Zhuo; Wang, Yilong; Ciais, Philippe; Yao, Yitong; Peng, Shushi; Chevallier, Frédéric; Friedlingstein, Pierre; Janssens, Ivan A; Peñuelas, Josep; Sitch, Stephen; Wang, Tao

2018-02-01

No consensus has yet been reached on the major factors driving the observed increase in the seasonal amplitude of atmospheric CO 2 in the northern latitudes. In this study, we used atmospheric CO 2 records from 26 northern hemisphere stations with a temporal coverage longer than 15 years, and an atmospheric transport model prescribed with net biome productivity (NBP) from an ensemble of nine terrestrial ecosystem models, to attribute change in the seasonal amplitude of atmospheric CO 2 . We found significant (p < .05) increases in seasonal peak-to-trough CO 2 amplitude (AMP P -T ) at nine stations, and in trough-to-peak amplitude (AMP T -P ) at eight stations over the last three decades. Most of the stations that recorded increasing amplitudes are in Arctic and boreal regions (>50°N), consistent with previous observations that the amplitude increased faster at Barrow (Arctic) than at Mauna Loa (subtropics). The multi-model ensemble mean (MMEM) shows that the response of ecosystem carbon cycling to rising CO 2 concentration (eCO 2 ) and climate change are dominant drivers of the increase in AMP P -T and AMP T -P in the high latitudes. At the Barrow station, the observed increase of AMP P -T and AMP T -P over the last 33 years is explained by eCO 2 (39% and 42%) almost equally than by climate change (32% and 35%). The increased carbon losses during the months with a net carbon release in response to eCO 2 are associated with higher ecosystem respiration due to the increase in carbon storage caused by eCO 2 during carbon uptake period. Air-sea CO 2 fluxes (10% for AMP P -T and 11% for AMP T -P ) and the impacts of land-use change (marginally significant 3% for AMP P -T and 4% for AMP T -P ) also contributed to the CO 2 measured at Barrow, highlighting the role of these factors in regulating seasonal changes in the global carbon cycle. © 2017 John Wiley & Sons Ltd.

SPRUCE Deep Peat Microbial Diversity, CO2 and CH4 Production in Response to Nutrient, Temperature, and pH Treatments during Incubation Studies.

DOE Data Explorer

A., Kluber Laurel [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Allen, Samantha A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hendershot, Nicholas [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hanson, Paul J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Schadt, Christopher W. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2014-09-01

This data set contains the results of a microcosm incubation study on deep peat collected from the SPRUCE experimental site in the S1 Bog in September 2014. Microcosms were monitored for CO2 and CH4 production, and microbial community dynamics were assessed using qPCR and amplicon sequencing.The experiment was designed with a full factorial design with elevated temperature, nitrogen (N), (P), and pH treatments was used with samples from each transect serving replicates. In all, 96 microcosms were constructed to account for the 16 treatment combinations (N x P x pH x temperature), 2 time points, and 3 replicates. Temperature treatments were 6 °C, to mimic the SPRUCE ambient plot temperatures, and 15 °C to mimic the SPRUCE +9 °C treatment.

Cellular Aspects of Prion Replication In Vitro

PubMed Central

Grassmann, Andrea; Wolf, Hanna; Hofmann, Julia; Graham, James; Vorberg, Ina

2013-01-01

Prion diseases or transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders in mammals that are caused by unconventional agents predominantly composed of aggregated misfolded prion protein (PrP). Prions self-propagate by recruitment of host-encoded PrP into highly ordered β-sheet rich aggregates. Prion strains differ in their clinical, pathological and biochemical characteristics and are likely to be the consequence of distinct abnormal prion protein conformers that stably replicate their alternate states in the host cell. Understanding prion cell biology is fundamental for identifying potential drug targets for disease intervention. The development of permissive cell culture models has greatly enhanced our knowledge on entry, propagation and dissemination of TSE agents. However, despite extensive research, the precise mechanism of prion infection and potential strain effects remain enigmatic. This review summarizes our current knowledge of the cell biology and propagation of prions derived from cell culture experiments. We discuss recent findings on the trafficking of cellular and pathologic PrP, the potential sites of abnormal prion protein synthesis and potential co-factors involved in prion entry and propagation. PMID:23340381

Frequent nasopharyngeal suctioning as a risk factor associated with neonatal coagulase-negative staphylococcal colonisation and sepsis

PubMed Central

Boo, Nem Yun; Suhaida, Abdul Rahman; Rohana, Jaafar

2015-01-01

INTRODUCTION This case-control study aimed to determine whether catheter use was significantly associated with coagulase-negative staphylococci (CoNS) colonisation and/or sepsis in neonates. METHODS Weekly swabs of the nose, umbilicus, rectum, wounds, eye discharge and intravenous catheter tips (after removal) of infants admitted to the neonatal intensive care unit of Universiti Kebangsaan Malaysia Medical Centre, Malaysia, were cultured. CoNS sepsis was diagnosed if pure growth of CoNS was cultured from the peripheral blood specimen of symptomatic infants. For each infant with CoNS colonisation or sepsis, a control infant was retrospectively and randomly selected from unaffected infants in the ward. Multivariate analyses were performed to determine whether catheter use was a significant risk factor. RESULTS CoNS colonisation was detected in 113 (8.7%) infants. CoNS sepsis was found in 12 (10.6%) infants with CoNS colonisation and 7 (0.6%) infants without CoNS colonisation. Multivariate analysis showed that the following were significantly associated with CoNS colonisation: conjunctivitis (adjusted odds ratio [OR] 8.2, 95% confidence interval [CI] 1.9–34.8, p = 0.005); central venous catheters (adjusted OR 5.8, 95% CI 1.9–17.8, p = 0.002); and nasopharyngeal and/or oral suctioning more than twice in the 48 hours before positive culture (adjusted OR 7.3, 95% CI 3.3–16.2, p < 0.001). Exposure to frequent nasopharyngeal and/or oral suctioning (adjusted OR 20.8, 95% CI 3.5–125.3, p = 0.001) was the only significant factor associated with CoNS sepsis. CONCLUSION Infants requiring more than two nasopharyngeal and/or oral suctions in the previous 48 hours were found to have a higher risk of developing CoNS colonisation and sepsis. PMID:25532513

The forkhead-like transcription factor (Fhl1p) maintains yeast replicative lifespan by regulating ribonucleotide reductase 1 (RNR1) gene transcription

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, Akiko; Kamei, Yuka; Mukai, Yukio

In eukaryotes, numerous genetic factors contribute to the lifespan including metabolic enzymes, signal transducers, and transcription factors. As previously reported, the forkhead-like transcription factor (FHL1) gene was required for yeast replicative lifespan and cell proliferation. To determine how Fhl1p regulates the lifespan, we performed a DNA microarray analysis of a heterozygous diploid strain deleted for FHL1. We discovered numerous Fhl1p-target genes, which were then screened for lifespan-regulating activity. We identified the ribonucleotide reductase (RNR) 1 gene (RNR1) as a regulator of replicative lifespan. RNR1 encodes a large subunit of the RNR complex, which consists of two large (Rnr1p/Rnr3p) and twomore » small (Rnr2p/Rnr4p) subunits. Heterozygous deletion of FHL1 reduced transcription of RNR1 and RNR3, but not RNR2 and RNR4. Chromatin immunoprecipitation showed that Fhl1p binds to the promoter regions of RNR1 and RNR3. Cells harboring an RNR1 deletion or an rnr1-C428A mutation, which abolishes RNR catalytic activity, exhibited a short lifespan. In contrast, cells with a deletion of the other RNR genes had a normal lifespan. Overexpression of RNR1, but not RNR3, restored the lifespan of the heterozygous FHL1 mutant to the wild-type (WT) level. The Δfhl1/FHL1 mutant conferred a decrease in dNTP levels and an increase in hydroxyurea (HU) sensitivity. These findings reveal that Fhl1p regulates RNR1 gene transcription to maintain dNTP levels, thus modulating longevity by protection against replication stress. - Highlights: • Fhl1p regulates replicative lifespan and transcription of RNR large subunit genes. • Rnr1p uniquely acts as a lifespan regulator independent of the RNR complex. • dNTP levels modulate longevity by protection against replication stress.« less

Forest soil CO2 fluxes as a function of understory removal and N-fixing species addition.

PubMed

Li, Haifang; Fu, Shenglei; Zhao, Hongting; Xia, Hanping

2011-01-01

We report on the effects of forest management practices of understory removal and N-fixing species (Cassia alata) addition on soil CO2 fluxes in an Eucalyptus urophylla plantation (EUp), Acacia crassicarpa plantation (ACp), 10-species-mixed plantation (Tp), and 30-species-mixed plantation (THp) using the static chamber method in southern China. Four forest management treatments, including (1) understory removal (UR); (2) C. alata addition (CA); (3) understory removal and replacement with C. alata (UR+CA); and (4) control without any disturbances (CK), were applied in the above four forest plantations with three replications for each treatment. The results showed that soil CO2 fluxes rates remained at a high level during the rainy season (from April to September), followed by a rapid decrease after October reaching a minimum in February. Soil CO2 fluxes were significantly higher (P < 0.01) in EUp (132.6 mg/(m2 x hr)) and ACp (139.8 mg/(m2 x hr)) than in Tp (94.0 mg/(m2 x hr)) and THp (102.9 mg/(m2 x hr)). Soil CO2 fluxes in UR and CA were significantly higher (P < 0.01) among the four treatments, with values of 105.7, 120.4, 133.6 and 112.2 mg/(m2 x hr) for UR+CA, UR, CA and CK, respectively. Soil CO2 fluxes were positively correlated with soil temperature (P < 0.01), soil moisture (P < 0.01), NO3(-)-N (P < 0.05), and litterfall (P < 0.01), indicating that all these factors might be important controlling variables for soil CO2 fluxes. This study sheds some light on our understanding of soil CO2 flux dynamics in forest plantations under various management practices.

3,3'-Diindolylmethane inhibits VEGF expression through the HIF-1α and NF-κB pathways in human retinal pigment epithelial cells under chemical hypoxic conditions.

PubMed

Park, Hongzoo; Lee, Dae-Sung; Yim, Mi-Jin; Choi, Yung Hyun; Park, Saegwang; Seo, Su-Kil; Choi, Jung Sik; Jang, Won Hee; Yea, Sung Su; Park, Won Sun; Lee, Chang-Min; Jung, Won-Kyo; Choi, Il-Whan

2015-07-01

Oxidative stress in the retinal pigment epithelium (RPE) can lead to the pathological causes of age-related macular degeneration (AMD). Hypoxia induces oxidative damage in retinal pigment epithelial cells (RPE cells). In this study, we investigated the capacity of 3,3'-diindolylmethane (DIM) to reduce the expression of vascular endothelial growth factor (VEGF) under hypoxic conditions, as well as the molecular mechanisms involved. Human RPE cells (ARPE-19 cells) were treated with cobalt chloride (CoCl2, 200 µM) and/or DIM (10 and 20 µM). The production of VEGF was measured by enzyme-linked immunosorbent assay. The translocation of hypoxia-inducible factor-1α (HIF-1α) and nuclear factor-κB (NF-κB) was determined by western blot analysis. The binding activity of HIF-1α and NF-κB was analyzed by electrophoretic mobility shift assay. The phosphorylation levels of mitogen-activated protein kinases (MAPKs) were measured by western blot analysis. The levels of mitochondrial reactive oxygen species (ROS) were detected by fluorescence microplate assay. The results revealed that DIM significantly attenuated the CoCl2-induced expression of VEGF in the ARPE-19 cells. The CoCl2-induced translocation and activation of HIF-1α and NF-κB were also attenuated by treatment with DIM. In addition, DIM inhibited the CoCl2-induced activation of p38 MAPK in the ARPE-19 cells. Pre-treatment with YCG063, a mitochondrial ROS inhibitor, led to the downregulation of the CoCl2-induced production of VEGF by suppressing HIF-1α and NF-κB activity. Taken together, the findings of our study demonstrate that DIM inhibits the CoCl2-induced production of VEGF by suppressing mitochondrial ROS production, thus attenuating the activation of HIF-1α and p38 MAPK/NF-κB.

Architecture and biogenesis of plus-strand RNA virus replication factories

PubMed Central

Paul, David; Bartenschlager, Ralf

2013-01-01

Plus-strand RNA virus replication occurs in tight association with cytoplasmic host cell membranes. Both, viral and cellular factors cooperatively generate distinct organelle-like structures, designated viral replication factories. This compartmentalization allows coordination of the different steps of the viral replication cycle, highly efficient genome replication and protection of the viral RNA from cellular defense mechanisms. Electron tomography studies conducted during the last couple of years revealed the three dimensional structure of numerous plus-strand RNA virus replication compartments and highlight morphological analogies between different virus families. Based on the morphology of virus-induced membrane rearrangements, we propose two separate subclasses: the invaginated vesicle/spherule type and the double membrane vesicle type. This review discusses common themes and distinct differences in the architecture of plus-strand RNA virus-induced membrane alterations and summarizes recent progress that has been made in understanding the complex interplay between viral and co-opted cellular factors in biogenesis and maintenance of plus-strand RNA virus replication factories. PMID:24175228

The Regulatory Interactions of p21 and PCNA in Human Breast Cancer

DTIC Science & Technology

2002-07-01

Proliferating cell nuclear antigen (PCNA) is a multifunctional enzyme involved in multiple cellular processes including DNA replication and repair...During DNA replication , PCNA function as an accessory factor- for the DNA polymerases E arid and are part of a multiprotein DNA replication complex...a cyclin-dependent kinase inhibitor, p21WAF1 ability to inhibit DNA replication in response to DNA damage has been wall characterized. Interestingly

IKZF1plus Defines a New Minimal Residual Disease-Dependent Very-Poor Prognostic Profile in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia.

PubMed

Stanulla, Martin; Dagdan, Elif; Zaliova, Marketa; Möricke, Anja; Palmi, Chiara; Cazzaniga, Giovanni; Eckert, Cornelia; Te Kronnie, Geertruy; Bourquin, Jean-Pierre; Bornhauser, Beat; Koehler, Rolf; Bartram, Claus R; Ludwig, Wolf-Dieter; Bleckmann, Kirsten; Groeneveld-Krentz, Stefanie; Schewe, Denis; Junk, Stefanie V; Hinze, Laura; Klein, Norman; Kratz, Christian P; Biondi, Andrea; Borkhardt, Arndt; Kulozik, Andreas; Muckenthaler, Martina U; Basso, Giuseppe; Valsecchi, Maria Grazia; Izraeli, Shai; Petersen, Britt-Sabina; Franke, Andre; Dörge, Petra; Steinemann, Doris; Haas, Oskar A; Panzer-Grümayer, Renate; Cavé, Hélène; Houlston, Richard S; Cario, Gunnar; Schrappe, Martin; Zimmermann, Martin

2018-04-20

Purpose Somatic deletions that affect the lymphoid transcription factor-coding gene IKZF1 have previously been reported as independently associated with a poor prognosis in pediatric B-cell precursor (BCP) acute lymphoblastic leukemia (ALL). We have now refined the prognostic strength of IKZF1 deletions by analyzing the effect of co-occurring deletions. Patients and Methods The analysis involved 991 patients with BCP ALL treated in the Associazione Italiana Ematologia ed Oncologia Pediatrica-Berlin-Frankfurt-Muenster (AIEOP-BFM) ALL 2000 trial with complete information for copy number alterations of IKZF1, PAX5, ETV6, RB1, BTG1, EBF1, CDKN2A, CDKN2B, Xp22.33/Yp11.31 (PAR1 region; CRLF2, CSF2RA, and IL3RA), and ERG; replication of findings involved 417 patients from the same trial. Results IKZF1 deletions that co-occurred with deletions in CDKN2A, CDKN2B, PAX5, or PAR1 in the absence of ERG deletion conferred the worst outcome and, consequently, were grouped as IKZF1 plus . The IKZF1 plus group comprised 6% of patients with BCP ALL, with a 5-year event-free survival of 53 ± 6% compared with 79 ± 5% in patients with IKZF1 deletion who did not fulfill the IKZF1 plus definition and 87 ± 1% in patients who lacked an IKZF1 deletion ( P ≤ .001). Respective 5-year cumulative relapse incidence rates were 44 ± 6%, 11 ± 4%, and 10 ± 1% ( P ≤ .001). Results were confirmed in the replication cohort, and multivariable analyses demonstrated independence of IKZF1 plus . The IKZF1 plus prognostic effect differed dramatically in analyses stratified by minimal residual disease (MRD) levels after induction treatment: 5-year event-free survival for MRD standard-risk IKZF1 plus patients was 94 ± 5% versus 40 ± 10% in MRD intermediate- and 30 ± 14% in high-risk IKZF1 plus patients ( P ≤ .001). Corresponding 5-year cumulative incidence of relapse rates were 6 ± 6%, 60 ± 10%, and 60 ± 17% ( P ≤ .001). Conclusion IKZF1 plus describes a new MRD-dependent very-poor prognostic profile in BCP ALL. Because current AIEOP-BFM treatment is largely ineffective for MRD-positive IKZF1 plus patients, new experimental treatment approaches will be evaluated in our upcoming trial AIEOP-BFM ALL 2017.

Solid Phase Extraction of Trace Elements in Waterand Tissue Samples on a Mini Column with Diphenylcarbazone Impregnated Nano-TiO2 and Their Determination by Inductively Coupled Plasma Optical Emission Spectrometry

PubMed Central

Baytak, Sıtkı; Arslan, Zikri

2015-01-01

This study presents a simple, robust and environmentally friendly solid phase preconcentration procedure for multielement determination by inductively coupled plasma optical emission spectrometry (ICP-OES) using diphenylcarbazone (DPC) impregnated TiO2 nanopowder (n-TiO2). DPC was successfully impregnated onto n-TiO2 in colloidal solution. A number of elements, including Co(II), Cr(III), Cu(II), Fe(III), Mn(II) and Zn(II) were quantitatively preconcentrated from aqueous solutions between pH 8 and 8.5 at a flow rate of 2 mL min−1, and then eluted with 2 mL of 5% (v/v) HNO3. A mini-column packed with 0.12 g DPC impregnated n-TiO2 retained all elements quantitatively from up to 250 mL multielement solution (2.5 μg per analyte) affording an enrichment factor of 125. The limits of detection (LOD) for preconcentration of 50 mL blank solutions (n = 12) were 0.28, 0.15, 0.25, 0.22, 0.12, and 0.10 μg L−1 for Co, Cr, Cu, Fe, Mn, and Zn, respectively. The relative standard deviation (RSD) for five replicate determinations was 0.8, 3.4, 2.6, 2.2, 1.2 and 3.3% for Co, Cr, Cu, Fe, Mn and Zn, respectively, at 5 μg L−1 level. The method was validated with analysis of Freshwater (SRM 1643e) and Lobster hepatopancreas (TORT-2) certified reference materials, and then applied to the determination of the elements from tap water and lake water samples by ICP-OES. PMID:26236403

Plasmid Replicons from Pseudomonas Are Natural Chimeras of Functional, Exchangeable Modules

PubMed Central

Bardaji, Leire; Añorga, Maite; Ruiz-Masó, José A.; del Solar, Gloria; Murillo, Jesús

2017-01-01

Plasmids are a main factor for the evolution of bacteria through horizontal gene exchange, including the dissemination of pathogenicity genes, resistance to antibiotics and degradation of pollutants. Their capacity to duplicate is dependent on their replication determinants (replicon), which also define their bacterial host range and the inability to coexist with related replicons. We characterize a second replicon from the virulence plasmid pPsv48C, from Pseudomonas syringae pv. savastanoi, which appears to be a natural chimera between the gene encoding a newly described replication protein and a putative replication control region present in the widespread family of PFP virulence plasmids. We present extensive evidence of this type of chimerism in structurally similar replicons from species of Pseudomonas, including environmental bacteria as well as plant, animal and human pathogens. We establish that these replicons consist of two functional modules corresponding to putative control (REx-C module) and replication (REx-R module) regions. These modules are functionally separable, do not show specificity for each other, and are dynamically exchanged among replicons of four distinct plasmid families. Only the REx-C module displays strong incompatibility, which is overcome by a few nucleotide changes clustered in a stem-and-loop structure of a putative antisense RNA. Additionally, a REx-C module from pPsv48C conferred replication ability to a non-replicative chromosomal DNA region containing features associated to replicons. Thus, the organization of plasmid replicons as independent and exchangeable functional modules is likely facilitating rapid replicon evolution, fostering their diversification and survival, besides allowing the potential co-option of appropriate genes into novel replicons and the artificial construction of new replicon specificities. PMID:28243228

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

PubMed Central

Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

2015-01-01

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. PMID:25155200

Human coronavirus EMC does not require the SARS-coronavirus receptor and maintains broad replicative capability in mammalian cell lines.

PubMed

Müller, Marcel A; Raj, V Stalin; Muth, Doreen; Meyer, Benjamin; Kallies, Stephan; Smits, Saskia L; Wollny, Robert; Bestebroer, Theo M; Specht, Sabine; Suliman, Tasnim; Zimmermann, Katrin; Binger, Tabea; Eckerle, Isabella; Tschapka, Marco; Zaki, Ali M; Osterhaus, Albert D M E; Fouchier, Ron A M; Haagmans, Bart L; Drosten, Christian

2012-12-11

A new human coronavirus (hCoV-EMC) has emerged very recently in the Middle East. The clinical presentation resembled that of the severe acute respiratory syndrome (SARS) as encountered during the epidemic in 2002/2003. In both cases, acute renal failure was observed in humans. HCoV-EMC is a member of the same virus genus as SARS-CoV but constitutes a sister species. Here we investigated whether it might utilize angiotensin-converting enzyme 2 (ACE2), the SARS-CoV receptor. Knowledge of the receptor is highly critical because the restriction of the SARS receptor to deep compartments of the human respiratory tract limited the spread of SARS. In baby hamster kidney (BHK) cells, lentiviral transduction of human ACE2 (hACE2) conferred permissiveness and replication for SARS-CoV but not for hCoV-EMC. Monkey and human kidney cells (LLC-MK2, Vero, and 769-P) and swine kidney cells were permissive for both viruses, but only SARS-CoV infection could be blocked by anti-hACE2 antibody and could be neutralized by preincubation of virus with soluble ACE2. Our data show that ACE2 is neither necessary nor sufficient for hCoV-EMC replication. Moreover, hCoV-EMC, but not SARS-CoV, replicated in cell lines from Rousettus, Rhinolophus, Pipistrellus, Myotis, and Carollia bats, representing four major chiropteran families from both suborders. As human CoV normally cannot replicate in bat cells from different families, this suggests that hCoV-EMC might use a receptor molecule that is conserved in bats, pigs, and humans, implicating a low barrier against cross-host transmission. IMPORTANCE A new human coronavirus (hCoV) emerged recently in the Middle East. The disease resembled SARS (severe acute respiratory syndrome), causing a fatal epidemic in 2002/2003. Coronaviruses have a reservoir in bats and because this novel virus is related to SARS-CoV, we investigated whether it might replicate in bat cells and use the same receptor (angiotensin-converting enzyme 2 [ACE2]). This knowledge is highly critical, because the SARS-CoV receptor influenced pathology, and its localization in the deep respiratory tract is thought to have restricted the transmissibility of SARS. Our data show that hCoV-EMC does not need the SARS-CoV receptor to infect human cells. Moreover, the virus is capable of infecting human, pig, and bat cells. This is remarkable, as human CoVs normally cannot replicate in bat cells as a consequence of host adaptation. Our results implicate that the new virus might use a receptor that is conserved between bats, pigs and humans suggesting a low barrier against cross-host transmission.

Impairment of Human Immunodeficiency Virus Type-1 Integrase SUMOylation Correlates with an Early Replication Defect*

PubMed Central

Zamborlini, Alessia; Coiffic, Audrey; Beauclair, Guillaume; Delelis, Olivier; Paris, Joris; Koh, Yashuiro; Magne, Fabian; Giron, Marie-Lou; Tobaly-Tapiero, Joelle; Deprez, Eric; Emiliani, Stephane; Engelman, Alan; de Thé, Hugues; Saïb, Ali

2011-01-01

HIV-1 integrase (IN) orchestrates the integration of the reverse transcribed viral cDNA into the host cell genome and participates also in other steps of HIV-1 replication. Cellular and viral factors assist IN in performing its multiple functions, and post-translational modifications contribute to modulate its activities. Here, we show that HIV-1 IN is modified by SUMO proteins and that phylogenetically conserved SUMOylation consensus motifs represent major SUMO acceptor sites. Viruses harboring SUMOylation site IN mutants displayed a replication defect that was mapped during the early stages of infection, before integration but after reverse transcription. Because SUMOylation-defective IN mutants retained WT catalytic activity, we hypothesize that SUMOylation might regulate the affinity of IN for co-factors, contributing to efficient HIV-1 replication. PMID:21454548

Coronaviruses and arteriviruses display striking differences in their cyclophilin A-dependence during replication in cell culture.

PubMed

de Wilde, Adriaan H; Zevenhoven-Dobbe, Jessika C; Beugeling, Corrine; Chatterji, Udayan; de Jong, Danielle; Gallay, Philippe; Szuhai, Karoly; Posthuma, Clara C; Snijder, Eric J

2018-04-01

Cyclophilin A (CypA) is an important host factor in the replication of a variety of RNA viruses. Also the replication of several nidoviruses was reported to depend on CypA, although possibly not to the same extent. These prior studies are difficult to compare, since different nidoviruses, cell lines and experimental set-ups were used. Here, we investigated the CypA dependence of three distantly related nidoviruses that can all replicate in Huh7 cells: the arterivirus equine arteritis virus (EAV), the alphacoronavirus human coronavirus 229E (HCoV-229E), and the betacoronavirus Middle East respiratory syndrome coronavirus (MERS-CoV). The replication of these viruses was compared in the same parental Huh7 cells and in CypA-knockout Huh7 cells generated using CRISPR/Cas9-technology. CypA depletion reduced EAV yields by ~ 3-log, whereas MERS-CoV progeny titers were modestly reduced (3-fold) and HCoV-229E replication was unchanged. This study reveals that the replication of nidoviruses can differ strikingly in its dependence on cellular CypA. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Inhibition of HBV Replication in HepG2.2.15 Cells by Human Peripheral Blood Mononuclear Cell-Derived Dendritic Cells.

PubMed

Liu, Tao; Song, Hong-Li; Zheng, Wei-Ping; Shen, Zhong-Yang

2015-01-01

Anti-HBV therapy is essential for patients awaiting liver transplantation. This study aimed to explore the effects of dendritic cells (DCs) derived from the peripheral blood of hepatitis B patients on the replication of HBV in vivo and to evaluate the biosafety of DCs in clinical therapy. Peripheral blood mononuclear cells (PBMCs) were isolated from HBV-infected patients and maturation-promoting factors and both HBsAg and HBcAg were used to induce DC maturation. Mature DCs and lymphocytes were co-cultured with human hepatocyte cell HL-7702 or HBV-producing human hepatocellular carcinoma cell HepG2.2.15. We found that mature lymphocytes exposed to DCs in vitro did not influence morphology or activities of HL-7702 and HepG2.2.15 cells. Liver function indexes and endotoxin levels in the cell supernatants did not change in these co-cultures. Additionally, supernatant and intracellular HBV DNA levels were reduced when HepG2.2.15 cells were co-cultured with mature lymphocytes that had been cultured with DCs, and HBV covalently closed circular DNA (cccDNA) levels in HepG2.2.15 cells also decreased. Importantly, DC-mediated immunotherapy had no mutagenic effect on HBV genomic DNA by gene sequencing of the P, S, X, and C regions of HBV genomic DNA. We conclude that PBMC-derived DCs from HBV-infected patients act on autologous lymphocytes to suppress HBV replication and these DC clusters showed favorable biosafety. © 2015 by the Association of Clinical Scientists, Inc.

Role of Accessory Proteins of HTLV-1 in Viral Replication, T Cell Activation, and Cellular Gene Expression

PubMed Central

Michael, Bindhu; Nair, Amithraj; Lairmore, Michael D.

2010-01-01

Human T-cell lymphotropic virus type 1 (HTLV-1), causes adult T cell leukemia/lymphoma (ATLL), and initiates a variety of immune mediated disorders. The viral genome encodes common structural and enzymatic proteins characteristic of all retroviruses and utilizes alternative splicing and alternate codon usage to make several regulatory and accessory proteins encoded in the pX region (pX ORF I to IV). Recent studies indicate that the accessory proteins p12I, p27I, p13II, and p30II, encoded by pX ORF I and II, contribute to viral replication and the ability of the virus to maintain typical in vivo expression levels. Proviral clones that are mutated in either pX ORF I or II, while fully competent in cell culture, are severely limited in their replicative capacity in a rabbit model. These HTLV-1 accessory proteins are critical for establishment of viral infectivity, enhance T- lymphocyte activation and potentially alter gene transcription and mitochondrial function. HTLV-1 pX ORF I expression is critical to the viral infectivity in resting primary lymphocytes suggesting a role for the calcineurin-binding protein p12I in lymphocyte activation. The endoplasmic reticulum and cis-Golgi localizing p12I activates NFAT, a key T cell transcription factor, through calcium-mediated signaling pathways and may lower the threshold of lymphocyte activation via the JAK/STAT pathway. In contrast p30II localizes to the nucleus and represses viral promoter activity, but may regulate cellular gene expression through p300/CBP or related co-activators of transcription. The mitochondrial localizing p13II induces morphologic changes in the organelle and may influence energy metabolism infected cells. Future studies of the molecular details HTLV-1 “accessory” proteins interactions will provide important new directions for investigations of HTLV-1 and related viruses associated with lymphoproliferative diseases. Thus, the accessory proteins of HTLV-1, once thought to be dispensable for viral replication, have proven to be directly involved in viral spread in vivo and represent potential targets for therapeutic intervention against HTLV-1 infection and disease. PMID:15358581

Exome-wide Association Study Identifies CLEC3B Missense Variant p.S106G as Being Associated With Extreme Longevity in East Asian Populations

PubMed Central

Tanisawa, Kumpei; Arai, Yasumichi; Hirose, Nobuyoshi; Shimokata, Hiroshi; Yamada, Yoshiji; Kawai, Hisashi; Kojima, Motonaga; Obuchi, Shuichi; Hirano, Hirohiko; Yoshida, Hideyo; Suzuki, Hiroyuki; Fujiwara, Yoshinori; Ihara, Kazushige; Sugaya, Maki; Arai, Tomio; Mori, Seijiro; Sawabe, Motoji; Sato, Noriko; Muramatsu, Masaaki; Higuchi, Mitsuru; Liu, Yao-Wen; Kong, Qing-Peng

2017-01-01

Abstract Life span is a complex trait regulated by multiple genetic and environmental factors; however, the genetic determinants of extreme longevity have been largely unknown. To identify the functional coding variants associated with extreme longevity, we performed an exome-wide association study (EWAS) on a Japanese population by using an Illumina HumanExome Beadchip and a focused replication study on a Chinese population. The EWAS on two independent Japanese cohorts consisting of 530 nonagenarians/centenarians demonstrated that the G allele of CLEC3B missense variant p.S106G was associated with extreme longevity at the exome-wide level of significance (p = 2.33×10–7, odds ratio [OR] = 1.50). The CLEC3B gene encodes tetranectin, a protein implicated in the mineralization process in osteogenesis as well as in the prognosis and metastasis of cancer. The replication study consisting of 448 Chinese nonagenarians/centenarians showed that the G allele of CLEC3B p.S106G was also associated with extreme longevity (p = .027, OR = 1.51), and the p value of this variant reached 1.87×10–8 in the meta-analysis of Japanese and Chinese populations. In conclusion, the present study identified the CLEC3B p.S106G as a novel longevity-associated variant, raising the novel hypothesis that tetranectin, encoded by CLEC3B, plays a role in human longevity and aging. PMID:27154906

A Role of hIPI3 in DNA Replication Licensing in Human Cells.

PubMed

Huang, Yining; Amin, Aftab; Qin, Yan; Wang, Ziyi; Jiang, Huadong; Liang, Lu; Shi, Linjing; Liang, Chun

2016-01-01

The yeast Ipi3p is required for DNA replication and cell viability in Sacharomyces cerevisiae. It is an essential component of the Rix1 complex (Rix1p/Ipi2p-Ipi1p-Ipi3p) that is required for the processing of 35S pre-rRNA in pre-60S ribosomal particles and for the initiation of DNA replication. The human IPI3 homolog is WDR18 (WD repeat domain 18), which shares significant homology with yIpi3p. Here we report that knockdown of hIPI3 resulted in substantial defects in the chromatin association of the MCM complex, DNA replication, cell cycle progression and cell proliferation. Importantly, hIPI3 silencing did not result in a reduction of the protein level of hCDC6, hMCM7, or the ectopically expressed GFP protein, indicating that protein synthesis was not defective in the same time frame of the DNA replication and cell cycle defects. Furthermore, the mRNA and protein levels of hIPI3 fluctuate in the cell cycle, with the highest levels from M phase to early G1 phase, similar to other pre-replicative (pre-RC) proteins. Moreover, hIPI3 interacts with other replication-initiation proteins, co-localizes with hMCM7 in the nucleus, and is important for the nuclear localization of hMCM7. We also found that hIPI3 preferentially binds to the origins of DNA replication including those at the c-Myc, Lamin-B2 and β-Globin loci. These results indicate that hIPI3 is involved in human DNA replication licensing independent of its role in ribosome biogenesis.

Methodological implications in pH standardization of exhaled breath condensate.

PubMed

Hoffmeyer, F; Berresheim, H; Beine, A; Sucker, K; Brüning, T; Bünger, J

2015-05-14

The variable amount of dissolved carbon dioxide is one of the main confounding factors of exhaled breath condensate (EBC) pH measurements. There have been many attempts at identifying the optimal approach to displace CO2 as a way to gain reproducible and valid pH values in EBC samples. The aim of the present study was to assess the correlation of pH and pCO2 in untreated, neat EBC samples and, after deaeration, to reevaluate the standardization of CO2 as a means to obtain valid pH values. A further aim was to evaluate the impact of deaeration on the acid-base balance in EBC samples. EBC was collected from seven female and 31 male subjects. The pH and pCO2 values immediately determined in untreated, neat EBC samples were strongly correlated (rp = -0.723, p <  0.0001). This correlation was not observed after deaeration with argon (rs = 0.264, p = 0.109). Based on a regression function for the pH/pCO2 relationship, the calculated pH at a pCO2 of 5.33 kPa was 6.07 (IQR 5.99, 6.20). No significant difference was observed between the pH measured in neat EBC samples and those calculated after deaeration with regression function and measured neat pCO2. Our data suggest that pCO2 is the most important confounder of pH measurement in EBC samples and, when adjusting for pCO2, the acid-base balance of EBC samples is not significantly influenced by the process of deaeration. Furthermore, measurement with a blood-gas analyzer and standardization of pH for pCO2 allows sensitive assaying of EBC samples. Therefore, this method provides a basis for detection of even small changes in airway pH due to inhalative exposure or respiratory disease.

Systemic Regulation of the Age-Related Decline of Pancreatic β-Cell Replication

PubMed Central

Salpeter, Seth J.; Khalaileh, Abed; Weinberg-Corem, Noa; Ziv, Oren; Glaser, Benjamin; Dor, Yuval

2013-01-01

The frequency of pancreatic β-cell replication declines dramatically with age, potentially contributing to the increased risk of type 2 diabetes in old age. Previous studies have shown the involvement of cell-autonomous factors in this phenomenon, particularly the decline of polycomb genes and accumulation of p16/INK4A. Here, we demonstrate that a systemic factor found in the circulation of young mice is able to increase the proliferation rate of old pancreatic β-cells. Old mice parabiosed to young mice have increased β-cell replication compared with unjoined old mice or old mice parabiosed to old mice. In addition, we demonstrate that old β-cells transplanted into young recipients have increased replication rate compared with cells transplanted into old recipients; conversely, young β-cells transplanted into old mice decrease their replication rate compared with young cells transplanted into young recipients. The expression of p16/INK4A mRNA did not change in heterochronic parabiosis, suggesting the involvement of other pathways. We conclude that systemic factors contribute to the replicative decline of old pancreatic β-cells. PMID:23630298

Myocyte enhancer factor (MEF)-2 plays essential roles in T-cell transformation associated with HTLV-1 infection by stabilizing complex between Tax and CREB.

PubMed

Jain, Pooja; Lavorgna, Alfonso; Sehgal, Mohit; Gao, Linlin; Ginwala, Rashida; Sagar, Divya; Harhaj, Edward W; Khan, Zafar K

2015-02-27

The exact molecular mechanisms regarding HTLV-1 Tax-mediated viral gene expression and CD4 T-cell transformation have yet to be fully delineated. Herein, utilizing virus-infected primary CD4+ T cells and the virus-producing cell line, MT-2, we describe the involvement and regulation of Myocyte enhancer factor-2 (specifically MEF-2A) during the course of HTLV-1 infection and associated disease syndrome. Inhibition of MEF-2 expression by shRNA and its activity by HDAC9 led to reduced viral replication and T-cell transformation in correlation with a heightened expression of MEF-2 in ATL patients. Mechanistically, MEF-2 was recruited to the viral promoter (LTR, long terminal repeat) in the context of chromatin, and constituted Tax/CREB transcriptional complex via direct binding to the HTLV-1 LTR. Furthermore, an increase in MEF-2 expression was observed upon infection in an extent similar to CREB (known Tax-interacting transcription factor), and HATs (p300, CBP, and p/CAF). Confocal imaging confirmed MEF-2 co-localization with Tax and these proteins were also shown to interact by co-immunoprecipitation. MEF-2 stabilization of Tax/CREB complex was confirmed by a novel promoter-binding assay that highlighted the involvement of NFAT (nuclear factor of activated T cells) in this process via Tax-mediated activation of calcineurin (a calcium-dependent serine-threonine phosphatase). MEF-2-integrated signaling pathways (PI3K/Akt, NF-κB, MAPK, JAK/STAT, and TGF-β) were also activated during HTLV-1 infection of primary CD4+ T cells, possibly regulating MEF-2 activity. We demonstrate the involvement of MEF-2 in Tax-mediated LTR activation, viral replication, and T-cell transformation in correlation with its heightened expression in ATL patients through direct binding to DNA within the HTLV-1 LTR.

Collagen type III alpha I is a gastro-oesophageal reflux disease susceptibility gene and a male risk factor for hiatus hernia.

PubMed

Asling, B; Jirholt, J; Hammond, P; Knutsson, M; Walentinsson, A; Davidson, G; Agreus, L; Lehmann, A; Lagerström-Fermer, M

2009-08-01

Gastro-oesophageal reflux disease (GORD) is a common gastrointestinal disorder with a genetic component. Our aim was to identify genetic factors associated with GORD. Four separate patient cohorts were analysed using a step-wise approach. (1) Whole genome linkage analysis was performed in 36 families. (2) Candidate genes were tested for GORD association in a trio cohort. (3) Genetic association was replicated in a case-control cohort. We also investigated genetic association to hiatus hernia (HH). (4) Protein expression was analysed in oesophageal biopsies. A region on chromosome 2, containing collagen type III alpha 1 (COL3A1), was identified (LOD = 3.3) in families with dominant transmission of GORD, stratified for hiatus hernia (HH). COL3A1 showed significant association with GORD in an independent paediatric trio cohort (p(corr) = 0.003). The association was male specific (p(corr) = 0.018). The COL3A1 association was replicated in an independent adult case control cohort (p(corr) = 0.022). Moreover, male specific association to HH (p(corr) = 0.019) was found for a SNP not associated to GORD. Collagen type III protein was more abundant in oesophageal biopsies from male patients with GORD (p = 0.03). COL3A1 is a disease-associated gene in both paediatric and adult GORD. Furthermore, we show that COL3A1 is genetically associated with HH in adult males. The GORD- and HH-associated alleles are different, indicating two separate mechanisms leading to disease. Our data provides new insight into GORD aetiology, identifying a connective tissue component and indicating a tissue remodelling mechanism in GORD. Our results implicate gender differences in the genetic risk for both for GORD and HH.

33. A.C. PANEL FOR MENTONE POWER HOUSE, P.L. & P. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

33. A.C. PANEL FOR MENTONE POWER HOUSE, P.L. & P. CO., LOS ANGELES. RETRACED FROM MASSON'S DRAWING NO. C-275. JAN. 20, 1909. SCE drawing no. 52880. - Santa Ana River Hydroelectric System, SAR-3 Powerhouse, San Bernardino National Forest, Redlands, San Bernardino County, CA

The G1/S Specific Cyclin D2 Is a Regulator of HIV-1 Restriction in Non-proliferating Cells

PubMed Central

Badia, Roger; Pujantell, Maria; Riveira-Muñoz, Eva; Puig, Teresa; Torres-Torronteras, Javier; Martí, Ramón; Clotet, Bonaventura; Ampudia, Rosa M.; Ballana, Ester

2016-01-01

Macrophages are a heterogeneous cell population strongly influenced by differentiation stimuli that become susceptible to HIV-1 infection after inactivation of the restriction factor SAMHD1 by cyclin-dependent kinases (CDK). Here, we have used primary human monocyte-derived macrophages differentiated through different stimuli to evaluate macrophage heterogeneity on cell activation and proliferation and susceptibility to HIV-1 infection. Stimulation of monocytes with GM-CSF induces a non-proliferating macrophage population highly restrictive to HIV-1 infection, characterized by the upregulation of the G1/S-specific cyclin D2, known to control early steps of cell cycle progression. Knockdown of cyclin D2, enhances HIV-1 replication in GM-CSF macrophages through inactivation of SAMHD1 restriction factor by phosphorylation. Co-immunoprecipitation experiments show that cyclin D2 forms a complex with CDK4 and p21, a factor known to restrict HIV-1 replication by affecting the function of the downstream cascade that leads to SAMHD1 deactivation. Thus, we demonstrate that cyclin D2 acts as regulator of cell cycle proteins affecting SAMHD1-mediated HIV-1 restriction in non-proliferating macrophages. PMID:27541004

Teaching primary prevention of Alzheimer's disease: does it make a difference?

PubMed

Clevenger, Carolyn K; Cantey, Shileah; Quinn, Mary Ellen

2010-07-01

Alzheimer's disease (AD) is one of the most feared illnesses among older adults. Although no cure exists, an emerging body of literature has outlined potentially risk-reducing behaviors. As evidence has become available on risk reduction, community organizations and advocacy groups have developed health education courses on the topic. This study examines the impact of one educational program on the audience's efficacy expectations and outcome expectations for behavior change. Participants included 53 older adults residing in a continuing care retirement community. The study used a pretest-posttest design with an experimental group (n = 33) and a control group (n = 20). Topics on weekly classes included the relationship between cardiovascular factors and AD, dietary factors implicated in AD, and mental stimulation to reduce AD risk. Class sessions consisted of lecture, discussion, and demonstration. Between-group differences were found for both efficacy (P = .016) and outcome expectations (P = .000). Within-group differences were only significant for increased outcome expectations related to literature-derived behaviors (P = .000). Future work should focus on action and prevention and on replication of the educational program's evaluation in a more diverse population.

A genome-wide association analysis identifies NMNAT2 and HCP5 as susceptibility loci for Kawasaki disease.

PubMed

Kim, Jae-Jung; Yun, Sin Weon; Yu, Jeong Jin; Yoon, Kyung Lim; Lee, Kyung-Yil; Kil, Hong-Ryang; Kim, Gi Beom; Han, Myung-Ki; Song, Min Seob; Lee, Hyoung Doo; Ha, Kee Soo; Sohn, Sejung; Johnson, Todd A; Takahashi, Atsushi; Kubo, Michiaki; Tsunoda, Tatsuhiko; Ito, Kaoru; Onouchi, Yoshihiro; Hong, Young Mi; Jang, Gi Young; Lee, Jong-Keuk

2017-12-01

Kawasaki disease (KD), a systemic vasculitis of infants and children, manifests as fever and mucocutaneous inflammation. Although its etiology is largely unknown, the epidemiological data suggest that genetic factors are important in KD susceptibility. To identify genetic variants influencing KD susceptibility, we performed a genome-wide association study (GWAS) and replication study using a total of 915 children with KD and 4553 controls in the Korean population. Six single-nucleotide polymorphisms (SNPs) in three loci were associated significantly with KD susceptibility (P<1.0 × 10 -5 ), including the previously reported BLK locus (rs6993775, odds ratio (OR)=1.52, P=2.52 × 10 -11 ). The other two loci were newly identified: NMNAT2 on chromosome 1q25.3 (rs2078087, OR=1.33, P=1.15 × 10 -6 ) and the human leukocyte antigen (HLA) region on chromosome 6p21.3 (HLA-C, HLA-B, MICA and HCP5) (rs9380242, rs9378199, rs9266669 and rs6938467; OR=1.33-1.51, P=8.93 × 10 -6 to 5.24 × 10 -8 ). Additionally, SNP rs17280682 in NLRP14 was associated significantly with KD with a family history (18 cases vs 4553 controls, OR=6.76, P=5.46 × 10 -6 ). These results provide new insights into the pathogenesis and pathophysiology of KD.

Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication.

PubMed

Sakai, Yusuke; Kawachi, Kengo; Terada, Yutaka; Omori, Hiroko; Matsuura, Yoshiharu; Kamitani, Wataru

2017-10-01

Infection with coronavirus rearranges the host cell membrane to assemble a replication/transcription complex in which replication of the viral genome and transcription of viral mRNA occur. Although coexistence of nsp3 and nsp4 is known to cause membrane rearrangement, the mechanisms underlying the interaction of these two proteins remain unclear. We demonstrated that binding of nsp4 with nsp3 is essential for membrane rearrangement and identified amino acid residues in nsp4 responsible for the interaction with nsp3. In addition, we revealed that the nsp3-nsp4 interaction is not sufficient to induce membrane rearrangement, suggesting the participation of other factors such as host proteins. Finally, we showed that loss of the nsp3-nsp4 interaction eliminated viral replication by using an infectious cDNA clone and replicon system of SARS-CoV. These findings provide clues to the mechanism of the replication/transcription complex assembly of SARS-CoV and could reveal an antiviral target for the treatment of betacoronavirus infection. Copyright © 2017 Elsevier Inc. All rights reserved.

The ORF1 Products of Tombusviruses Play a Crucial Role in Lethal Necrosis of Virus-Infected Plants

PubMed Central

Burgyán, József; Hornyik, Csaba; Szittya, György; Silhavy, Dániel; Bisztray, György

2000-01-01

Hybrids of cymbidium ringspot (CymRSV) and carnation Italian ringspot (CIRV) tombusviruses were used to identify viral symptom determinants responsible for the generalized necrosis in tombusvirus-infected plants. Surprisingly, symptoms of Nicotiana benthamiana infected with CymRSV/CIRV hybrids were distinctly different. It was demonstrated that not all chimeras expressing wild-type (wt) levels of p19 protein caused systemic necrosis as both parents CymRSV and CIRV did. We showed here that hybrids containing chimeric ORF1 were not able to induce lethal necrosis even if the viral replication of these constructs was not altered significantly. However, if a wt p33 (product of ORF1) of CymRSV was provided in trans in transgenic plants expressing p33 and its readthrough product p92, the lethal necrosis characteristic to tombusvirus infection was restored. In addition, the expression of p33 by a potato virus X viral vector in N. benthamiana caused severe chlorosis and occasionally necrosis, indicating the importance of p33 in wt symptoms of tombusviruses. Thus, our results provide evidence that elicitation of the necrotic phenotype requires the presence of the wt p33 in addition to the p19 protein of tombusviruses. PMID:11069981

Salicylates inhibit flavivirus replication independently of blocking nuclear factor kappa B activation.

PubMed

Liao, C L; Lin, Y L; Wu, B C; Tsao, C H; Wang, M C; Liu, C I; Huang, Y L; Chen, J H; Wang, J P; Chen, L K

2001-09-01

Flaviviruses comprise a positive-sense RNA genome that replicates exclusively in the cytoplasm of infected cells. Whether flaviviruses require an activated nuclear factor(s) to complete their life cycle and trigger apoptosis in infected cells remains elusive. Flavivirus infections quickly activate nuclear factor kappa B (NF-kappaB), and salicylates have been shown to inhibit NF-kappaB activation. In this study, we investigated whether salicylates suppress flavivirus replication and virus-induced apoptosis in cultured cells. In a dose-dependent inhibition, we found salicylates within a range of 1 to 5 mM not only restricted flavivirus replication but also abrogated flavivirus-triggered apoptosis. However, flavivirus replication was not affected by a specific NF-kappaB peptide inhibitor, SN50, and a proteosome inhibitor, lactacystin. Flaviviruses also replicated and triggered apoptosis in cells stably expressing IkappaBalpha-DeltaN, a dominant-negative mutant that antagonizes NF-kappaB activation, as readily as in wild-type BHK-21 cells, suggesting that NF-kappaB activation is not essential for either flavivirus replication or flavivirus-induced apoptosis. Salicylates still diminished flavivirus replication and blocked apoptosis in the same IkappaBalpha-DeltaN cells. This inhibition of flaviviruses by salicylates could be partially reversed by a specific p38 mitogen-activated protein (MAP) kinase inhibitor, SB203580. Together, these results show that the mechanism by which salicylates suppress flavivirus infection may involve p38 MAP kinase activity but is independent of blocking the NF-kappaB pathway.

A GWAS meta-analysis and replication study identifies a novel locus within CLPTM1L/TERT associated with nasopharyngeal carcinoma in individuals of Chinese ancestry

PubMed Central

Yu, Kai; Chin, Yoon-Ming; Lou, Pei-Jen; Hsu, Wan-Lun; McKay, James D.; Chen, Chien-Jen; Chang, Yu-Sun; Chen, Li-Zhen; Chen, Ming-Yuan; Cui, Qian; Feng, Fu-Tuo; Feng, Qi-Shen; Guo, Yun-Miao; Jia, Wei-Hua; Khoo, Alan Soo-Beng; Liu, Wen-Sheng; Mo, Hao-Yuan; Pua, Kin-Choo; Teo, Soo-Hwang; Tse, Ka-Po; Xia, Yun-Fei; Zhang, Hongxin; Zhou, Gang-Qiao; Liu, Jian-Jun; Zeng, Yi-Xin; Hildesheim, Allan

2015-01-01

Background Genetic loci within the major histocompatibility complex (MHC) have been associated with nasopharyngeal carcinoma (NPC), an Epstein-Barr virus (EBV)-associated cancer, in several GWAS. Results outside this region have varied. Methods We conducted a meta-analysis of four NPC GWAS among Chinese individuals (2,152 cases;3,740 controls). 43 noteworthy findings outside the MHC region were identified and targeted for replication in a pooled analysis of 4 independent case-control studies across 3 regions in Asia (4,716 cases;5,379 controls). A meta-analysis that combined results from the initial GWA and replication studies was performed. Results In the combined meta-analysis, rs31489, located within the CLPTM1L/TERT region on chromosome 5p15.33, was strongly associated with NPC (OR=0.81;p-value 6.3*10−13). Our results also provide support for associations reported from published NPC GWAS - rs6774494 (p = 1.5*10−12;located in the MECOM gene region), rs9510787 (p = 5.0*10−10;located in the TNFRSF19 gene region), and rs1412829/rs4977756/rs1063192 (p = 2.8*10−8,p = 7.0*10−7,and p = 8.4*10−7 respectively;located in the CDKN2A/B gene region). Conclusion We have identified a novel association between genetic variation in the CLPTM1L/TERT region and NPC. Supporting our finding, rs31489 and other SNPs in this region have been reported to be associated with multiple cancer sites, candidate-based studies have reported associations between polymorphisms in this region and NPC, the TERT gene is important for telomere maintenance and has been reported to be over-expressed in NPC, and an EBV protein expressed in NPC (LMP1) modulates TERT expression/telomerase activity. Impact Our finding suggests that factors involved in telomere length maintenance are involved in NPC pathogenesis. PMID:26545403

Cyclophilin A Interacts with Viral VP4 and Inhibits the Replication of Infectious Bursal Disease Virus.

PubMed

Wang, Nian; Zhang, Lizhou; Chen, Yuming; Lu, Zhen; Gao, Li; Wang, Yongqiang; Gao, Yulong; Gao, Honglei; Cui, Hongyu; Li, Kai; Liu, Changjun; Zhang, Yanping; Qi, Xiaole; Wang, Xiaomei

2015-01-01

Nonstructural protein VP4, a serine protease of infectious bursal disease virus (IBDV) that catalyzes the hydrolysis of polyprotein pVP2-VP4-VP3 to form the viral proteins VP2, VP4, and VP3, is essential to the replication of IBDV. However, the interacting partners of VP4 in host cells and the effects of the interaction on the IBDV lifecycle remain incompletely elucidated. In this study, using the yeast two-hybrid system, the putative VP4-interacting partner cyclophilin A (CypA) was obtained from a chicken embryo fibroblast (CEF) expression library. CypA was further confirmed to interact with VP4 of IBDV using co-immunoprecipitation (CO-IP), GST pull-down, and confocal microscopy assays. Moreover, we found that the overexpression of CypA suppressed IBDV replication, whereas the knock-down of CypA by small interfering RNAs promoted the replication of IBDV. Taken together, our findings indicate that the host cell protein CypA interacts with viral VP4 and inhibits the replication of IBDV.

Comparative study of regulated and unregulated air pollutant emissions before and after conversion of automobiles from gasoline power to liquefied petroleum gas/gasoline dual-fuel retrofits.

PubMed

Yang, Hsi-Hsien; Chien, Shu-Mei; Cheng, Man-Ting; Peng, Chiung-Yu

2007-12-15

Liquefied petroleum gas (LPG) is increasingly being examined as an alternative to gasoline use in automobiles as interest grows in reducing air pollutant emissions. In this study, emissions of regulated (CO, THC, NO(x)) and unregulated air pollutants, including CO2, particulate matter (PM), polycyclic aromatic hydrocarbons (PAHs), and BTEX (acronym for benzene, toluene, ethylbenzene, xylene), were measured before and after conversion of nine gasoline-powered automobiles to LPG/ gasoline dual-fuel retrofits. The tests were conducted on a standard chassis dynamometer in accordance with the United States Environmental Protection Agency FTP-75 test procedure, with the exception that all tests were conducted under hot-start driving conditions. The influences of LPG on air pollutant emission levels and carcinogenic potency were investigated and compared with gasoline. The results showed average emission factors of 0.14 g/km, 0.33 mg/km, 0.09 g/km, 0.44 g/km, and 197 g/km for CO, THC, NO(x), PM, and CO2, respectively, for LPG/ gasoline dual-fuel retrofits. Paired-sample t-test results indicated that the emissions of CO (p = 0.03), THC (p = 0.04), and CO2 (p = 4.6 x 10(-8)) were significantly reduced with the retrofit in comparison with gasoline-powered automobiles. The reduction percentages were 71%, 89%, and 14% for CO, THC, and CO2, respectively. The average total PAH emission factor for LPG was 217 microg/km, which is significantly lower than gasoline (863 microg/km; p = 0.05). The PAH corresponding carcinogenicities (BaP(eq)) were calculated via toxic equivalencies based on benzo(a)pyrene (BaP). Paired-sample t-test results fortotal BaP(eq) emissions showed no significant difference between gasoline (30.0 microg/km) and LPG (24.8 microg/km) at a confidence level of 95%. The discrepancy between PAH and BaP(eq) emissions resulted from the higher emission percentages of high molecular weight PAHs for LPG, which might be from lubricant oil. The average emission factors of benzene, toluene, ethylbenzene, and xylene were 351, 4400, 324, and 1100 microg/ km, respectively, with LPG as fuel, which were all significantly lower than those for gasoline (95% confidence level). The average reduction percentages were 78%, 61%, 57%, and 58% for benzene, toluene, ethylbenzene, and xylene, respectively.

Crystal Structure, Piezoelectric and Dielectric Properties of (Li, Ce)4+, Nb5+ and Mn2+ Co-doped CaBi4Ti4O15 High-Temperature Ceramics

NASA Astrophysics Data System (ADS)

Xin, Deqiong; Chen, Qiang; Wu, Jiagang; Bao, Shaoming; Zhang, Wen; Xiao, Dingquan; Zhu, Jianguo

2016-07-01

Bismuth-layered structured ceramics Ca0.85(Li,Ce)0.075Bi4Ti4- x Nb x O15-0.01MnCO3 were prepared by the conventional solid-state reaction method. The evolution of microstructure and corresponding electrical properties were studied. All the samples presented a single bismuth layered-structural phase with m = 4, indicating that (Li, Ce)4+, Nb5+ and Mn2+ adequately enter into the pseudo-perovskite structure and form solid solutions. It was found that Ca0.85(Li,Ce)0.075Bi4Ti3.98Nb0.02O15-0.01MnCO3 (CBTLCM-0.02Nb) ceramics possess the optimum electrical properties. The piezoelectric coefficient d 33, dielectric constant ɛ r, loss tan δ, planar electromechanical coupling factor k p and Curie-temperature T C of CBTLCM-0.02Nb ceramics were found to be ˜19.6 pC/N, 160, 0.16%, 8.1% and 767°C, respectively. Furthermore, the thermal depoling behavior demonstrates that the d 33 value of x = 0.02 content remains at 16.8 pC/N after annealing at 500°C. These results suggest that the (Li, Ce)4+-, Nb5+- and Mn2+-doped CBT-based ceramics are promising candidates for high-temperature piezoelectric applications.

Improved biocompatibility of poly(lactic-co-glycolic acid) orv and poly-L-lactic acid blended with nanoparticulate amorphous calcium phosphate in vascular stent applications.

PubMed

Zheng, Xiaoxin; Wang, Yujue; Lan, Zhiyuan; Lyu, Yongnan; Feng, Gaoke; Zhang, Yipei; Tagusari, Shizu; Kislauskis, Edward; Robich, Michael P; McCarthy, Stephen; Sellke, Frank W; Laham, Roger; Jiang, Xuejun; Gu, Wei Wang; Wu, Tim

2014-06-01

Biodegradable polymers used as vascular stent coatings and stent platforms encounter a major challenge: biocompatibility in vivo, which plays an important role in in-stent restenosis (ISR). Co-formulating amorphous calcium phosphate (ACP) into poly(lactic-co-glycolic acid) (PLGA) or poly-L-lactic acid (PLLA) was investigated to address the issue. For stent coating applications, metal stents were coated with polyethylene-co-vinyl acetate/poly-n-butyl methacrylate (PEVA/PBMA), PLGA or PLGA/ACP composites, and implanted into rat aortas for one and three months. Comparing with both PEVA/PBMA and PLGA groups after one month, the results showed that stents coated with PLGA/ACP had significantly reduced restenosis (PLGA/ACP vs. PEVA/PBMA vs. PLGA: 21.24 +/- 2.59% vs. 27.54 +/- 1.19% vs. 32.12 +/- 3.93%, P < 0.05), reduced inflammation (1.25 +/- 0.35 vs. 1.77 +/- 0.38 vs. 2.30 +/- 0.21, P < 0.05) and increased speed of re-endothelialization (1.78 +/- 0.46 vs. 1.17 +/- 0.18 vs. 1.20 +/- 0.18, P < 0.05). After three months, the PLGA/ACP group still displayed lower inflammation score (1.33 +/- 0.33 vs. 2.27 +/- 0.55, P < 0.05) and higher endothelial scores (2.33 +/- 0.33 vs. 1.20 +/- 0.18, P < 0.05) as compared with the PEVA/PBMA group. Moreover, for stent platform applications, PLLA/ACP stent tube significantly reduced the inflammatory cells infiltration in the vessel walls of rabbit iliac arteries relative to their PLLA cohort (NF-kappaB-positive cells: 23.31 +/- 2.33/mm2 vs. 9.34 +/- 1.35/mm2, P < 0.05). No systemic biochemical or pathological evidence of toxicity was found in either PLGA/ACP or PLLA/ACP. The co-formulation of ACP into PLGA and PLLA resulted in improved biocompatibility without systemic toxicity.

Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polonskaya, Zhanna; Benham, Craig J.; Hearing, Janet

The minimal replicator of the Epstein-Barr virus (EBV) latent cycle origin of DNA replication oriP is composed of two binding sites for the Epstein-Barr virus nuclear antigen-1 (EBNA-1) and flanking inverted repeats that bind the telomere repeat binding factor TRF2. Although not required for minimal replicator activity, additional binding sites for EBNA-1 and TRF2 and one or more auxiliary elements located to the right of the EBNA-1/TRF2 sites are required for the efficient replication of oriP plasmids. Another region of oriP that is predicted to be destabilized by DNA supercoiling is shown here to be an important functional component ofmore » oriP. The ability of DNA fragments of unrelated sequence and possessing supercoiled-induced DNA duplex destabilized (SIDD) structures, but not fragments characterized by helically stable DNA, to substitute for this component of oriP demonstrates a role for the SIDD region in the initiation of oriP-plasmid DNA replication.« less

The sequence of the CA-SP1 junction accounts for the differential sensitivity of HIV-1 and SIV to the small molecule maturation inhibitor 3-O-{3',3'-dimethylsuccinyl}-betulinic acid.

PubMed

Zhou, Jing; Chen, Chin Ho; Aiken, Christopher

2004-06-29

Despite the effectiveness of currently available antiretroviral therapies in the treatment of HIV-1 infection, a continuing need exists for novel compounds that can be used in combination with existing drugs to slow the emergence of drug-resistant viruses. We previously reported that the small molecule 3-O-{3',3'-dimethylsuccinyl}-betulinic acid (DSB) specifically inhibits HIV-1 replication by delaying the processing of the CA-SP1 junction in Pr55Gag. By contrast, SIVmac239 replicates efficiently in the presence of high concentrations of DSB. To determine whether sequence differences in the CA-SP1 junction can fully account for the differential sensitivity of HIV-1 and SIV to DSB, we engineered mutations in this region of two viruses and tested their sensitivity to DSB in replication assays using activated human primary CD4+ T cells. Substitution of the P2 and P1 residues of HIV-1 by the corresponding amino acids of SIV resulted in strong resistance to DSB, but the mutant virus replicated with reduced efficiency. Conversely, replication of an SIV mutant containing three amino acid substitutions in the CA-SP1 cleavage site was highly sensitive to DSB, and the mutations resulted in delayed cleavage of the CA-SP1 junction in the presence of the drug. These results demonstrate that the CA-SP1 junction in Pr55Gag represents the primary viral target of DSB. They further suggest that the therapeutic application of DSB will be accompanied by emergence of mutant viruses that are highly resistant to the drug but which exhibit reduced fitness relative to wild type HIV-1.

Poliovirus replication requires the N-terminus but not the catalytic Sec7 domain of ArfGEF GBF1.

PubMed

Belov, George A; Kovtunovych, Gennadiy; Jackson, Catherine L; Ehrenfeld, Ellie

2010-10-01

Viruses are intracellular parasites whose reproduction relies on factors provided by the host. The cellular protein GBF1 is critical for poliovirus replication. Here we show that the contribution of GBF1 to virus replication is different from its known activities in uninfected cells. Normally GBF1 activates the ADP-ribosylation factor (Arf) GTPases necessary for formation of COPI transport vesicles. GBF1 function is modulated by p115 and Rab1b. However, in polio-infected cells, p115 is degraded and neither p115 nor Rab1b knock-down affects virus replication. Poliovirus infection is very sensitive to brefeldin A (BFA), an inhibitor of Arf activation by GBF1. BFA targets the catalytic Sec7 domain of GBF1. Nevertheless the BFA block of polio replication is rescued by expression of only the N-terminal region of GBF1 lacking the Sec7 domain. Replication of BFA-resistant poliovirus in the presence of BFA is uncoupled from Arf activation but is dependent on GBF1. Thus the function(s) of this protein essential for viral replication can be separated from those required for cellular metabolism. © Published 2010. This article is a US Government work and is in the public domain in the USA.

CDC-48/p97 coordinates CDT-1 degradation with GINS chromatin dissociation to ensure faithful DNA replication.

PubMed

Franz, André; Orth, Michael; Pirson, Paul A; Sonneville, Remi; Blow, J Julian; Gartner, Anton; Stemmann, Olaf; Hoppe, Thorsten

2011-10-07

Faithful transmission of genomic information requires tight spatiotemporal regulation of DNA replication factors. In the licensing step of DNA replication, CDT-1 is loaded onto chromatin to subsequently promote the recruitment of additional replication factors, including CDC-45 and GINS. During the elongation step, the CDC-45/GINS complex moves with the replication fork; however, it is largely unknown how its chromatin association is regulated. Here, we show that the chaperone-like ATPase CDC-48/p97 coordinates degradation of CDT-1 with release of the CDC-45/GINS complex. C. elegans embryos lacking CDC-48 or its cofactors UFD-1/NPL-4 accumulate CDT-1 on mitotic chromatin, indicating a critical role of CDC-48 in CDT-1 turnover. Strikingly, CDC-48(UFD-1/NPL-4)-deficient embryos show persistent chromatin association of CDC-45/GINS, which is a consequence of CDT-1 stabilization. Moreover, our data confirmed a similar regulation in Xenopus egg extracts, emphasizing a conserved coordination of licensing and elongation events during eukaryotic DNA replication by CDC-48/p97. Copyright © 2011 Elsevier Inc. All rights reserved.

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas.

PubMed

Schaub, Franz X; Dhankani, Varsha; Berger, Ashton C; Trivedi, Mihir; Richardson, Anne B; Shaw, Reid; Zhao, Wei; Zhang, Xiaoyang; Ventura, Andrea; Liu, Yuexin; Ayer, Donald E; Hurlin, Peter J; Cherniack, Andrew D; Eisenman, Robert N; Bernard, Brady; Grandori, Carla

2018-03-28

Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers is lacking. Using computational approaches, we define genomic and proteomic features associated with MYC and the PMN across the 33 cancers of The Cancer Genome Atlas. Pan-cancer, 28% of all samples had at least one of the MYC paralogs amplified. In contrast, the MYC antagonists MGA and MNT were the most frequently mutated or deleted members, proposing a role as tumor suppressors. MYC alterations were mutually exclusive with PIK3CA, PTEN, APC, or BRAF alterations, suggesting that MYC is a distinct oncogenic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such as immune response and growth factor signaling; chromatin, translation, and DNA replication/repair were conserved pan-cancer. This analysis reveals insights into MYC biology and is a reference for biomarkers and therapeutics for cancers with alterations of MYC or the PMN. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Nuclear IL-33 is a transcriptional regulator of NF-{kappa}B p65 and induces endothelial cell activation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Yeon-Sook; Park, Jeong Ae; Kim, Jihye

2012-05-04

Highlights: Black-Right-Pointing-Pointer IL-33 as nuclear factor regulated expression of ICAM-1 and VCAM-1. Black-Right-Pointing-Pointer Nuclear IL-33 increased the transcription of NF-{kappa}B p65 by binding to the p65 promoter. Black-Right-Pointing-Pointer Nuclear IL-33 controls NF-{kappa}B-dependent inflammatory responses. -- Abstract: Interleukin (IL)-33, an IL-1 family member, acts as an extracellular cytokine by binding its cognate receptor, ST2. IL-33 is also a chromatin-binding transcriptional regulator highly expressed in the nuclei of endothelial cells. However, the function of IL-33 as a nuclear factor is poorly defined. Here, we show that IL-33 is a novel transcriptional regulator of the p65 subunit of the NF-{kappa}B complex and ismore » involved in endothelial cell activation. Quantitative reverse transcriptase PCR and Western blot analyses indicated that IL-33 mediates the expression of intercellular adhesion molecule (ICAM)-1 and vascular cell adhesion molecule (VCAM)-1 in endothelial cells basally and in response to tumor necrosis factor-{alpha}-treatment. IL-33-induced ICAM-1/VCAM-1 expression was dependent on the regulatory effect of IL-33 on the nuclear factor (NF)-{kappa}B pathway; NF-{kappa}B p65 expression was enhanced by IL-33 overexpression and, conversely, reduced by IL-33 knockdown. Moreover, NF-{kappa}B p65 promoter activity and chromatin immunoprecipitation analysis revealed that IL-33 binds to the p65 promoter region in the nucleus. Our data provide the first evidence that IL-33 in the nucleus of endothelial cells participates in inflammatory reactions as a transcriptional regulator of NF-{kappa}B p65.« less

Diminished origin licensing capacity specifically sensitises tumour cells to replication stress

PubMed Central

Zimmerman, Kristin M.; Jones, Rebecca M.; Petermann, Eva; Jeggo, Penelope A.

2013-01-01

Previous studies have shown that dormant licensed replication origins can be exploited to enhance recovery from replication stress. Since tumour cells express high levels of origin licensing proteins, we examined whether depletion of such factors might specifically sensitise tumour versus non-tumour cells. Consistent with previous findings, we observed that three tumour-derived cell lines overexpress ORC1, a licensing component, compared to four non-tumour cell lines and that a greater level of ORC1 was required to maintain viability in the tumour cells. We determined siRNA-mediated knockdown conditions for each line that maximally reduced ORC1 but did not impact upon viability, which we considered would optimally deplete dormant origins. ORC1 depletion hypersensitised the tumour-derived cells to hydroxyurea (HU) and H202 but did not affect the sensitivity of the non-tumour lines. Similar results were observed following depletion of ORC6 or CDC6. Further, co-depletion of p53 and ORC1 modestly impaired viability of 1BR3hTERT non-tumour fibroblasts and more dramatically caused hypersensitivity to HU. Finally, overexpression of the c-Myc oncogene combined with ORC1 depletion in non-tumour BJhTERT cells diminished viability. Collectively, these findings suggest that tumour cells may have a reliance on origin licensing capacity, suggesting that licensing factors could represent a target for drug-based cancer therapy. PMID:23364533

Analysis of Breast Cell-Lineage Response Differences to Taxol Using a Novel Co-Culture System

DTIC Science & Technology

2005-06-01

as the Hayflick limit [159], is thought to be a "mitotic clock" preventing cumulative cell damage from progressing to tumorigenesis [164-166] and...TERMS Breast cancer, co-culture, gene expression profiles, Taxol, transport mechanisms 16. SECURITY CLASSIFICATION OF: 17. LIMITATION 18. NUMBER 19a...proteins have been shown to bind and inactivate p53 and pRb respectively [25]. While the mortal cells have limited replicative potential in culture and

Shared Genetic Risk Factors of Intracranial, Abdominal, and Thoracic Aneurysms.

PubMed

van 't Hof, Femke N G; Ruigrok, Ynte M; Lee, Cue Hyunkyu; Ripke, Stephan; Anderson, Graig; de Andrade, Mariza; Baas, Annette F; Blankensteijn, Jan D; Böttinger, Erwin P; Bown, Matthew J; Broderick, Joseph; Bijlenga, Philippe; Carrell, David S; Crawford, Dana C; Crosslin, David R; Ebeling, Christian; Eriksson, Johan G; Fornage, Myriam; Foroud, Tatiana; von Und Zu Fraunberg, Mikael; Friedrich, Christoph M; Gaál, Emília I; Gottesman, Omri; Guo, Dong-Chuan; Harrison, Seamus C; Hernesniemi, Juha; Hofman, Albert; Inoue, Ituro; Jääskeläinen, Juha E; Jones, Gregory T; Kiemeney, Lambertus A L M; Kivisaari, Riku; Ko, Nerissa; Koskinen, Seppo; Kubo, Michiaki; Kullo, Iftikhar J; Kuivaniemi, Helena; Kurki, Mitja I; Laakso, Aki; Lai, Dongbing; Leal, Suzanne M; Lehto, Hanna; LeMaire, Scott A; Low, Siew-Kee; Malinowski, Jennifer; McCarty, Catherine A; Milewicz, Dianna M; Mosley, Thomas H; Nakamura, Yusuke; Nakaoka, Hirofumi; Niemelä, Mika; Pacheco, Jennifer; Peissig, Peggy L; Pera, Joanna; Rasmussen-Torvik, Laura; Ritchie, Marylyn D; Rivadeneira, Fernando; van Rij, Andre M; Santos-Cortez, Regie Lyn P; Saratzis, Athanasios; Slowik, Agnieszka; Takahashi, Atsushi; Tromp, Gerard; Uitterlinden, André G; Verma, Shefali S; Vermeulen, Sita H; Wang, Gao T; Han, Buhm; Rinkel, Gabriël J E; de Bakker, Paul I W

2016-07-14

Intracranial aneurysms (IAs), abdominal aortic aneurysms (AAAs), and thoracic aortic aneurysms (TAAs) all have a familial predisposition. Given that aneurysm types are known to co-occur, we hypothesized that there may be shared genetic risk factors for IAs, AAAs, and TAAs. We performed a mega-analysis of 1000 Genomes Project-imputed genome-wide association study (GWAS) data of 4 previously published aneurysm cohorts: 2 IA cohorts (in total 1516 cases, 4305 controls), 1 AAA cohort (818 cases, 3004 controls), and 1 TAA cohort (760 cases, 2212 controls), and observed associations of 4 known IA, AAA, and/or TAA risk loci (9p21, 18q11, 15q21, and 2q33) with consistent effect directions in all 4 cohorts. We calculated polygenic scores based on IA-, AAA-, and TAA-associated SNPs and tested these scores for association to case-control status in the other aneurysm cohorts; this revealed no shared polygenic effects. Similarly, linkage disequilibrium-score regression analyses did not show significant correlations between any pair of aneurysm subtypes. Last, we evaluated the evidence for 14 previously published aneurysm risk single-nucleotide polymorphisms through collaboration in extended aneurysm cohorts, with a total of 6548 cases and 16 843 controls (IA) and 4391 cases and 37 904 controls (AAA), and found nominally significant associations for IA risk locus 18q11 near RBBP8 to AAA (odds ratio [OR]=1.11; P=4.1×10(-5)) and for TAA risk locus 15q21 near FBN1 to AAA (OR=1.07; P=1.1×10(-3)). Although there was no evidence for polygenic overlap between IAs, AAAs, and TAAs, we found nominally significant effects of two established risk loci for IAs and TAAs in AAAs. These two loci will require further replication. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Genetic associations between fibrinogen and cognitive performance in three Scottish cohorts.

PubMed

Marioni, Riccardo E; Deary, Ian J; Murray, Gordon D; Lowe, Gordon D O; Strachan, Mark W J; Luciano, Michelle; Houlihan, Lorna M; Gow, Alan J; Harris, Sarah E; Rumley, Ann; Stewart, Marlene C; Fowkes, F Gerry R; Price, Jackie F

2011-09-01

There is increasing evidence to suggest that elevated plasma levels of fibrinogen are associated with late-life cognitive performance. This study tested the association of single nucleotide polymorphisms in the fibrinogen α (FGA) and β (FGB) genes with cognitive performance. Data were analysed from three community-dwelling populations of older persons (>50 years) in central Scotland: the Aspirin for Asymptomatic Atherosclerosis (AAA) Trial (n = 2,091), the Edinburgh Type 2 Diabetes Study (ET2DS, n = 1,066), and the Lothian Birth Cohort 1936 (LBC1936, n = 1,091). Cognition was assessed using a battery of five, seven, and four psychometric tests, respectively. This information was used to derive a general cognitive factor. Weakly significant associations were found between the rs4220 (FGB), and rs2227412 (FGB) SNPs and a single test of cognitive performance in the AAA Trial (p < 0.05). These findings did not replicate in the LBC1936 or ET2DS cohorts, except for the rs2227412 SNP, which was significantly associated with the general cognitive factor in the ET2DS (p = 3.3 × 10(-4)). A summary term that combined results from all three studies suggested that the rs2227412 genotype associated with reduced cognitive ability also associated with higher plasma fibrinogen levels. These findings suggest a tentative role for fibrinogen as a determinant of late-life cognitive performance and justify further attempts at replication in older persons.

DNA damage tolerance pathway involving DNA polymerase ι and the tumor suppressor p53 regulates DNA replication fork progression.

PubMed

Hampp, Stephanie; Kiessling, Tina; Buechle, Kerstin; Mansilla, Sabrina F; Thomale, Jürgen; Rall, Melanie; Ahn, Jinwoo; Pospiech, Helmut; Gottifredi, Vanesa; Wiesmüller, Lisa

2016-07-26

DNA damage tolerance facilitates the progression of replication forks that have encountered obstacles on the template strands. It involves either translesion DNA synthesis initiated by proliferating cell nuclear antigen monoubiquitination or less well-characterized fork reversal and template switch mechanisms. Herein, we characterize a novel tolerance pathway requiring the tumor suppressor p53, the translesion polymerase ι (POLι), the ubiquitin ligase Rad5-related helicase-like transcription factor (HLTF), and the SWI/SNF catalytic subunit (SNF2) translocase zinc finger ran-binding domain containing 3 (ZRANB3). This novel p53 activity is lost in the exonuclease-deficient but transcriptionally active p53(H115N) mutant. Wild-type p53, but not p53(H115N), associates with POLι in vivo. Strikingly, the concerted action of p53 and POLι decelerates nascent DNA elongation and promotes HLTF/ZRANB3-dependent recombination during unperturbed DNA replication. Particularly after cross-linker-induced replication stress, p53 and POLι also act together to promote meiotic recombination enzyme 11 (MRE11)-dependent accumulation of (phospho-)replication protein A (RPA)-coated ssDNA. These results implicate a direct role of p53 in the processing of replication forks encountering obstacles on the template strand. Our findings define an unprecedented function of p53 and POLι in the DNA damage response to endogenous or exogenous replication stress.

Human Cytomegalovirus Nuclear Capsids Associate with the Core Nuclear Egress Complex and the Viral Protein Kinase pUL97

PubMed Central

Sonntag, Eric; Wagner, Sabrina; Strojan, Hanife; Wangen, Christina; Lenac Rovis, Tihana; Lisnic, Berislav; Jonjic, Stipan; Schlötzer-Schrehardt, Ursula; Marschall, Manfred

2018-01-01

The nuclear phase of herpesvirus replication is regulated through the formation of regulatory multi-component protein complexes. Viral genomic replication is followed by nuclear capsid assembly, DNA encapsidation and nuclear egress. The latter has been studied intensely pointing to the formation of a viral core nuclear egress complex (NEC) that recruits a multimeric assembly of viral and cellular factors for the reorganization of the nuclear envelope. To date, the mechanism of the association of human cytomegalovirus (HCMV) capsids with the NEC, which in turn initiates the specific steps of nuclear capsid budding, remains undefined. Here, we provide electron microscopy-based data demonstrating the association of both nuclear capsids and NEC proteins at nuclear lamina budding sites. Specifically, immunogold labelling of the core NEC constituent pUL53 and NEC-associated viral kinase pUL97 suggested an intranuclear NEC-capsid interaction. Staining patterns with phospho-specific lamin A/C antibodies are compatible with earlier postulates of targeted capsid egress at lamina-depleted areas. Important data were provided by co-immunoprecipitation and in vitro kinase analyses using lysates from HCMV-infected cells, nuclear fractions, or infectious virions. Data strongly suggest that nuclear capsids interact with pUL53 and pUL97. Combined, the findings support a refined concept of HCMV nuclear trafficking and NEC-capsid interaction. PMID:29342872

Human Cytomegalovirus Nuclear Capsids Associate with the Core Nuclear Egress Complex and the Viral Protein Kinase pUL97.

PubMed

Milbradt, Jens; Sonntag, Eric; Wagner, Sabrina; Strojan, Hanife; Wangen, Christina; Lenac Rovis, Tihana; Lisnic, Berislav; Jonjic, Stipan; Sticht, Heinrich; Britt, William J; Schlötzer-Schrehardt, Ursula; Marschall, Manfred

2018-01-13

The nuclear phase of herpesvirus replication is regulated through the formation of regulatory multi-component protein complexes. Viral genomic replication is followed by nuclear capsid assembly, DNA encapsidation and nuclear egress. The latter has been studied intensely pointing to the formation of a viral core nuclear egress complex (NEC) that recruits a multimeric assembly of viral and cellular factors for the reorganization of the nuclear envelope. To date, the mechanism of the association of human cytomegalovirus (HCMV) capsids with the NEC, which in turn initiates the specific steps of nuclear capsid budding, remains undefined. Here, we provide electron microscopy-based data demonstrating the association of both nuclear capsids and NEC proteins at nuclear lamina budding sites. Specifically, immunogold labelling of the core NEC constituent pUL53 and NEC-associated viral kinase pUL97 suggested an intranuclear NEC-capsid interaction. Staining patterns with phospho-specific lamin A/C antibodies are compatible with earlier postulates of targeted capsid egress at lamina-depleted areas. Important data were provided by co-immunoprecipitation and in vitro kinase analyses using lysates from HCMV-infected cells, nuclear fractions, or infectious virions. Data strongly suggest that nuclear capsids interact with pUL53 and pUL97. Combined, the findings support a refined concept of HCMV nuclear trafficking and NEC-capsid interaction.

Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis)

PubMed Central

Saade, Evelyne; Pirozhkova, Iryna; Aimbetov, Rakhan; Lipinski, Marc; Ogryzko, Vasily

2015-01-01

The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed. PMID:25720734

The influence of HCl concentration and demineralization temperature of Atrina pectinata shells on quality of chitin

NASA Astrophysics Data System (ADS)

Nugroho, Intan Lazuardi; Pursetyo, Kustiawan Tri; Masithah, Endang Dewi

2017-02-01

Atrina pectinata is one of shells species widely consumed by people, which means the high consumption will generate the availability of shells in the environment as waste. Chitin can be produced from the shells. Shells contain quite high minerals that it should be demineralized to reduce the mineral content from the shells. This study aimed to determine the effect of HCl concentration and temperature affect chitin characteristics as the result of demineralization process from pen shells. The method based on two steps, there were demineralization and deproteination. This study used Completely Randomized Design (CRD) with two factors, including HCl concentration (2N, 4N, and 6N) and temperature (33°C and 60°C) which consists six combination treatments and three replications. Data was analyzed by using Analysis of Variance (ANOVA) and followed by Duncan's Multiple Range Test. The results showed that interaction of HCl concentration and temperature has significant effect (p<0.05) to ash content of chitin. The use concentration of 6N and 33°C produced the lowest ash content. Characteristics chitin resulted from the treatment of 6N and 33°C produced ash content 25.33% ± 6.82, moisture content 3.67% ± 1.10, yield 0.72% ± 0.12 and protein content 5.86%.

Genome-wide association analysis implicates dysregulation of immunity genes in chronic lymphocytic leukaemia.

PubMed

Law, Philip J; Berndt, Sonja I; Speedy, Helen E; Camp, Nicola J; Sava, Georgina P; Skibola, Christine F; Holroyd, Amy; Joseph, Vijai; Sunter, Nicola J; Nieters, Alexandra; Bea, Silvia; Monnereau, Alain; Martin-Garcia, David; Goldin, Lynn R; Clot, Guillem; Teras, Lauren R; Quintela, Inés; Birmann, Brenda M; Jayne, Sandrine; Cozen, Wendy; Majid, Aneela; Smedby, Karin E; Lan, Qing; Dearden, Claire; Brooks-Wilson, Angela R; Hall, Andrew G; Purdue, Mark P; Mainou-Fowler, Tryfonia; Vajdic, Claire M; Jackson, Graham H; Cocco, Pierluigi; Marr, Helen; Zhang, Yawei; Zheng, Tongzhang; Giles, Graham G; Lawrence, Charles; Call, Timothy G; Liebow, Mark; Melbye, Mads; Glimelius, Bengt; Mansouri, Larry; Glenn, Martha; Curtin, Karen; Diver, W Ryan; Link, Brian K; Conde, Lucia; Bracci, Paige M; Holly, Elizabeth A; Jackson, Rebecca D; Tinker, Lesley F; Benavente, Yolanda; Boffetta, Paolo; Brennan, Paul; Maynadie, Marc; McKay, James; Albanes, Demetrius; Weinstein, Stephanie; Wang, Zhaoming; Caporaso, Neil E; Morton, Lindsay M; Severson, Richard K; Riboli, Elio; Vineis, Paolo; Vermeulen, Roel C H; Southey, Melissa C; Milne, Roger L; Clavel, Jacqueline; Topka, Sabine; Spinelli, John J; Kraft, Peter; Ennas, Maria Grazia; Summerfield, Geoffrey; Ferri, Giovanni M; Harris, Robert J; Miligi, Lucia; Pettitt, Andrew R; North, Kari E; Allsup, David J; Fraumeni, Joseph F; Bailey, James R; Offit, Kenneth; Pratt, Guy; Hjalgrim, Henrik; Pepper, Chris; Chanock, Stephen J; Fegan, Chris; Rosenquist, Richard; de Sanjose, Silvia; Carracedo, Angel; Dyer, Martin J S; Catovsky, Daniel; Campo, Elias; Cerhan, James R; Allan, James M; Rothman, Nathanial; Houlston, Richard; Slager, Susan

2017-02-06

Several chronic lymphocytic leukaemia (CLL) susceptibility loci have been reported; however, much of the heritable risk remains unidentified. Here we perform a meta-analysis of six genome-wide association studies, imputed using a merged reference panel of 1,000 Genomes and UK10K data, totalling 6,200 cases and 17,598 controls after replication. We identify nine risk loci at 1p36.11 (rs34676223, P=5.04 × 10 -13 ), 1q42.13 (rs41271473, P=1.06 × 10 -10 ), 4q24 (rs71597109, P=1.37 × 10 -10 ), 4q35.1 (rs57214277, P=3.69 × 10 -8 ), 6p21.31 (rs3800461, P=1.97 × 10 -8 ), 11q23.2 (rs61904987, P=2.64 × 10 -11 ), 18q21.1 (rs1036935, P=3.27 × 10 -8 ), 19p13.3 (rs7254272, P=4.67 × 10 -8 ) and 22q13.33 (rs140522, P=2.70 × 10 -9 ). These new and established risk loci map to areas of active chromatin and show an over-representation of transcription factor binding for the key determinants of B-cell development and immune response.

Tombusvirus RNA replication depends on the TOR pathway in yeast and plants.

PubMed

Inaba, Jun-Ichi; Nagy, Peter D

2018-06-01

Similar to other (+)RNA viruses, tomato bushy stunt virus (TBSV) utilizes metabolites, lipids, membranes, and co-opted host factors during replication. The coordination of cell metabolism and growth with environmental cues is performed by the target of rapamycin (TOR) kinase in eukaryotic cells. In this paper, we find that TBSV replication partially inhibits TOR activity, likely due to recruitment of glycolytic enzymes to the viral replication compartment, which results in reduced ATP levels in the cytosol. Complete inhibition of TOR activity with rapamycin in yeast or AZD8055 inhibitor in plants reduces tombusvirus replication. We find that high glucose concentration, which stimulates TOR activity, enhanced tombusvirus replication in yeast. Depletion of yeast Sch9 or plant S6K1 kinase, a downstream effector of TOR, also inhibited tombusvirus replication in yeast and plant or the assembly of the viral replicase in vitro. Altogether, the TOR pathway is crucial for TBSV to replicate efficiently in hosts. Copyright © 2018 Elsevier Inc. All rights reserved.

Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis.

PubMed

Li, Caroline M; Miao, Yunan; Lingeman, Robert G; Hickey, Robert J; Malkas, Linda H

2016-01-01

We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE). In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40) origin of DNA replication and the viral large tumor antigen (T-antigen) protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA), DNA topoisomerase I (topo I), DNA polymerase δ (Pol δ), DNA polymerase ɛ (Pol ɛ), replication protein A (RPA) and replication factor C (RFC). Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

Hypovitaminosis D increases TB co-infection risk on HIV patients

NASA Astrophysics Data System (ADS)

Gayatri, Y. A. A. A.; Sukmawati, D. D.; Utama, S. M.; Somia, I. K. A.; Merati, T. P.

2018-03-01

Tuberculosis is causes of mortality and morbidity in patients with HIV. Hypovitaminosis D, a defective cell-mediated immune response to Mycobacterium tuberculosis infection has been extensively described in HIV patients, but studies assessing the role of vitamin D in TB-HIV co-infection are lacking. We, therefore, conducted a 1:1 pair- matched case-control study to verify hypovitaminosis D possible risk factor of TB- HIV co- infection. Consecutive HIV patients starting ARV and sex, age and CD4 cell count matched were by recruiting. Tuberculosis has confirmed by thepresence of acid-fast bacilli in sputum or mycobacterium detected in specimens culture/Gene Xpert/PCR. Vitamin D levels were by measuring direct chemiluminescent immunoassay on a LIAISON®25OH analyzer. The study comprised 25 cases and 25 controls, median (interquartile range) 25(OH)D3 serum concentration were 19.80 (12.15-27.45) ng/mL in cases and 33.30 (27.2-39.4) ng/mL in controls (P<0.001). After adjustment for potential confounders included anemia, smoking,and low BMI, with multivariate logistic regression analysis, hypovitaminosis Dindependently associated with the development of active tuberculosis in HIV patients.(OR 26.154 (90% CI: 4.371-156.541); p <0.001). The finding indicates that hypovitaminosis D was a risk factor of TB-HIV co-infection.

Replicating viral vector platform exploits alarmin signals for potent CD8+ T cell-mediated tumour immunotherapy

PubMed Central

Kallert, Sandra M.; Darbre, Stephanie; Bonilla, Weldy V.; Kreutzfeldt, Mario; Page, Nicolas; Müller, Philipp; Kreuzaler, Matthias; Lu, Min; Favre, Stéphanie; Kreppel, Florian; Löhning, Max; Luther, Sanjiv A.; Zippelius, Alfred; Merkler, Doron; Pinschewer, Daniel D.

2017-01-01

Viral infections lead to alarmin release and elicit potent cytotoxic effector T lymphocyte (CTLeff) responses. Conversely, the induction of protective tumour-specific CTLeff and their recruitment into the tumour remain challenging tasks. Here we show that lymphocytic choriomeningitis virus (LCMV) can be engineered to serve as a replication competent, stably-attenuated immunotherapy vector (artLCMV). artLCMV delivers tumour-associated antigens to dendritic cells for efficient CTL priming. Unlike replication-deficient vectors, artLCMV targets also lymphoid tissue stroma cells expressing the alarmin interleukin-33. By triggering interleukin-33 signals, artLCMV elicits CTLeff responses of higher magnitude and functionality than those induced by replication-deficient vectors. Superior anti-tumour efficacy of artLCMV immunotherapy depends on interleukin-33 signalling, and a massive CTLeff influx triggers an inflammatory conversion of the tumour microenvironment. Our observations suggest that replicating viral delivery systems can release alarmins for improved anti-tumour efficacy. These mechanistic insights may outweigh safety concerns around replicating viral vectors in cancer immunotherapy. PMID:28548102

Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans

PubMed Central

Zhang, Mingfeng; Song, Fengju; Liang, Liming; Nan, Hongmei; Zhang, Jiangwen; Liu, Hongliang; Wang, Li-E.; Wei, Qingyi; Lee, Jeffrey E.; Amos, Christopher I.; Kraft, Peter; Qureshi, Abrar A.; Han, Jiali

2013-01-01

Aiming to identify novel genetic loci for pigmentation and skin cancer, we conducted a series of genome-wide association studies on hair color, eye color, number of sunburns, tanning ability and number of non-melanoma skin cancers (NMSCs) among 10 183 European Americans in the discovery stage and 4504 European Americans in the replication stage (for eye color, 3871 males in the discovery stage and 2496 males in the replication stage). We targeted novel chromosome regions besides the known ones for replication. As a result, we identified a new region downstream of the EDNRB gene on 13q22 associated with hair color and the strongest association was the single-nucleotide polymorphism (SNP) rs975739 (P = 2.4 × 10−14; P = 5.4 × 10−9 in the discovery set and P = 1.2 × 10−6 in the replication set). Using blue, intermediate (including green) and brown eye colors as co-dominant outcomes, we identified the SNP rs3002288 in VASH2 on 1q32.3 associated with brown eye (P = 7.0 × 10−8; P = 5.3 × 10−5 in the discovery set and P = 0.02 in the replication set). Additionally, we identified a significant interaction between the SNPs rs7173419 and rs12913832 in the OCA2 gene region on brown eye color (P-value for interaction = 3.8 × 10−3). As for the number of NMSCs, we identified two independent SNPs on chr6 and one SNP on chromosome 14: rs12203592 in IRF4 (P = 7.2 × 10−14; P = 1.8 × 10−8 in the discovery set and P = 6.7 × 10−7 in the replication set), rs12202284 between IRF4 and EXOC2 (P = 5.0 × 10−8; P = 6.6 × 10−7 in the discovery set and P = 3.0 × 10−3 in the replication set) and rs8015138 upstream of GNG2 (P = 6.6 × 10−8; P = 5.3 × 10−7 in the discovery set and P = 0.01 in the replication set). PMID:23548203

Severe Acute Respiratory Syndrome Coronavirus Replication Is Severely Impaired by MG132 due to Proteasome-Independent Inhibition of M-Calpain

PubMed Central

Schneider, Martha; Ackermann, Kerstin; Stuart, Melissa; Wex, Claudia; Protzer, Ulrike; Schätzl, Hermann M.

2012-01-01

The ubiquitin-proteasome system (UPS) is involved in the replication of a broad range of viruses. Since replication of the murine hepatitis virus (MHV) is impaired upon proteasomal inhibition, the relevance of the UPS for the replication of the severe acute respiratory syndrome coronavirus (SARS-CoV) was investigated in this study. We demonstrate that the proteasomal inhibitor MG132 strongly inhibits SARS-CoV replication by interfering with early steps of the viral life cycle. Surprisingly, other proteasomal inhibitors (e.g., lactacystin and bortezomib) only marginally affected viral replication, indicating that the effect of MG132 is independent of proteasomal impairment. Induction of autophagy by MG132 treatment was excluded from playing a role, and no changes in SARS-CoV titers were observed during infection of wild-type or autophagy-deficient ATG5−/− mouse embryonic fibroblasts overexpressing the human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2). Since MG132 also inhibits the cysteine protease m-calpain, we addressed the role of calpains in the early SARS-CoV life cycle using calpain inhibitors III (MDL28170) and VI (SJA6017). In fact, m-calpain inhibition with MDL28170 resulted in an even more pronounced inhibition of SARS-CoV replication (>7 orders of magnitude) than did MG132. Additional m-calpain knockdown experiments confirmed the dependence of SARS-CoV replication on the activity of the cysteine protease m-calpain. Taken together, we provide strong experimental evidence that SARS-CoV has unique replication requirements which are independent of functional UPS or autophagy pathways compared to other coronaviruses. Additionally, this work highlights an important role for m-calpain during early steps of the SARS-CoV life cycle. PMID:22787216

Progress and Challenges in Predicting Crop Responses to Atmospheric [CO2

NASA Astrophysics Data System (ADS)

Kent, J.; Paustian, K.

2017-12-01

Increasing atmospheric [CO2] directly accelerates photosynthesis in C3 crops, and indirectly promotes yields by reducing stomatal conductance and associated water losses in C3 and C4 crops. Several decades of experiments have exposed crops to eCO2 in greenhouses and other enclosures and observed yield increases on the order of 33%. FACE systems were developed in the early 1990s to better replicate open-field growing conditions. Some authors contend that FACE results indicate lower crop yield responses than enclosure studies, while others maintain no significant difference or attribute differences to various methodological factors. The crop CO2 response processes in many crop models were developed using results from enclosure experiments. This work tested the ability of one such model, DayCent, to reproduce crop responses to CO2 enrichment from several FACE experiments. DayCent performed well at simulating yield and transpiration responses in C4 crops, but significantly overestimated yield responses in C3 crops. After adjustment of CO2-response parameters, DayCent was able to reproduce mean yield responses for specific crops. However, crop yield responses from FACE experiments vary widely across years and sites, and likely reflect complex interactions between conditions such as weather, soils, cultivars, and biotic stressors. Further experimental work is needed to identify the secondary variables that explain this variability so that models can more reliably forecast crop yields under climate change. Likewise, CO2 impacts on crop outcomes such as belowground biomass allocation and grain N content have implications for agricultural C fluxes and human nutrition, respectively, but are poorly understood and thus difficult to simulate with confidence.

Effectiveness of Reducing P Fertilizer and Adding Fish Pond Mud Waste on Growth and Yield of Soybean in Peatland

NASA Astrophysics Data System (ADS)

Asie, Erina Riak; Rumbang, Nyahu; Winarti, Sih; Sinaga, Soaloon

2018-02-01

The objective of the study was to assess the effectiveness of P fertilizer reduction and the addition of fish pond sludge waste on the growth and yield of soybean crop in peatland. Research used Complete Randomized Design factorial with two factors. The first factor was the reduction of P fertilizer from the dose of 150 kg.ha-1 consisting of 4 levels, namely P0: 100% (2.944 g/polybag), P1: 75% (2.208 g/polybag), P2: 50% (1.472 g/polybag), and P3: 25% (0.736 g/polybag). The second factor was the addition of fish pond mud waste (L) from the dose of 15 ton.ha-1 consisting of 4 levels, namely L0: 25% (73.595 g/polybag), L1: 50% (147.19 g/polybag), L2: 75% (220.78 g/polybag), and L3: 100% (294.38 g/polybag). Each treatment combination was replicated 3 times to obtain 48 experimental units. The results showed that (1) fish pond mud waste was effective to reduce the use of P fertilizer, (2) the reduction of P fertilizer up to 50% from recommendation dosage by addition of fish pond sludge waste at 75% dose of 15 ton/ha was the best combination due to providing the best plant growth and the highest P concentration of plant tissue. The highest number of pods and weight of seed obtained in the combination were 60.33 pods/plant and 7.30 g/plant, respectively.

Homocysteine is the confounding factor of metabolic syndrome-confirmed by siMS score.

PubMed

Srećković, Branko; Soldatovic, Ivan; Colak, Emina; Mrdovic, Igor; Sumarac-Dumanovic, Mirjana; Janeski, Hristina; Janeski, Nenad; Gacic, Jasna; Dimitrijevic-Sreckovic, Vesna

2018-04-06

Abdominal adiposity has a central role in developing insulin resistance (IR) by releasing pro-inflammatory cytokines. Patients with metabolic syndrome (MS) have higher values of homocysteine. Hyperhomocysteinemia correlates with IR, increasing the oxidative stress. Oxidative stress causes endothelial dysfunction, hypertension and atherosclerosis. The objective of the study was to examine the correlation of homocysteine with siMS score and siMS risk score and with other MS co-founding factors. The study included 69 obese individuals (age over 30, body mass index [BMI] >25 kg/m2), classified into two groups: I-with MS (33 patients); II-without MS (36 patients). Measurements included: anthropometric parameters, lipids, glucose regulation parameters and inflammation parameters. IR was determined by homeostatic model assessment for insulin resistance (HOMA-IR). ATP III classification was applied for diagnosing MS. SiMS score was used as continuous measure of metabolic syndrome. A significant difference between groups was found for C-reactive protein (CRP) (p<0.01) apolipoprotein (Apo) B, HOMA-IR and acidum uricum (p<0.05). siMS risk score showed a positive correlation with homocysteine (p=0.023), while siMS score correlated positively with fibrinogen (p=0.013), CRP and acidum uricum (p=0.000) and homocysteine (p=0.08). Homocysteine correlated positively with ApoB (p=0.036), HbA1c (p=0.047), HOMA-IR (p=0.008) and negatively with ApoE (p=0.042). Correlation of siMS score with homocysteine, fibrinogen, CRP and acidum uricum indicates that they are co-founding factors of MS. siMS risk score correlation with homocysteine indicates that hyperhomocysteinemia increases with age. Hyperhomocysteinemia is linked with genetic factors and family nutritional scheme, increasing the risk for atherosclerosis.

Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins

PubMed Central

Soler, Nicolas; Marguet, Evelyne; Cortez, Diego; Desnoues, Nicole; Keller, Jenny; van Tilbeurgh, Herman; Sezonov, Guennadi; Forterre, Patrick

2010-01-01

Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (∼12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication. PMID:20403814

Case–Control Genome-Wide Association Study of Persistent Attention-Deficit Hyperactivity Disorder Identifies FBXO33 as a Novel Susceptibility Gene for the Disorder

PubMed Central

Sánchez-Mora, Cristina; Ramos-Quiroga, Josep A; Bosch, Rosa; Corrales, Montse; Garcia-Martínez, Iris; Nogueira, Mariana; Pagerols, Mireia; Palomar, Gloria; Richarte, Vanesa; Vidal, Raquel; Arias-Vasquez, Alejandro; Bustamante, Mariona; Forns, Joan; Gross-Lesch, Silke; Guxens, Monica; Hinney, Anke; Hoogman, Martine; Jacob, Christian; Jacobsen, Kaya K; Kan, Cornelis C; Kiemeney, Lambertus; Kittel-Schneider, Sarah; Klein, Marieke; Onnink, Marten; Rivero, Olga; Zayats, Tetyana; Buitelaar, Jan; Faraone, Stephen V; Franke, Barbara; Haavik, Jan; Johansson, Stefan; Lesch, Klaus-Peter; Reif, Andreas; Sunyer, Jordi; Bayés, Mònica; Casas, Miguel; Cormand, Bru; Ribasés, Marta

2015-01-01

Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with high heritability. At least 30% of patients diagnosed in childhood continue to suffer from ADHD during adulthood and genetic risk factors may play an essential role in the persistence of the disorder throughout lifespan. To date, genome-wide association studies (GWAS) of ADHD have been completed in seven independent datasets, six of which were pediatric samples and one on persistent ADHD using a DNA-pooling strategy, but none of them reported genome-wide significant associations. In an attempt to unravel novel genes for the persistence of ADHD into adulthood, we conducted the first two-stage GWAS in adults with ADHD. The discovery sample included 607 ADHD cases and 584 controls. Top signals were subsequently tested for replication in three independent follow-up samples of 2104 ADHD patients and 1901 controls. None of the findings exceeded the genome-wide threshold for significance (PGC<5e−08), but we found evidence for the involvement of the FBXO33 (F-box only protein 33) gene in combined ADHD in the discovery sample (P=9.02e−07) and in the joint analysis of both stages (P=9.7e−03). Additional evidence for a FBXO33 role in ADHD was found through gene-wise and pathway enrichment analyses in our genomic study. Risk alleles were associated with lower FBXO33 expression in lymphoblastoid cell lines and with reduced frontal gray matter volume in a sample of 1300 adult subjects. Our findings point for the first time at the ubiquitination machinery as a new disease mechanism for adult ADHD and establish a rationale for searching for additional risk variants in ubiquitination-related genes. PMID:25284319

Global genomics and proteomics approaches to identify host factors as targets to induce resistance against Tomato bushy stunt virus.

PubMed

Nagy, Peter D; Pogany, Judit

2010-01-01

The success of RNA viruses as pathogens of plants, animals, and humans depends on their ability to reprogram the host cell metabolism to support the viral infection cycle and to suppress host defense mechanisms. Plus-strand (+)RNA viruses have limited coding potential necessitating that they co-opt an unknown number of host factors to facilitate their replication in host cells. Global genomics and proteomics approaches performed with Tomato bushy stunt virus (TBSV) and yeast (Saccharomyces cerevisiae) as a model host have led to the identification of 250 host factors affecting TBSV RNA replication and recombination or bound to the viral replicase, replication proteins, or the viral RNA. The roles of a dozen host factors involved in various steps of the replication process have been validated in yeast as well as a plant host. Altogether, the large number of host factors identified and the great variety of cellular functions performed by these factors indicate the existence of a truly complex interaction between TBSV and the host cell. This review summarizes the advantages of using a simple plant virus and yeast as a model host to advance our understanding of virus-host interactions at the molecular and cellular levels. The knowledge of host factors gained can potentially be used to inhibit virus replication via gene silencing, expression of dominant negative mutants, or design of specific chemical inhibitors leading to novel specific or broad-range resistance and antiviral tools against (+)RNA plant viruses. Copyright © 2010 Elsevier Inc. All rights reserved.

Cellular and molecular mechanisms of HIV-1 integration targeting.

PubMed

Engelman, Alan N; Singh, Parmit K

2018-07-01

Integration is central to HIV-1 replication and helps mold the reservoir of cells that persists in AIDS patients. HIV-1 interacts with specific cellular factors to target integration to interior regions of transcriptionally active genes within gene-dense regions of chromatin. The viral capsid interacts with several proteins that are additionally implicated in virus nuclear import, including cleavage and polyadenylation specificity factor 6, to suppress integration into heterochromatin. The viral integrase protein interacts with transcriptional co-activator lens epithelium-derived growth factor p75 to principally position integration within gene bodies. The integrase additionally senses target DNA distortion and nucleotide sequence to help fine-tune the specific phosphodiester bonds that are cleaved at integration sites. Research into virus-host interactions that underlie HIV-1 integration targeting has aided the development of a novel class of integrase inhibitors and may help to improve the safety of viral-based gene therapy vectors.

The Impact of Donor Viral Replication at Transplant on Recipient Infections Posttransplant: A Prospective Study

PubMed Central

Verghese, Priya S.; Schmeling, David O.; Knight, Jennifer A.; Matas, Arthur J.; Balfour, Henry H.

2014-01-01

Background Organ donors are often implicated as the source of posttransplant recipient infection. We prospectively studied kidney and liver donor-recipient pairs to determine if donor viral replication of cytomegalovirus (CMV), Epstein-Barr virus (EBV), and BK polyomavirus (BKV) at transplant was a risk factor for posttransplant recipient infection and disease. Methods Donors and recipients were studied for antibodies against CMV and EBV and for quantitative viral replication of CMV, EBV and BKV in oral washes, urine, and whole blood pretransplant. Recipient testing continued every 3 months posttransplant. Demographic and clinical data on infections and graft and subject outcomes were obtained. Results The 98 donor-recipient pairs included 15 liver and 83 kidney transplants (18 of whom were children). No donor had detectable CMV replication; therefore its impact on recipient CMV replication could not be analyzed. Donor EBV replication occurred in 22%, mostly in the oral wash and had no impact on posttransplant recipient EBV replication (p 0.9) or EBV viremia (p 0.6) in kidney or liver recipients. Donor BKV replication occurred in 17%, mostly in the urine and although not associated with posttransplant recipient urinary BKV replication in recipients, it was associated with BKV viremia (p 0.02), and a significantly shorter time to BKV viremia (p 0.01) in kidney recipients. Conclusion Donor replication of CMV or EBV did not impact posttransplant recipient viral replication in kidney/liver transplants. Donor urinary BKV replication is associated with recipient BKV viremia in kidney transplants. PMID:25148381

CRTC2 polymorphism as a risk factor for the incidence of metabolic syndrome in patients with solid organ transplantation.

PubMed

Quteineh, L; Bochud, P-Y; Golshayan, D; Crettol, S; Venetz, J-P; Manuel, O; Kutalik, Z; Treyer, A; Lehmann, R; Mueller, N J; Binet, I; van Delden, C; Steiger, J; Mohacsi, P; Dufour, J-F; Soccal, P M; Pascual, M; Eap, C B

2017-01-01

Metabolic syndrome after transplantation is a major concern following solid organ transplantation (SOT). The CREB-regulated transcription co-activator 2 (CRTC2) regulates glucose metabolism. The effect of CRTC2 polymorphisms on new-onset diabetes after transplantation (NODAT) was investigated in a discovery sample of SOT recipients (n 1 =197). Positive results were tested for replication in two samples from the Swiss Transplant Cohort Study (STCS, n 2 =1294 and n 3 =759). Obesity and other metabolic traits were also tested. Associations with metabolic traits in population-based samples (n 4 =46'186, n 5 =123'865, n 6 >100,000) were finally analyzed. In the discovery sample, CRTC2 rs8450-AA genotype was associated with NODAT, fasting blood glucose and body mass index (P corrected <0.05). CRTC2 rs8450-AA genotype was associated with NODAT in the second STCS replication sample (odd ratio (OR)=2.01, P=0.04). In the combined STCS replication samples, the effect of rs8450-AA genotype on NODAT was observed in patients having received SOT from a deceased donor and treated with tacrolimus (n=395, OR=2.08, P=0.02) and in non-kidney transplant recipients (OR=2.09, P=0.02). Moreover, rs8450-AA genotype was associated with overweight or obesity (n=1215, OR=1.56, P=0.02), new-onset hyperlipidemia (n=1007, OR=1.76, P=0.007), and lower high-density lipoprotein-cholesterol (n=1214, β=-0.08, P=0.001). In the population-based samples, a proxy of rs8450G>A was significantly associated with several metabolic abnormalities. CRTC2 rs8450G>A appears to have an important role in the high prevalence of metabolic traits observed in patients with SOT. A weak association with metabolic traits was also observed in the population-based samples.

Mitochondrial nucleoid clusters protect newly synthesized mtDNA during Doxorubicin- and Ethidium Bromide-induced mitochondrial stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alán, Lukáš, E-mail: lukas.alan@fgu.cas.cz; Špaček

Mitochondrial DNA (mtDNA) is compacted in ribonucleoprotein complexes called nucleoids, which can divide or move within the mitochondrial network. Mitochondrial nucleoids are able to aggregate into clusters upon reaction with intercalators such as the mtDNA depletion agent Ethidium Bromide (EB) or anticancer drug Doxorobicin (DXR). However, the exact mechanism of nucleoid clusters formation remains unknown. Resolving these processes may help to elucidate the mechanisms of DXR-induced cardiotoxicity. Therefore, we addressed the role of two key nucleoid proteins; mitochondrial transcription factor A (TFAM) and mitochondrial single-stranded binding protein (mtSSB); in the formation of mitochondrial nucleoid clusters during the action of intercalators.more » We found that both intercalators cause numerous aberrations due to perturbing their native status. By blocking mtDNA replication, both agents also prevented mtDNA association with TFAM, consequently causing nucleoid aggregation into large nucleoid clusters enriched with TFAM, co-existing with the normal nucleoid population. In the later stages of intercalation (> 48 h), TFAM levels were reduced to 25%. In contrast, mtSSB was released from mtDNA and freely distributed within the mitochondrial network. Nucleoid clusters mostly contained nucleoids with newly replicated mtDNA, however the nucleoid population which was not in replication mode remained outside the clusters. Moreover, the nucleoid clusters were enriched with p53, an anti-oncogenic gatekeeper. We suggest that mitochondrial nucleoid clustering is a mechanism for protecting nucleoids with newly replicated DNA against intercalators mediating genotoxic stress. These results provide new insight into the common mitochondrial response to mtDNA stress and can be implied also on DXR-induced mitochondrial cytotoxicity. - Highlights: • The mechanism for mitochondrial nucleoid clustering is proposed. • DNA intercalators (Doxorubicin or Ethidium Bromide) prevent TFAM binding to mtDNA. • Replicating nucleoids are less prone to DNA intercalator and preserve more TFAM. • Nucleoid clusters mostly contain nucleoids with newly replicated mtDNA. • Recently replicated nucleoids are protected in clusters by increased TFAM and p53.« less

Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis).

PubMed

Saade, Evelyne; Pirozhkova, Iryna; Aimbetov, Rakhan; Lipinski, Marc; Ogryzko, Vasily

2015-06-01

The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed. © 2015 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Perturbation of ribosome biogenesis drives cells into senescence through 5S RNP-mediated p53 activation.

PubMed

Nishimura, Kazuho; Kumazawa, Takuya; Kuroda, Takao; Katagiri, Naohiro; Tsuchiya, Mai; Goto, Natsuka; Furumai, Ryohei; Murayama, Akiko; Yanagisawa, Junn; Kimura, Keiji

2015-03-03

The 5S ribonucleoprotein particle (RNP) complex, consisting of RPL11, RPL5, and 5S rRNA, is implicated in p53 regulation under ribotoxic stress. Here, we show that the 5S RNP contributes to p53 activation and promotes cellular senescence in response to oncogenic or replicative stress. Oncogenic stress accelerates rRNA transcription and replicative stress delays rRNA processing, resulting in RPL11 and RPL5 accumulation in the ribosome-free fraction, where they bind MDM2. Experimental upregulation of rRNA transcription or downregulation of rRNA processing, mimicking the nucleolus under oncogenic or replicative stress, respectively, also induces RPL11-mediated p53 activation and cellular senescence. We demonstrate that exogenous expression of certain rRNA-processing factors rescues the processing defect, attenuates p53 accumulation, and increases replicative lifespan. To summarize, the nucleolar-5S RNP-p53 pathway functions as a senescence inducer in response to oncogenic and replicative stresses. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

The Chromatin Remodeling Factor SMARCB1 Forms a Complex with Human Cytomegalovirus Proteins UL114 and UL44

PubMed Central

Ranneberg-Nilsen, Toril; Rollag, Halvor; Slettebakk, Ragnhild; Backe, Paul Hoff; Olsen, Øyvind; Luna, Luisa; Bjørås, Magnar

2012-01-01

Background Human cytomegalovirus (HCMV) uracil DNA glycosylase, UL114, is required for efficient viral DNA replication. Presumably, UL114 functions as a structural partner to other factors of the DNA-replication machinery and not as a DNA repair protein. UL114 binds UL44 (HCMV processivity factor) and UL54 (HCMV-DNA-polymerase). In the present study we have searched for cellular partners of UL114. Methodology/Principal Findings In a yeast two-hybrid screen SMARCB1, a factor of the SWI/SNF chromatin remodeling complex, was found to be an interacting partner of UL114. This interaction was confirmed in vitro by co-immunoprecipitation and pull-down. Immunofluorescence microscopy revealed that SMARCB1 along with BRG-1, BAF170 and BAF155, which are the core SWI/SNF components required for efficient chromatin remodeling, were present in virus replication foci 24–48 hours post infection (hpi). Furthermore a direct interaction was also demonstrated for SMARCB1 and UL44. Conclusions/Significance The core SWI/SNF factors required for efficient chromatin remodeling are present in the HCMV replication foci throughout infection. The proteins UL44 and UL114 interact with SMARCB1 and may participate in the recruitment of the SWI/SNF complex to the chromatinized virus DNA. Thus, the presence of the SWI/SNF chromatin remodeling complex in replication foci and its association with UL114 and with UL44 might imply its involvement in different DNA transactions. PMID:22479537

Deletion of the Clostridium thermocellum recA gene reveals that it is required for thermophilic plasmid replication but not plasmid integration at homologous DNA sequences.

PubMed

Groom, Joseph; Chung, Daehwan; Kim, Sun-Ki; Guss, Adam; Westpheling, Janet

2018-05-28

A limitation to the engineering of cellulolytic thermophiles is the availability of functional, thermostable (≥ 60 °C) replicating plasmid vectors for rapid expression and testing of genes that provide improved or novel fuel molecule production pathways. A series of plasmid vectors for genetic manipulation of the cellulolytic thermophile Caldicellulosiruptor bescii has recently been extended to Clostridium thermocellum, another cellulolytic thermophile that very efficiently solubilizes plant biomass and produces ethanol. While the C. bescii pBAS2 replicon on these plasmids is thermostable, the use of homologous promoters, signal sequences and genes led to undesired integration into the bacterial chromosome, a result also observed with less thermostable replicating vectors. In an attempt to overcome undesired plasmid integration in C. thermocellum, a deletion of recA was constructed. As expected, C. thermocellum ∆recA showed impaired growth in chemically defined medium and an increased susceptibility to UV damage. Interestingly, we also found that recA is required for replication of the C. bescii thermophilic plasmid pBAS2 in C. thermocellum, but it is not required for replication of plasmid pNW33N. In addition, the C. thermocellum recA mutant retained the ability to integrate homologous DNA into the C. thermocellum chromosome. These data indicate that recA can be required for replication of certain plasmids, and that a recA-independent mechanism exists for the integration of homologous DNA into the C. thermocellum chromosome. Understanding thermophilic plasmid replication is not only important for engineering of these cellulolytic thermophiles, but also for developing genetic systems in similar new potentially useful non-model organisms.

Deletion of the Clostridium thermocellum recA Gene Reveals that it is Required for Thermophilic Plasmid Replication but not Plasmid Integration at Homologous DNA Sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Daehwan; Groom, Joseph; Kim, Sun-Ki

A limitation to the engineering of cellulolytic thermophiles is the availability of functional, thermostable (>/= 60 degrees C) replicating plasmid vectors for rapid expression and testing of genes that provide improved or novel fuel molecule production pathways. A series of plasmid vectors for genetic manipulation of the cellulolytic thermophile Caldicellulosiruptor bescii has recently been extended to Clostridium thermocellum, another cellulolytic thermophile that very efficiently solubilizes plant biomass and produces ethanol. While the C. bescii pBAS2 replicon on these plasmids is thermostable, the use of homologous promoters, signal sequences and genes led to undesired integration into the bacterial chromosome, a resultmore » also observed with less thermostable replicating vectors. In an attempt to overcome undesired plasmid integration in C. thermocellum, a deletion of recA was constructed. As expected, C. thermocellum ..delta..recA showed impaired growth in chemically defined medium and an increased susceptibility to UV damage. Interestingly, we also found that recA is required for replication of the C. bescii thermophilic plasmid pBAS2 in C. thermocellum, but it is not required for replication of plasmid pNW33N. In addition, the C. thermocellum recA mutant retained the ability to integrate homologous DNA into the C. thermocellum chromosome. These data indicate that recA can be required for replication of certain plasmids, and that a recA-independent mechanism exists for the integration of homologous DNA into the C. thermocellum chromosome. Understanding thermophilic plasmid replication is not only important for engineering of these cellulolytic thermophiles, but also for developing genetic systems in similar new potentially useful non-model organisms.« less

Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study.

PubMed

Beaty, T H; Taub, M A; Scott, A F; Murray, J C; Marazita, M L; Schwender, H; Parker, M M; Hetmanski, J B; Balakrishnan, P; Mansilla, M A; Mangold, E; Ludwig, K U; Noethen, M M; Rubini, M; Elcioglu, N; Ruczinski, I

2013-07-01

A collection of 1,108 case-parent trios ascertained through an isolated, nonsyndromic cleft lip with or without cleft palate (CL/P) was used to replicate the findings from a genome-wide association study (GWAS) conducted by Beaty et al. (Nat Genet 42:525-529, 2010), where four different genes/regions were identified as influencing risk to CL/P. Tagging SNPs for 33 different genes were genotyped (1,269 SNPs). All four of the genes originally identified as showing genome-wide significance (IRF6, ABCA4 and MAF, plus the 8q24 region) were confirmed in this independent sample of trios (who were primarily of European and Southeast Asian ancestry). In addition, eight genes classified as 'second tier' hits in the original study (PAX7, THADA, COL8A1/FILIP1L, DCAF4L2, GADD45G, NTN1, RBFOX3 and FOXE1) showed evidence of linkage and association in this replication sample. Meta-analysis between the original GWAS trios and these replication trios showed PAX7, COL8A1/FILIP1L and NTN1 achieved genome-wide significance. Tests for gene-environment interaction between these 33 genes and maternal smoking found evidence for interaction with two additional genes: GRID2 and ELAVL2 among European mothers (who had a higher rate of smoking than Asian mothers). Formal tests for gene-gene interaction (epistasis) failed to show evidence of statistical interaction in any simple fashion. This study confirms that many different genes influence risk to CL/P.

Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study

PubMed Central

Beaty, TH; Taub, MA; Scott, AF; Murray, JC; Marazita, ML; Schwender, H; Parker, MM; Hetmanski, JB; Balakrishnan, P; Mansilla, MA; Mangold, E; Ludwig, KU; Noethen, MM; Rubini, M; Elcioglu, N; Ruczinski, I

2013-01-01

A collection of 1,108 case-parent trios ascertained through an isolated, non-syndromic cleft lip with or without cleft palate (CL/P) was used to replicate the findings from a genome-wide association study (GWAS) conducted by Beaty et al. (2010) where four different genes/regions were identified as influencing risk to CL/P. Tagging SNPs for 33 different genes were genotyped (1,269 SNPs). All four of the genes originally identified as showing genome-wide significance (IRF6, ABCA4 and MAF, plus the 8q24 region) were confirmed in this independent sample of trios (who were primarily of European and Southeast Asian ancestry). In addition, eight genes classified as ‘second tier’ hits in the original study (PAX7, THADA, COL8A1/FILIP1L, DCAF4L2, GADD45G, NTN1, RBFOX3 and FOXE1) showed evidence of linkage and association in this replication sample. Meta-analysis between the original GWAS trios and these replication trios showed PAX7, COL8A1/FILIP1L and NTN1 achieved genome-wide significance. Tests for gene-environment interaction between these 33 genes and maternal smoking found evidence for interaction with two additional genes: GRID2 and ELAVL2 among European mothers (who had a higher rate of smoking than Asian mothers). Formal tests for gene-gene interaction (epistasis) failed to show evidence of statistical interaction in any simple fashion. This study confirms that many different genes influence risk to CL/P. PMID:23512105

Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: implications for replication and genome packaging.

PubMed

Chaturvedi, Sonali; Rao, A L N

2014-09-01

In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein-protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase. Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Genetic susceptibility loci for subtypes of breast cancer in an African American population

PubMed Central

Palmer, Julie R.; Ruiz-Narvaez, Edward A.; Rotimi, Charles N.; Cupples, L. Adrienne; Cozier, Yvette C.; Adams-Campbell, Lucile L.; Rosenberg, Lynn

2012-01-01

Background Most genome-wide association scans (GWAS) have been carried out in European ancestry populations; no risk variants for breast cancer have been identified solely from African ancestry GWAS data. Few GWAS hits have replicated in African ancestry populations. Methods In a nested case-control study of breast cancer in the Black Women’s Health Study (1,199 cases/1,948 controls), we evaluated index SNPs in 21 loci from GWAS of European or Asian ancestry populations, overall, in subtypes defined by estrogen (ER) and progesterone (PR) receptor status (ER+/PR+, n=336; ER−/PR−, n=229), and in triple-negative breast cancer (TNBC, N=81). To evaluate the contribution of genetic factors to population differences in breast cancer subtype, we also examined global percent African ancestry. Results Index SNPs in five loci were replicated, including three associated with ER−/PR− breast cancer (TERT rs10069690 in 5p15.33, rs704010 in 10q22.3, and rs8170 in 19p13.11): per allele odds ratios were 1.29 (95% confidence interval (CI) 1.04–1.59), p=0.02, 1.52 (95% CI 1.12–2.08), p=0.01, and 1.30 (95% CI 1.01–1.68), p=0.04, respectively. Stronger associations were observed for TNBC. Furthermore, cases in the highest quintile of percent African ancestry were three times more likely to have TNBC than ER+/PR+ cancer. Conclusions These findings provide the first confirmation of the TNBC SNP rs8170 in an African ancestry population, and independent confirmation of the TERT ER− SNP. Further, the risk of developing ER− breast cancer, particularly TNBC, increased with increasing proportion of global African ancestry. Impact The findings demonstrate the importance of genetic factors in the disproportionately high occurrence of TNBC in African American women. PMID:23136140

Complex and interactive effects of ocean acidification and temperature on epilithic and endolithic coral-reef turf algal assemblages

NASA Astrophysics Data System (ADS)

Johnson, Maggie D.; Comeau, Steeve; Lantz, Coulson A.; Smith, Jennifer E.

2017-12-01

Turf algal assemblages are ubiquitous primary producers on coral reefs, but little is known about the response of this diverse group to ocean acidification (OA) across different temperatures. We tested the hypothesis that CO2 influences the functional response of epilithic and endolithic turf assemblages to increasing temperature. Replicate carbonate plugs covered by turf were collected from the reef and exposed to ambient and high pCO2 (1000 µatm) conditions for 3 weeks. Each pCO2 treatment was replicated across six temperatures (24.0-31.5 °C) that spanned the full seasonal temperature range on a fringing reef in Moorea, French Polynesia, and included one warming treatment (3 °C above daily average temperatures). Temperature and CO2 enrichment had complex, and sometimes interactive, effects on turf metabolism and growth. Photosynthetic and respiration rates were enhanced by increasing temperature, with an interactive effect of CO2 enrichment. Photosynthetic rates were amplified by high CO2 in the warmest temperatures, while the increase in respiration rates with temperature were enhanced under ambient CO2. Epilithic turf growth rates were not affected by temperature, but increased in response to CO2 enrichment. We found that CO2 and temperature interactively affected the endolithic assemblage, with the highest growth rates under CO2 enrichment, but only at the warmest temperatures. These results demonstrate how OA may influence algal physiology and growth across a range of ecologically relevant temperatures, and indicate that the effects of CO2 enrichment on coral-reef turf assemblages can be temperature dependent. The complex effects of CO2 enrichment and temperature across a suite of algal responses illustrates the importance of incorporating multiple stressors into global change experiments.

Characterization of the influence of mediator complex in HIV-1 transcription.

PubMed

Ruiz, Alba; Pauls, Eduardo; Badia, Roger; Riveira-Muñoz, Eva; Clotet, Bonaventura; Ballana, Ester; Esté, José A

2014-10-03

HIV-1 exploits multiple host proteins during infection. siRNA-based screenings have identified new proteins implicated in different pathways of the viral cycle that participate in a broad range of cellular functions. The human Mediator complex (MED) is composed of 28 elements and represents a fundamental component of the transcription machinery, interacting with the RNA polymerase II enzyme and regulating its ability to express genes. Here, we provide an evaluation of the MED activity on HIV replication. Knockdown of 9 out of 28 human MED proteins significantly impaired viral replication without affecting cell viability, including MED6, MED7, MED11, MED14, MED21, MED26, MED27, MED28, and MED30. Impairment of viral replication by MED subunits was at a post-integration step. Inhibition of early HIV transcripts was observed by siRNA-mediated knockdown of MED6, MED7, MED11, MED14, and MED28, specifically affecting the transcription of the nascent viral mRNA transactivation-responsive element. In addition, MED14 and MED30 were shown to have special relevance during the formation of unspliced viral transcripts (p < 0.0005). Knockdown of the selected MED factors compromised HIV transcription induced by Tat, with the strongest inhibitory effect shown by siMED6 and siMED14 cells. Co-immunoprecipitation experiments suggested physical interaction between MED14 and HIV-1 Tat protein. A better understanding of the mechanisms and factors controlling HIV-1 transcription is key to addressing the development of new strategies required to inhibit HIV replication or reactivate HIV-1 from the latent reservoirs. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Weed diversity identification on growth phases of twelve maize varieties

NASA Astrophysics Data System (ADS)

Rahayu, M.; Yudono, P.; Indradewa, D.; Hanudin, E.

2018-03-01

Weed is one of the factors that disturb maize cultivation. Each maize variety has specific characteristics which will lead to weeds diversity in particular farm. This study aimed to identify the effect of maize variety on weed diversity on maize’s growth phases. The research was conducted from March to July 2016 in Banguntapan, Bantul, Yogyakarta, Indonesia. The field research was arranged by using Randomised Complete Block Design with three replications. The treatments were maize varieties, consist of 12 levels: ‘Bisi 18’, ‘Bisi 2’, ‘Pertiwi 3’, ‘NK 22’, ‘NK 33’, ‘DK 959’, ‘P23’, ‘DK 771’, ‘DK 95’, ‘Bima 19 Uri’, ‘Bisma’, and ‘Sukmaraga’. The results showed that at four weeks after planting (WAP) the most of weeds were growing on varieties ‘Bisi 18’, ‘NK 33’, ‘P 23’, and ‘DK 95’, there were 14 species. Bulbostylispuberula and Cyperusrotundus were growing on all maize varieties with the highest SDR on ‘Sukmaraga’ and ‘DK 959’. At six WAP, weeds that grew, most consists of four species of sedges, six species of grasses and 24 species of broadleaf. While at the age of eight WAP, the weeds that grow at least on ‘NK 33’ that were 13 species and the most on ‘P23’ that were 21 species. Dactyloctenium aeghypthium having highest SDR in all maize varieties except Bisi 18. The highest SDR value on Bisi 18 was Boerhaavia erecta about 16.23%.

The eukaryotic bell-shaped temporal rate of DNA replication origin firing emanates from a balance between origin activation and passivation.

PubMed

Arbona, Jean-Michel; Goldar, Arach; Hyrien, Olivier; Arneodo, Alain; Audit, Benjamin

2018-06-01

The time-dependent rate I(t) of origin firing per length of unreplicated DNA presents a universal bell shape in eukaryotes that has been interpreted as the result of a complex time-evolving interaction between origins and limiting firing factors. Here we show that a normal diffusion of replication fork components towards localized potential replication origins (p-oris) can more simply account for the I(t) universal bell shape, as a consequence of a competition between the origin firing time and the time needed to replicate DNA separating two neighboring p-oris . We predict the I(t) maximal value to be the product of the replication fork speed with the squared p-ori density. We show that this relation is robustly observed in simulations and in experimental data for several eukaryotes. Our work underlines that fork-component recycling and potential origins localization are sufficient spatial ingredients to explain the universality of DNA replication kinetics. © 2018, Arbona et al.

Validation of the self-beliefs related to social anxiety scale: a replication and extension.

PubMed

Wong, Quincy J J; Moulds, Michelle L; Rapee, Ronald M

2014-06-01

The importance of self-beliefs in prominent models of social phobia has led to the development of measures that tap this cognitive construct. The Self-Beliefs Related to Social Anxiety (SBSA) Scale is one such measure and taps the three maladaptive belief types proposed in Clark and Wells's model of social phobia. This study aimed to replicate and extend previous research on the psychometric properties of the SBSA. Replicating previous research, in an (undiagnosed) undergraduate sample (n = 235), the SBSA was found to have a correlated three-factor structure using confirmatory factor analyses, and the SBSA and its subscales demonstrated good internal consistency and test-retest reliability. The SBSA and its subscales also had unique relationships with social anxiety and depression, the majority of which replicated previous research. Extending previous research, the SBSA and its subscales showed good incremental validity in the undergraduate sample and good discriminative validity using the undergraduate sample and a sample of individuals with social phobia (n = 33). The SBSA's strong theoretical basis and the findings of this study suggest that the SBSA is an ideal research and clinical tool to assess the cognitions characteristic of social phobia. © The Author(s) 2013.

Feeling the future: A meta-analysis of 90 experiments on the anomalous anticipation of random future events.

PubMed

Bem, Daryl; Tressoldi, Patrizio; Rabeyron, Thomas; Duggan, Michael

2015-01-01

In 2011, one of the authors (DJB) published a report of nine experiments in the Journal of Personality and Social Psychology purporting to demonstrate that an individual's cognitive and affective responses can be influenced by randomly selected stimulus events that do not occur until after his or her responses have already been made and recorded, a generalized variant of the phenomenon traditionally denoted by the term precognition. To encourage replications, all materials needed to conduct them were made available on request. We here report a meta-analysis of 90 experiments from 33 laboratories in 14 countries which yielded an overall effect greater than 6 sigma, z = 6.40, p = 1.2 × 10 (-10 ) with an effect size (Hedges' g) of 0.09. A Bayesian analysis yielded a Bayes Factor of 5.1 × 10 (9), greatly exceeding the criterion value of 100 for "decisive evidence" in support of the experimental hypothesis. When DJB's original experiments are excluded, the combined effect size for replications by independent investigators is 0.06, z = 4.16, p = 1.1 × 10 (-5), and the BF value is 3,853, again exceeding the criterion for "decisive evidence." The number of potentially unretrieved experiments required to reduce the overall effect size of the complete database to a trivial value of 0.01 is 544, and seven of eight additional statistical tests support the conclusion that the database is not significantly compromised by either selection bias or by intense " p-hacking"-the selective suppression of findings or analyses that failed to yield statistical significance. P-curve analysis, a recently introduced statistical technique, estimates the true effect size of the experiments to be 0.20 for the complete database and 0.24 for the independent replications, virtually identical to the effect size of DJB's original experiments (0.22) and the closely related "presentiment" experiments (0.21). We discuss the controversial status of precognition and other anomalous effects collectively known as psi.

Epigenetic associations of type 2 diabetes and BMI in an Arab population.

PubMed

Al Muftah, Wadha A; Al-Shafai, Mashael; Zaghlool, Shaza B; Visconti, Alessia; Tsai, Pei-Chien; Kumar, Pankaj; Spector, Tim; Bell, Jordana; Falchi, Mario; Suhre, Karsten

2016-01-01

The prevalence of type 2 diabetes (T2D) and obesity has dramatically increased within a few generations, reaching epidemic levels. In addition to genetic risk factors, epigenetic mechanisms triggered by changing environment are investigated for their role in the pathogenesis of these complex diseases. Epigenome-wide association studies (EWASs) have revealed significant associations of T2D, obesity, and BMI with DNA methylation. However, populations from the Middle East, where T2D and obesity rates are highest worldwide, have not been investigated so far. We performed the first EWAS in an Arab population with T2D and BMI and attempted to replicate 47 EWAS associations previously reported in Caucasians. We used the Illumina Infinium HumanMethylation450 BeadChip to quantify DNA methylation in whole blood DNA from 123 subjects of 15 multigenerational families from Qatar. To investigate the effect of differing genetic background and environment on the epigenetic associations, we further assessed the effect of replicated loci in 810 twins from UK. Our EWAS suggested a novel association between T2D and cg06721411 (DQX1; p value = 1.18 × 10(-9)). We replicated in the Qatari population seven CpG associations with BMI (SOCS3, p value = 3.99 × 10(-6); SREBF1, p value = 4.33 × 10(-5); SBNO2, p value = 5.87 × 10(-5); CPT1A, p value = 7.99 × 10(-5); PRR5L, p value = 1.85 × 10(-4); cg03078551, intergenic region on chromosome 17; p value = 1.00 × 10(-3); LY6G6E, p value = 1.10 × 10(-3)) and one with T2D (TXNIP, p value = 2.46 × 10(-5)). All the associations were further confirmed in the UK cohort for both BMI and T2D. Meta-analysis increased the significance of the observed associations and revealed strong heterogeneity of the effect sizes (apart from CPT1A), although associations at these loci showed concordant direction in the two populations. Our study replicated eight known CpG associations with T2D or BMI in an Arab population. Heterogeneity of the effects at all loci except CPT1A between the Qatari and UK studies suggests that the underlying mechanisms might depend on genetic background and environmental pressure. Our EWAS results provide a basis for comparison with other ethnicities.

Characterization of protein-protein interaction domains within the baculovirus Autographa californica multiple nucleopolyhedrovirus late expression factor LEF-3.

PubMed

Downie, Kelsey; Adetola, Gbolagade; Carstens, Eric B

2013-11-01

Autographa californica nucleopolyhedrovirus late expression factor 3 (LEF-3) is required for late viral gene expression probably through its numerous functions related to DNA replication, including nuclear localization of the virus helicase P143 and binding to ssDNA. LEF-3 appears to interact with itself as a homo-oligomer, although the details of this oligomeric structure are not yet known. To examine LEF-3-LEF-3 interactions, a bimolecular fluorescent protein complementation assay was used. Pairs of recombinant plasmids expressing full-length LEF-3 fused to one of two complementary fragments (V1 or V2) of a variant of yellow fluorescent protein named 'Venus' were constructed. Plasmids expressing fusions with complementary fragments of Venus were co-transfected into Sf21 cells and analysed by fluorescence microscopy. Co-transfected plasmids expressing full-length V1-LEF-3 and V2-LEF-3 showed positive fluorescence, confirming the formation of homo-oligomers. A series of truncated V1/V2-LEF-3 fusions was constructed and used to investigate interactions with one another as well as with full-length LEF-3.

A GWAS Meta-analysis and Replication Study Identifies a Novel Locus within CLPTM1L/TERT Associated with Nasopharyngeal Carcinoma in Individuals of Chinese Ancestry.

PubMed

Bei, Jin-Xin; Su, Wen-Hui; Ng, Ching-Ching; Yu, Kai; Chin, Yoon-Ming; Lou, Pei-Jen; Hsu, Wan-Lun; McKay, James D; Chen, Chien-Jen; Chang, Yu-Sun; Chen, Li-Zhen; Chen, Ming-Yuan; Cui, Qian; Feng, Fu-Tuo; Feng, Qi-Shen; Guo, Yun-Miao; Jia, Wei-Hua; Khoo, Alan Soo-Beng; Liu, Wen-Sheng; Mo, Hao-Yuan; Pua, Kin-Choo; Teo, Soo-Hwang; Tse, Ka-Po; Xia, Yun-Fei; Zhang, Hongxin; Zhou, Gang-Qiao; Liu, Jian-Jun; Zeng, Yi-Xin; Hildesheim, Allan

2016-01-01

Genetic loci within the major histocompatibility complex (MHC) have been associated with nasopharyngeal carcinoma (NPC), an Epstein-Barr virus (EBV)-associated cancer, in several GWAS. Results outside this region have varied. We conducted a meta-analysis of four NPC GWAS among Chinese individuals (2,152 cases; 3,740 controls). Forty-three noteworthy findings outside the MHC region were identified and targeted for replication in a pooled analysis of four independent case-control studies across three regions in Asia (4,716 cases; 5,379 controls). A meta-analysis that combined results from the initial GWA and replication studies was performed. In the combined meta-analysis, rs31489, located within the CLPTM1L/TERT region on chromosome 5p15.33, was strongly associated with NPC (OR = 0.81; P value 6.3 × 10(-13)). Our results also provide support for associations reported from published NPC GWAS-rs6774494 (P = 1.5 × 10(-12); located in the MECOM gene region), rs9510787 (P = 5.0 × 10(-10); located in the TNFRSF19 gene region), and rs1412829/rs4977756/rs1063192 (P = 2.8 × 10(-8), P = 7.0 × 10(-7), and P = 8.4 × 10(-7), respectively; located in the CDKN2A/B gene region). We have identified a novel association between genetic variation in the CLPTM1L/TERT region and NPC. Supporting our finding, rs31489 and other SNPs in this region have been reported to be associated with multiple cancer sites, candidate-based studies have reported associations between polymorphisms in this region and NPC, the TERT gene has been shown to be important for telomere maintenance and has been reported to be overexpressed in NPC, and an EBV protein expressed in NPC (LMP1) has been reported to modulate TERT expression/telomerase activity. Our finding suggests that factors involved in telomere length maintenance are involved in NPC pathogenesis. ©2015 American Association for Cancer Research.

Variants in DENND1A Are Associated with Polycystic Ovary Syndrome in Women of European Ancestry

PubMed Central

Styrkarsdottir, Unnur; Ehrmann, David A.; Thorleifsson, Gudmar; Arason, Gudmundur; Gudmundsson, Jens A.; Ober, Carole; Rosenfield, Robert L.; Saxena, Richa; Thorsteinsdottir, Unnur; Crowley, William F.

2012-01-01

Context: A genome-wide association study has identified three loci (five independent signals) that confer risk for polycystic ovary syndrome (PCOS) in Han Chinese women. Replication is necessary to determine whether the same variants confer risk for PCOS in women of European ancestry. Objective: The objective of the study was to test whether these PCOS risk variants in Han Chinese women confer risk for PCOS in women of European ancestry. Design: This was a case-control study. Setting: The study was conducted at deCODE Genetics in Iceland and two academic medical centers in the United States. Patients: Cases were 376 Icelandic women and 565 and 203 women from Boston, MA, and Chicago, IL, respectively, all diagnosed with PCOS by the National Institutes of Health criteria. Controls were 16,947, 483, and 189 women not known to have PCOS from Iceland, Boston, and Chicago, respectively. Intervention: There were no interventions. Main Outcomes: Main outcomes were allele frequencies for seven variants in PCOS cases and controls. Results: Two strongly correlated Han Chinese PCOS risk variants on chromosome 9q33.3, rs10986105[C], and rs10818854[A], were replicated in samples of European ancestry with odds ratio of 1.68 (P = 0.00033) and odds ratio of 1.53 (P = 0.0019), respectively. Other risk variants at 2p16.3 (rs13405728), 2p21 (rs12468394, rs12478601, and rs13429458), and 9q33.3 (rs2479106), or variants correlated with them, did not associate with PCOS. The same allele of rs10986105 that increased the risk of PCOS also increased the risk of hyperandrogenism in women without PCOS from Iceland and demonstrated a stronger risk for PCOS defined by the National Institutes of Health criteria than the Rotterdam criteria. Conclusions: We replicated one of the five Chinese PCOS association signals, represented by rs10986105 and rs10818854 on 9q33, in individuals of European ancestry. Examination of the subjects meeting at least one of the Rotterdam criteria for PCOS suggests that the variant may be involved in the hyperandrogenism and possibly the irregular menses of PCOS. PMID:22547425

Variants in DENND1A are associated with polycystic ovary syndrome in women of European ancestry.

PubMed

Welt, Corrine K; Styrkarsdottir, Unnur; Ehrmann, David A; Thorleifsson, Gudmar; Arason, Gudmundur; Gudmundsson, Jens A; Ober, Carole; Rosenfield, Robert L; Saxena, Richa; Thorsteinsdottir, Unnur; Crowley, William F; Stefansson, Kari

2012-07-01

A genome-wide association study has identified three loci (five independent signals) that confer risk for polycystic ovary syndrome (PCOS) in Han Chinese women. Replication is necessary to determine whether the same variants confer risk for PCOS in women of European ancestry. The objective of the study was to test whether these PCOS risk variants in Han Chinese women confer risk for PCOS in women of European ancestry. This was a case-control study. The study was conducted at deCODE Genetics in Iceland and two academic medical centers in the United States. Cases were 376 Icelandic women and 565 and 203 women from Boston, MA, and Chicago, IL, respectively, all diagnosed with PCOS by the National Institutes of Health criteria. Controls were 16,947, 483, and 189 women not known to have PCOS from Iceland, Boston, and Chicago, respectively. There were no interventions. Main outcomes were allele frequencies for seven variants in PCOS cases and controls. Two strongly correlated Han Chinese PCOS risk variants on chromosome 9q33.3, rs10986105[C], and rs10818854[A], were replicated in samples of European ancestry with odds ratio of 1.68 (P = 0.00033) and odds ratio of 1.53 (P = 0.0019), respectively. Other risk variants at 2p16.3 (rs13405728), 2p21 (rs12468394, rs12478601, and rs13429458), and 9q33.3 (rs2479106), or variants correlated with them, did not associate with PCOS. The same allele of rs10986105 that increased the risk of PCOS also increased the risk of hyperandrogenism in women without PCOS from Iceland and demonstrated a stronger risk for PCOS defined by the National Institutes of Health criteria than the Rotterdam criteria. We replicated one of the five Chinese PCOS association signals, represented by rs10986105 and rs10818854 on 9q33, in individuals of European ancestry. Examination of the subjects meeting at least one of the Rotterdam criteria for PCOS suggests that the variant may be involved in the hyperandrogenism and possibly the irregular menses of PCOS.

Impact of Nb vacancies and p-type doping of the NbCoSn-NbCoSb half-Heusler thermoelectrics.

PubMed

Ferluccio, Daniella A; Smith, Ronald I; Buckman, Jim; Bos, Jan-Willem G

2018-02-07

The half-Heuslers NbCoSn and NbCoSb have promising thermoelectric properties. Here, an investigation of the NbCo 1+y Sn 1-z Sb z (y = 0, 0.05; 0 ≤ z ≤ 1) solid-solution is presented. In addition, the p-type doping of NbCoSn using Ti and Zr substitution is investigated. Rietveld analysis reveals the gradual creation of Nb vacancies to compensate for the n-type doping caused by the substitution of Sb in NbCoSn. This leads to a similar valence electron count (∼18.25) for the NbCo 1+y Sn 1-z Sb z samples (z > 0). Mass fluctuation disorder due to the Nb vacancies strongly decreases the lattice thermal conductivity from 10 W m -1 K -1 (z = 0) to 4.5 W m -1 K -1 (z = 0.5, 1). This is accompanied by a transition to degenerate semiconducting behaviour leading to large power factors, S 2 /ρ = 2.5-3 mW m -1 K -2 and figures of merit, ZT = 0.25-0.33 at 773 K. Ti and Zr can be used to achieve positive Seebeck values, e.g. S = +150 μV K -1 for 20% Zr at 773 K. However, the electrical resistivity, ρ 323K = 27-35 mΩ cm, remains too large for these materials to be considered useful p-type materials.

Kis antitoxin couples plasmid R1 replication and parD (kis,kid) maintenance modules.

PubMed

López-Villarejo, Juan; Diago-Navarro, Elizabeth; Hernández-Arriaga, Ana María; Díaz-Orejas, Ramón

2012-03-01

The coupling between the replication and parD (kis, kid) maintenance modules of R1 has been revisited here by the isolation of a significant collection of conditional replication mutants in the pKN1562 mini-R1 plasmid, and in its derivative, pJLV01, specifically affected in the RNase activity of the Kid toxin. This new analysis aims to identify key factors in this coupling. For this purpose we have quantified and characterized the restriction introduced by parD to isolate conditional replication mutants of this plasmid, a signature of the modular coupling. This restriction depends on the RNase activity of the Kid toxin and it is relieved by either over-expression of the Kis antitoxin or by preventing its degradation by Lon and ClpAP proteases. Based on these data and on the correlation between copy numbers and parD transcriptional levels obtained in the different mutants, it is proposed that a reduction of Kis antitoxin levels in response to inefficient plasmid replication is the key factor for coupling plasmid replication and parD modules. Copyright © 2012 Elsevier Inc. All rights reserved.

Do the Reasons for Ceramic-on-ceramic Revisions Differ From Other Bearings in Total Hip Arthroplasty?

PubMed

Migaud, Henri; Putman, Sophie; Kern, Grégory; Isida, Ronald; Girard, Julien; Ramdane, Nassima; Delaunay, Christian P; Hamadouche, Moussa

2016-10-01

Despite widespread use of ceramic-on-ceramic (CoC) in total hip arthroplasty (THA) during the past 10 years, little is known about why revisions are performed in hips with this bearing or the time elapsed before revision. The purposes of this study were: (1) Do the reasons for first revision differ between CoC bearings and other bearing couples? (2) Does the time to revision differ between CoC and other bearing couples? (3) Are there unique reasons for revisions of CoC bearings? All members of the Société Française de Chirurgie Orthopédique et Traumatologique (SoFCOT) who performed ≥ 30 revisions per year were invited to participate in this multicenter, prospective, observational study. Our data represent 12% of the revision procedures performed in France. A total of 2107 first revisions of THA (from January 2010 to December 2011) were done in 2107 patients (1201 females [57%] and 906 males [43%]; median age, 73 years; age range, 17-104 years) at the time of surgery after a median of 11 years (range, 0 day-42 years) after the primary THA. There were 238 of 2107 (11%) CoC, 148 of 2107 (7%) metal-on-metal (MoM), and 1721 of 2017 (82%) metal-on-polyethylene (MoP) bearings. The reasons for reoperation differed according to the bearing component: (1) for the MoP reference bearing (odds ratio [OR]; 95% confidence interval), cup loosening occurred in 698 of 1721 hips (41%), periprosthetic fracture in 220 of 1721 hips (13%), and osteolysis in 213 of 1721 hips (12%); (2) for CoC, cup loosening occurred in 41 of 238 hips (17%) (OR, 0.31 [0.22-0.43; p < 0.001), infection in 39 of 238 hips (16%) (OR, 1.63 [1.12-2.37]; p = 0.01), and dislocation in 23 of 238 hips (10%) (OR, 0.9 [0.57-1.42]; p = 0.9); (3) for MoM, cup loosening occurred in 28 of 148 hips (19%) (OR, 0.34 [0.22-0.52]; p < 0.001), adverse reaction to metallic debris in 26 of 148 hips (18%) (OR, 18.12 [9.84-33.4]; p < 0.001), and infection in 16 of 148 hips (11%) (OR, 1 [0.59-1.73]; p = 0.9). In comparison with MoP, osteolysis was rarely the reason for revision in CoC (four of 238 hips [2%]; OR, 0.12 [0.05-0.33]; p < 0.001), but this bearing was frequently revised because of iliopsoas irritation (18 of 238 hips [8%]; OR, 4.9 [2.7-9]; p < 0.001). The time elapsed before revision differed between bearings: median of 3 years (range, 3 days to 28 years) for CoC and 4 years (range, 14 days to 37 years) for MoM versus a median 13 years (range, 0 day to 42 years) for MoP (p < 0.001). Thirty-seven of the 238 revisions (16%) were directly related to ceramic use (ceramic breakage [n = 23], squeaking [n = 6], impingement [n = 7], incorrect ceramic insert insertion [n = 1]). No factors were identified that contributed to breakage of the 12 bulk ceramic components (eight heads, four inserts, four of 12 Delta ceramic). No factors were associated with squeaking, iliopsoas irritation, or impingement, but component orientation was not assessed. The reasons and time to first revision differed between CoC and other bearings. CoC THAs are revised earlier and are sensitive to mechanical problems such as impingement, squeaking, and ceramic rupture that did not disappear with introduction of Delta ceramics and large-diameter (≥ 36 mm) bearings. CoC was rarely revised for osteolysis, but a high rate of iliopsoas irritation requires further investigation. Level III, therapeutic study.

Screening and identification of host factors interacting with UL14 of herpes simplex virus 1.

PubMed

Wu, Fuqing; Xing, Junji; Wang, Shuai; Li, Meili; Zheng, Chunfu

2011-08-01

The UL14 protein of herpes simplex virus type 1 (HSV-1) is highly conserved in herpesvirus family. However, its exact function during the HSV-1 replication cycle is little known. In the present study, a high throughput yeast two-hybrid system was employed to screen the cellular factors interacting with UL14, and five target candidates were yielded: (1) TSC22 domain family protein 3 (TSC22D3); (2) Mediator of RNA polymerase II transcription subunit 8 isoform 1(MED8); (3) Runt-related transcription factor 3 (RUNX3); (4) Arrestin beta-2 (ARRB2); (5) Cereblon (CRBN). Indirect immunofluorescent assay showed that both TSC22D3 and MED8 co-localized with UL14. Co-immunoprecipitation assay demonstrated that UL14 could be immunoprecipitated by TSC22D3, suggesting that UL14 interacted with TSC22D3 under physiological condition. In summary, this study opened up new avenues toward delineating the function and physiological significance of UL14 during the HSV-1 replication cycle.

The influence of tumour necrosis factor-alpha on the cardiovascular system of anaesthetized rats.

PubMed

Tabrizchi, R

2001-03-01

The effects of two vasoactive agents (adenosine A2A agonist, CGS 21680, and adrenoceptor agonist, noradrenaline) were examined on cardiac output (CO), heart rate (HR), blood pressure (BP), mean circulatory filling pressure (Pmcf), resistance to venous return, arterial resistance, dP/dt, plasma levels of NO2-/NO3-, and inducible nitric oxide synthase (iNOS) activity in lungs ex vivo, following treatment with tumour necrosis factor-alpha (TNF-alpha; 30 microg/kg) in anaesthetized rats. Treatment with TNF-alpha produced significant reduction in CO (41+/-2%), dP/dt (26+/-3%), BP (26+/-2%) and Pmcf (27+/-4%; n=6; mean+/-SEM), but increased arterial resistance. There were no significant changes in the plasma levels of NO2-/NO3-levels over time following treatment with TNF-alpha, but there was a significant increase (approximately twofold) in the activity of the iNOS in the lungs of animals treated with TNF-alpha. Administration of CGS 21680 (1.0 microg/kg per min) significantly increased CO (44+/-6%), HR (12+/-2%), Pmcf (24+/-4%) and dP/dt (24+/-5%) in TNF-alpha-treated rats. CGS 21680 also significantly reduced arterial resistance (33+/-2%) without altering resistance to venous return in TNF-alpha-treated rats. While noradrenaline (1.0 microg/kg per min) infusion did not significantly increase CO, it did significantly increase HR (12+/-1%), BP (55+/-9%), Pmcf (47+/-5%), dP/dt (65+/-7%), resistance to venous return (64+/-20%), and arterial resistance (41+/-16%) in TNF-alpha-treated animals. The reduction in BP due to administration of TNF-alpha is the result of significant reduction in CO. Consequently, the decline in CO can be attributed to a combination of a negative inotropic effect as well as a reduction in Pmcf. It is evident that infusion with CGS 21680 could reverse the negative impact of TNF-alpha on CO by increasing dP/dt, Pmcf and HR as well as a reduction in arterial resistance. The fact that noradrenaline did not significantly increase CO in TNF-alpha-treated rats can be attributed to increased arterial resistance as well increase in resistance to venous return.

Platelet factor 4 (CXCL4) facilitates human macrophage infection with HIV-1 and potentiates virus replication.

PubMed

Schwartzkopff, Franziska; Grimm, Tobias A; Lankford, Carla S R; Fields, Karen; Wang, Jiun; Brandt, Ernst; Clouse, Kathleen A

2009-12-01

Platelet factor 4 (CXCL4), a member of the CXC chemokine subfamily released in high amounts by activated platelets, has been identified as a monocyte survival factor that induces monocyte differentiation into macrophages. Although CXCL4 has been shown to have biological effects unique to chemokines, nothing is known about the role of CXCL4-derived human macrophages or CXCL4 in human immunodeficiency virus (HIV) disease. In this study, CXCL4-derived macrophages are compared with macrophage-colony stimulating factor (M-CSF)-derived macrophages for their ability to support HIV-1 replication. We show that CXCL4-derived macrophages can be infected with macrophage-tropic HIV-1 that uses either CC-chemokine receptor 5 (CCR5) or CXC-chemokine receptor 4 (CXCR4) as a co-receptor for viral entry. We also find that M-CSF and the chemokines, monocyte chemoattractant protein 1 (MCP-1; CCL2) and macrophage-inflammatory-protein-1-alpha (MIP-1alpha; CCL3) are produced upon R5- and X4-tropic HIV-1 replication in both M-CSF- and CXCL4-derived human macrophages. In addition, CXCL4 added to M-CSF-derived macrophages after virus adsorption and maintained throughout the infection enhances HIV-1 replication. We thus propose a novel role for CXCL4 in HIV disease.

Enterovirus 3A Facilitates Viral Replication by Promoting Phosphatidylinositol 4-Kinase IIIβ–ACBD3 Interaction

PubMed Central

Xiao, Xia; Lei, Xiaobo; Zhang, Zhenzhen; Ma, Yijie; Qi, Jianli; Wu, Chao; Xiao, Yan; Li, Li

2017-01-01

ABSTRACT Like other enteroviruses, enterovirus 71 (EV71) relies on phosphatidylinositol 4-kinase IIIβ (PI4KB) for genome RNA replication. However, how PI4KB is recruited to the genome replication sites of EV71 remains elusive. Recently, we reported that a host factor, ACBD3, is needed for EV71 replication by interacting with viral 3A protein. Here, we show that ACBD3 is required for the recruitment of PI4KB to RNA replication sites. Overexpression of viral 3A or EV71 infection stimulates the interaction of PI4KB and ACBD3. Consistently, EV71 infection induces the production of phosphatidylinositol-4-phosphate (PI4P). Furthermore, PI4KB, ACBD3, and 3A are all localized to the viral-RNA replication sites. Accordingly, PI4KB or ACBD3 depletion by small interfering RNA (siRNA) leads to a reduction in PI4P production after EV71 infection. I44A or H54Y substitution in 3A interrupts the stimulation of PI4KB and ACBD3. Further analysis suggests that stimulation of ACBD3-PI4KB interaction is also important for the replication of enterovirus 68 but disadvantageous to human rhinovirus 16. These results reveal a mechanism of enterovirus replication that involves a selective strategy for recruitment of PI4KB to the RNA replication sites. IMPORTANCE Enterovirus 71, like other human enteroviruses, replicates its genome within host cells, where viral proteins efficiently utilize cellular machineries. While multiple factors are involved, it is largely unclear how viral replication is controlled. We show that the 3A protein of enterovirus 71 recruits an enzyme, phosphatidylinositol 4-kinase IIIβ, by interacting with ACBD3, which alters cellular membranes through the production of a lipid, PI4P. Consequently, the viral and host proteins form a large complex that is necessary for RNA synthesis at replication sites. Notably, PI4KB-ACBD3 interaction also differentially mediates the replication of enterovirus 68 and rhinovirus 16. These results provide new insight into the molecular network of enterovirus replication. PMID:28701404

Efficacy of integrated school based de-worming and prompt malaria treatment on helminths -Plasmodium falciparum co-infections: A 33 months follow up study.

PubMed

Midzi, Nicholas; Mtapuri-Zinyowera, Sekesai; Sangweme, Davison; Paul, Noah H; Makware, Godfrey; Mapingure, Munyaradzi P; Brouwer, Kimberly C; Mudzori, James; Hlerema, Gibson; Chadukura, Vivian; Mutapi, Francisca; Kumar, Nirbhay; Mduluza, Takafira

2011-06-22

The geographical congruency in distribution of helminths and Plasmodium falciparum makes polyparasitism a common phenomenon in Sub Saharan Africa. The devastating effects of helminths-Plasmodium co-infections on primary school health have raised global interest for integrated control. However little is known on the feasibility, timing and efficacy of integrated helminths-Plasmodium control strategies. A study was conducted in Zimbabwe to evaluate the efficacy of repeated combined school based antihelminthic and prompt malaria treatment. A cohort of primary schoolchildren (5-17 years) received combined Praziquantel, albendazole treatment at baseline, and again during 6, 12 and 33 months follow up surveys and sustained prompt malaria treatment. Sustained prompt malaria treatment was carried out throughout the study period. Children's infection status with helminths, Plasmodium and helminths-Plasmodium co-infections was determined by parasitological examinations at baseline and at each treatment point. The prevalence of S. haematobium, S. mansoni, STH, malaria, helminths-Plasmodium co-infections and helminths infection intensities before and after treatment were analysed. Longitudinal data showed that two rounds of combined Praziquantel and albendazole treatment for schistosomiasis and STHs at 6 monthly intervals and sustained prompt malaria treatment significantly reduced the overall prevalence of S. haematobium, S. mansoni, hookworms and P. falciparum infection in primary schoolchildren by 73.5%, 70.8%, 67.3% and 58.8% respectively (p < 0.001, p < 0.001, p < 0.001, p < 0.001 respectively). More importantly, the prevalence of STH + schistosomes, P. f + schistosomes, and P. f + STHs + schistosomes co-infections were reduced by 68.0%, 84.2%, and 90.7%, respectively. The absence of anti-helminthic treatment between the 12 mth and 33 mth follow-up surveys resulted in the sharp increase in STHs + schistosomes co-infection from 3.3% at 12 months follow up survey to 10.7%, slightly more than the baseline level (10.3%) while other co-infection combinations remained significantly low. The overall prevalence of heavy S. haematobium, S. mansoni and hookworms infection intensities were significantly reduced from: 17.9-22.4% to 2.6-5.1%, 1.6-3.3% to 0.0% and 0.0-0.7% to 0.0% respectively. Biannual Integrated school based antihelminthic and sustained prompt malaria treatment has a potential to reduce the burden of helminths-plasmodium co-infections in primary school children. In areas of stable malaria transmission, active case finding is recommended to track and treat asymptomatic malaria cases as these may sustain transmission in the community.

Efficacy of integrated school based de-worming and prompt malaria treatment on helminths -Plasmodium falciparum co-infections: A 33 months follow up study

PubMed Central

2011-01-01

Background The geographical congruency in distribution of helminths and Plasmodium falciparum makes polyparasitism a common phenomenon in Sub Saharan Africa. The devastating effects of helminths-Plasmodium co-infections on primary school health have raised global interest for integrated control. However little is known on the feasibility, timing and efficacy of integrated helminths-Plasmodium control strategies. A study was conducted in Zimbabwe to evaluate the efficacy of repeated combined school based antihelminthic and prompt malaria treatment. Methods A cohort of primary schoolchildren (5-17 years) received combined Praziquantel, albendazole treatment at baseline, and again during 6, 12 and 33 months follow up surveys and sustained prompt malaria treatment. Sustained prompt malaria treatment was carried out throughout the study period. Children's infection status with helminths, Plasmodium and helminths-Plasmodium co-infections was determined by parasitological examinations at baseline and at each treatment point. The prevalence of S. haematobium, S. mansoni, STH, malaria, helminths-Plasmodium co-infections and helminths infection intensities before and after treatment were analysed. Results Longitudinal data showed that two rounds of combined Praziquantel and albendazole treatment for schistosomiasis and STHs at 6 monthly intervals and sustained prompt malaria treatment significantly reduced the overall prevalence of S. haematobium, S. mansoni, hookworms and P. falciparum infection in primary schoolchildren by 73.5%, 70.8%, 67.3% and 58.8% respectively (p < 0.001, p < 0.001, p < 0.001, p < 0.001 respectively). More importantly, the prevalence of STH + schistosomes, P. f + schistosomes, and P. f + STHs + schistosomes co-infections were reduced by 68.0%, 84.2%, and 90.7%, respectively. The absence of anti-helminthic treatment between the 12 mth and 33 mth follow-up surveys resulted in the sharp increase in STHs + schistosomes co-infection from 3.3% at 12 months follow up survey to 10.7%, slightly more than the baseline level (10.3%) while other co-infection combinations remained significantly low. The overall prevalence of heavy S. haematobium, S. mansoni and hookworms infection intensities were significantly reduced from: 17.9-22.4% to 2.6-5.1%, 1.6-3.3% to 0.0% and 0.0-0.7% to 0.0% respectively. Conclusion Biannual Integrated school based antihelminthic and sustained prompt malaria treatment has a potential to reduce the burden of helminths-plasmodium co-infections in primary school children. In areas of stable malaria transmission, active case finding is recommended to track and treat asymptomatic malaria cases as these may sustain transmission in the community. PMID:21696629

Cdt1p, through its interaction with Mcm6p, is required for the formation, nuclear accumulation and chromatin loading of the MCM complex.

PubMed

Wu, Rentian; Wang, Jiafeng; Liang, Chun

2012-01-01

Regulation of DNA replication initiation is essential for the faithful inheritance of genetic information. Replication initiation is a multi-step process involving many factors including ORC, Cdt1p, Mcm2-7p and other proteins that bind to replication origins to form a pre-replicative complex (pre-RC). As a prerequisite for pre-RC assembly, Cdt1p and the Mcm2-7p heterohexameric complex accumulate in the nucleus in G1 phase in an interdependent manner in budding yeast. However, the nature of this interdependence is not clear, nor is it known whether Cdt1p is required for the assembly of the MCM complex. In this study, we provide the first evidence that Cdt1p, through its interaction with Mcm6p with the C-terminal regions of the two proteins, is crucial for the formation of the MCM complex in both the cytoplasm and nucleoplasm. We demonstrate that disruption of the interaction between Cdt1p and Mcm6p prevents the formation of the MCM complex, excludes Mcm2-7p from the nucleus, and inhibits pre-RC assembly and DNA replication. Our findings suggest a function for Cdt1p in promoting the assembly of the MCM complex and maintaining its integrity by interacting with Mcm6p.

HIV skews the lineage-defining transcriptional profile of Mycobacterium tuberculosis-specific CD4+ T cells

PubMed Central

Riou, Catherine; Strickland, Natalie; Soares, Andreia P.; Corleis, Bjorn; Kwon, Douglas; Wherry, E. John; Wilkinson, Robert J.; Burgers, Wendy A.

2016-01-01

HIV-infected persons are at greater risk of developing tuberculosis (TB) even before profound CD4 loss occurs, suggesting that HIV alters CD4+T cell functions capable of containing bacterial replication. An effective immune response to Mycobacterium tuberculosis likely relies on the development of a balanced CD4 response, where distinct CD4+T helper subsets act in synergy to control the infection. To define the diversity of Mtb-specific CD4+Th subsets and determine whether HIV infection impacts such responses, the expression of lineage-defining transcription factors T-bet, Gata3, RORγt and Foxp3 was measured in Mtb-specific CD4+T cells in HIV-uninfected (n=20) and HIV-infected individuals (n=20) with latent TB infection. Our results show that upon 5 day restimulation in vitro, Mtb-specific CD4+T cells from healthy individuals have the ability to exhibit a broad spectrum of T helper subsets, defined by specific patterns of transcription factor co-expression. These transcription factor profiles were skewed in HIV-infected individuals where the proportion of T-bethighFoxp3+ Mtb-specific CD4+T cells was significantly decreased (p=0.002) compared to HIV-uninfected individuals, a change that correlated inversely with HIV viral load (p=0.0007) and plasma TNF-α (p=0.027). Our data demonstrate an important balance in T helper subset diversity defined by lineage-defining transcription factor co-expression profiles that is disrupted by HIV infection and suggest a role for HIV in impairing TB immunity by altering the equilibrium of Mtb-specific CD4+T helper subsets. PMID:26927799

A multiple chamber, semicontinuous, crop carbon dioxide exchange system: design, calibration, and data interpretation

NASA Technical Reports Server (NTRS)

van Iersel, M. W.; Bugbee, B.

2000-01-01

Long-term, whole crop CO2 exchange measurements can be used to study factors affecting crop growth. These factors include daily carbon gain, cumulative carbon gain, and carbon use efficiency, which cannot be determined from short-term measurements. We describe a system that measures semicontinuously crop CO2 exchange in 10 chambers over a period of weeks or months. Exchange of CO2 in every chamber can be measured at 5 min intervals. The system was designed to be placed inside a growth chamber, with additional environmental control provided by the individual gas exchange chambers. The system was calibrated by generating CO2 from NaHCO3 inside the chambers, which indicated that accuracy of the measurements was good (102% and 98% recovery for two separate photosynthesis systems). Since the systems measure net photosynthesis (P-net, positive) and dark respiration(R-dark, negative), the data can be used to estimate gross photosynthesis, daily carbon gain, cumulative carbon gain, and carbon use efficiency. Continuous whole-crop measurements are a valuable tool that complements leaf photosynthesis measurements. Multiple chambers allow for replication and comparison among several environmental or cultural treatments that may affect crop growth. Example data from a 2 week study with petunia (Petunia x hybrida Hort. Vilm.-Andr.) are presented to illustrate some of the capabilities of this system.

The leukemia-associated Rho guanine nucleotide exchange factor LARG is required for efficient replication stress signaling

PubMed Central

Beveridge, Ryan D; Staples, Christopher J; Patil, Abhijit A; Myers, Katie N; Maslen, Sarah; Skehel, J Mark; Boulton, Simon J; Collis, Spencer J

2014-01-01

We previously identified and characterized TELO2 as a human protein that facilitates efficient DNA damage response (DDR) signaling. A subsequent yeast 2-hybrid screen identified LARG; Leukemia-Associated Rho Guanine Nucleotide Exchange Factor (also known as Arhgef12), as a potential novel TELO2 interactor. LARG was previously shown to interact with Pericentrin (PCNT), which, like TELO2, is required for efficient replication stress signaling. Here we confirm interactions between LARG, TELO2 and PCNT and show that a sub-set of LARG co-localizes with PCNT at the centrosome. LARG-deficient cells exhibit replication stress signaling defects as evidenced by; supernumerary centrosomes, reduced replication stress-induced γH2AX and RPA nuclear foci formation, and reduced activation of the replication stress signaling effector kinase Chk1 in response to hydroxyurea. As such, LARG-deficient cells are sensitive to replication stress-inducing agents such as hydroxyurea and mitomycin C. Conversely we also show that depletion of TELO2 and the replication stress signaling kinase ATR leads to RhoA signaling defects. These data therefore reveal a level of crosstalk between the RhoA and DDR signaling pathways. Given that mutations in both ATR and PCNT can give rise to the related primordial dwarfism disorders of Seckel Syndrome and Microcephalic osteodysplastic primordial dwarfism type II (MOPDII) respectively, which both exhibit defects in ATR-dependent checkpoint signaling, these data also raise the possibility that mutations in LARG or disruption to RhoA signaling may be contributory factors to the etiology of a sub-set of primordial dwarfism disorders. PMID:25485589

40 CFR 261.33 - Discarded commercial chemical products, off-specification species, container residues, and spill...

Code of Federal Regulations, 2011 CFR

2011-07-01

... P073 13463-39-3 Nickel carbonyl Ni(CO)4, (T-4)- P074 557-19-7 Nickel cyanide P074 557-19-7 Nickel cyanide Ni(CN)2 P075 1 54-11-5 Nicotine, & salts P076 10102-43-9 Nitric oxide P077 100-01-6 p-Nitroaniline... 13463-39-3 Nickel carbonyl P073 13463-39-3 Nickel carbonyl Ni(CO)4, (T-4)- P074 557-19-7 Nickel cyanide...

40 CFR 261.33 - Discarded commercial chemical products, off-specification species, container residues, and spill...

Code of Federal Regulations, 2010 CFR

2010-07-01

... P073 13463-39-3 Nickel carbonyl Ni(CO)4, (T-4)- P074 557-19-7 Nickel cyanide P074 557-19-7 Nickel cyanide Ni(CN)2 P075 1 54-11-5 Nicotine, & salts P076 10102-43-9 Nitric oxide P077 100-01-6 p-Nitroaniline... 13463-39-3 Nickel carbonyl P073 13463-39-3 Nickel carbonyl Ni(CO)4, (T-4)- P074 557-19-7 Nickel cyanide...

The carbon dioxide system on the Mississippi River‐dominated continental shelf in the northern Gulf of Mexico: 1. Distribution and air‐sea CO2 flux

PubMed Central

Huang, Wei‐Jen; Wang, Yongchen; Lohrenz, Steven E.; Murrell, Michael C.

2015-01-01

Abstract River‐dominated continental shelf environments are active sites of air‐sea CO2 exchange. We conducted 13 cruises in the northern Gulf of Mexico, a region strongly influenced by fresh water and nutrients delivered from the Mississippi and Atchafalaya River system. The sea surface partial pressure of carbon dioxide (pCO2) was measured, and the air‐sea CO2 flux was calculated. Results show that CO2 exchange exhibited a distinct seasonality: the study area was a net sink of atmospheric CO2 during spring and early summer, and it was neutral or a weak source of CO2 to the atmosphere during midsummer, fall, and winter. Along the salinity gradient, across the shelf, the sea surface shifted from a source of CO2 in low‐salinity zones (0≤S<17) to a strong CO2 sink in the middle‐to‐high‐salinity zones (17≤S<33), and finally was a near‐neutral state in the high‐salinity areas (33≤S<35) and in the open gulf (S≥35). High pCO2 values were only observed in narrow regions near freshwater sources, and the distribution of undersaturated pCO2 generally reflected the influence of freshwater inputs along the shelf. Systematic analyses of pCO2 variation demonstrated the importance of riverine nitrogen export; that is, riverine nitrogen‐enhanced biological removal, along with mixing processes, dominated pCO2 variation along the salinity gradient. In addition, extreme or unusual weather events were observed to alter the alongshore pCO2 distribution and to affect regional air‐sea CO2 flux estimates. Overall, the study region acted as a net CO2 sink of 0.96 ± 3.7 mol m−2 yr−1 (1.15 ± 4.4 Tg C yr−1). PMID:27656331

DOE Office of Scientific and Technical Information (OSTI.GOV)

Versteeg, Gijs A.; Bredenbeek, Peter J.; Worm, Sjoerd H.E. van den

Many viruses encode antagonists to prevent interferon (IFN) induction. Infection of fibroblasts with the murine hepatitis coronavirus (MHV) and SARS-coronavirus (SARS-CoV) did not result in nuclear translocation of interferon-regulatory factor 3 (IRF3), a key transcription factor involved in IFN induction, and induction of IFN mRNA transcription. Furthermore, MHV and SARS-CoV infection could not prevent IFN induction by poly (I:C) or Sendai virus, suggesting that these CoVs do not inactivate IRF3-mediated transcription regulation, but apparently prevent detection of replicative RNA by cellular sensory molecules. Our data indicate that shielding of viral RNA to host cell sensors might be the main generalmore » mechanism for coronaviruses to prevent IFN induction.« less

Expression of interleukin-33 and its receptor ST2 in periapical granulomas and radicular cysts.

PubMed

Velickovic, Milena; Pejnovic, Nada; Petrovic, Renata; Mitrovic, Slobodanka; Jeftic, Ilija; Kanjevac, Tatjana; Lukic, Aleksandra

2016-01-01

Interleukin-33 (IL-33) is a recently identified cytokine belonging to the IL-1 family and ligand for the IL-1 receptor-related protein ST2. IL-33/ST2 signaling plays a critical role in allergy, autoimmunity, and chronic inflammatory disorders, but its role in the pathogenesis of periapical lesions is unknown. We aimed to investigate the expression patterns of IL-33 and ST2 in human periapical lesions. Periapical lesions (n = 36) and healthy periapical tissues (n = 10) were evaluated by immunohistochemistry using antibodies specific for human IL-33 and ST2. Lesion samples were further analyzed by double immunofluorescence to assess IL-33/ST2 co-expression. The numbers of IL-33- and ST2-positive fibroblasts were significantly higher in periapical lesions compared to healthy periapical tissues (both P < 0.05), while the numbers of IL-33- and ST2-positive endothelial cells were similar (both P > 0.05). There were no significant differences in the numbers of IL-33- and ST2-positive fibroblasts and endothelial cells between periapical granulomas and radicular cysts (all P > 0.05). Similarly, numbers of ST2-positive mononuclear cells did not differ between periapical granulomas and radicular cysts (P > 0.05). The majority of epithelial cells in radicular cysts were IL-33 positive, while the small proportion of epithelial cells was ST2 positive. Double immunofluorescence analysis revealed IL-33/ST2 co-expression in fibroblasts and endothelial cells. IL-33 and ST2 are expressed in periapical granulomas and radicular cysts. Increased numbers of IL-33- and ST2-positive fibroblasts in periapical lesions when compared to healthy periapical tissues suggest that IL-33/ST2 signaling may be involved in periapical inflammation and tissue fibrosis. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Genome-wide association analysis implicates dysregulation of immunity genes in chronic lymphocytic leukaemia

PubMed Central

Law, Philip J.; Berndt, Sonja I.; Speedy, Helen E.; Camp, Nicola J.; Sava, Georgina P.; Skibola, Christine F.; Holroyd, Amy; Joseph, Vijai; Sunter, Nicola J.; Nieters, Alexandra; Bea, Silvia; Monnereau, Alain; Martin-Garcia, David; Goldin, Lynn R.; Clot, Guillem; Teras, Lauren R.; Quintela, Inés; Birmann, Brenda M.; Jayne, Sandrine; Cozen, Wendy; Majid, Aneela; Smedby, Karin E.; Lan, Qing; Dearden, Claire; Brooks-Wilson, Angela R.; Hall, Andrew G.; Purdue, Mark P.; Mainou-Fowler, Tryfonia; Vajdic, Claire M.; Jackson, Graham H.; Cocco, Pierluigi; Marr, Helen; Zhang, Yawei; Zheng, Tongzhang; Giles, Graham G.; Lawrence, Charles; Call, Timothy G.; Liebow, Mark; Melbye, Mads; Glimelius, Bengt; Mansouri, Larry; Glenn, Martha; Curtin, Karen; Diver, W Ryan; Link, Brian K.; Conde, Lucia; Bracci, Paige M.; Holly, Elizabeth A.; Jackson, Rebecca D.; Tinker, Lesley F.; Benavente, Yolanda; Boffetta, Paolo; Brennan, Paul; Maynadie, Marc; McKay, James; Albanes, Demetrius; Weinstein, Stephanie; Wang, Zhaoming; Caporaso, Neil E.; Morton, Lindsay M.; Severson, Richard K.; Riboli, Elio; Vineis, Paolo; Vermeulen, Roel C. H.; Southey, Melissa C.; Milne, Roger L.; Clavel, Jacqueline; Topka, Sabine; Spinelli, John J.; Kraft, Peter; Ennas, Maria Grazia; Summerfield, Geoffrey; Ferri, Giovanni M.; Harris, Robert J.; Miligi, Lucia; Pettitt, Andrew R.; North, Kari E.; Allsup, David J.; Fraumeni, Joseph F.; Bailey, James R.; Offit, Kenneth; Pratt, Guy; Hjalgrim, Henrik; Pepper, Chris; Chanock, Stephen J.; Fegan, Chris; Rosenquist, Richard; de Sanjose, Silvia; Carracedo, Angel; Dyer, Martin J. S.; Catovsky, Daniel; Campo, Elias; Cerhan, James R.; Allan, James M.; Rothman, Nathanial; Houlston, Richard; Slager, Susan

2017-01-01

Several chronic lymphocytic leukaemia (CLL) susceptibility loci have been reported; however, much of the heritable risk remains unidentified. Here we perform a meta-analysis of six genome-wide association studies, imputed using a merged reference panel of 1,000 Genomes and UK10K data, totalling 6,200 cases and 17,598 controls after replication. We identify nine risk loci at 1p36.11 (rs34676223, P=5.04 × 10−13), 1q42.13 (rs41271473, P=1.06 × 10−10), 4q24 (rs71597109, P=1.37 × 10−10), 4q35.1 (rs57214277, P=3.69 × 10−8), 6p21.31 (rs3800461, P=1.97 × 10−8), 11q23.2 (rs61904987, P=2.64 × 10−11), 18q21.1 (rs1036935, P=3.27 × 10−8), 19p13.3 (rs7254272, P=4.67 × 10−8) and 22q13.33 (rs140522, P=2.70 × 10−9). These new and established risk loci map to areas of active chromatin and show an over-representation of transcription factor binding for the key determinants of B-cell development and immune response. PMID:28165464

Inhibition of rotavirus replication by downregulation of fatty acid synthesis.

PubMed

Gaunt, Eleanor R; Cheung, Winsome; Richards, James E; Lever, Andrew; Desselberger, Ulrich

2013-06-01

Recently the recruitment of lipid droplets (LDs) to sites of rotavirus (RV) replication was reported. LDs are polymorphic organelles that store triacylglycerols, cholesterol and cholesterol esters. The neutral fats are derived from palmitoyl-CoA, synthesized via the fatty acid biosynthetic pathway. RV-infected cells were treated with chemical inhibitors of the fatty acid biosynthetic pathway, and the effects on viral replication kinetics were assessed. Treatment with compound C75, an inhibitor of the fatty acid synthase enzyme complex (FASN), reduced RV infectivity 3.2-fold (P = 0.07) and modestly reduced viral RNA synthesis (1.2-fold). Acting earlier in the fatty acid synthesis pathway, TOFA [5-(Tetradecyloxy)-2-furoic acid] inhibits the enzyme acetyl-CoA carboxylase 1 (ACC1). TOFA reduced the infectivity of progeny RV 31-fold and viral RNA production 6-fold. The effect of TOFA on RV infectivity and RNA replication was dose-dependent, and infectivity was reduced by administering TOFA up to 4 h post-infection. Co-treatment of RV-infected cells with C75 and TOFA synergistically reduced viral infectivity. Knockdown by siRNA of FASN and ACC1 produced findings similar to those observed by inhibiting these proteins with the chemical compounds. Inhibition of fatty acid synthesis using a range of approaches uniformly had a more marked impact on viral infectivity than on viral RNA yield, inferring a role for LDs in virus assembly and/or egress. Specific inhibitors of fatty acid metabolism may help pinpoint the critical structural and biochemical features of LDs that are essential for RV replication, and facilitate the development of antiviral therapies.

Serum adipokines and HIV viral replication in patients undergoing antiretroviral therapy

PubMed Central

Aramă, Victoria; Tilişcan, Cătălin; Ion, Daniela Adriana; Mihăilescu, Raluca; Munteanu, Daniela; Streinu-Cercel, Anca; Tudor, Ana Maria; Hristea, Adriana; Leoveanu, Viorica; Olaru, Ioana; Aramă, Ştefan Sorin

2012-01-01

Introduction Several studies have reported that cytokines secreted by adipose tissue (adipokines) may be linked to HIV replication. The aim of the study was to evaluate the relationship between HIV replication and serum levels of adipokines, in a Caucasian HIV-infected population of men and women undergoing complex antiretroviral therapy. Methods A cross-sectional study was conducted in an unselected sample of 77 HIV-1-positive patients. Serum adipokines levels were measured including circulating adiponectin, leptin, resistin, tumor necrosis factor alpha (TNF-alpha) and interleukin-6 (IL-6). Patients were divided into two groups: Group 1 - with undetectable viral load and Group 2 - with persistent HIV viral replication. Differences between groups ? were tested using independent-sample t-test for Gaussian variables and Mann–Whitney–Wilcoxon test for non-parametric variables. Pearson's chi-squared test was used for correlation analysis. Results A total of 77 patients (age range: 17-65, mean: 32.5 years) including 44 men (57.1% men, age range: 17–63 years, mean: 34.1 years) and 33 women (42.9% women age range: 19–65 years, mean: 30.3 years) were included in the study. TNF-alpha had significantly higher serum levels in patients with detectable viral load (16.89 vs. 9.35 pg/mL), (p=0.043), but correlation analysis lacked statistical significance. Adiponectin had median serum levels of 9.22 ìg/mL in Group 1 vs. 16.50 ìg/mL in Group 2 but the results lacked statistical significance (p=0.059). Higher leptin, IL-6 and resistin serum levels were noted in patients with undetectable HIV viral load, without statistical significance. Conclusions The present study reported higher TNF-alpha serum levels in patients with persistent HIV viral load. We found no statistically significant correlations between adiponectin, leptin, resistin and IL-6 and HIV viral load in our Caucasian HIV-positive study population, undergoing antiretroviral therapy. PMID:24432258

Altered postural control strategies in quiet standing more than 20 years after rupture of the anterior cruciate ligament.

PubMed

Stensdotter, Ann-Katrin; Tengman, Eva; Häger, Charlotte

2016-05-01

To explore long-term consequences of anterior cruciate ligament (ACL) rupture on postural sway and control strategies during bilateral quiet standing, in subjects treated with or without reconstructive surgery compared to uninjured controls. 70 individuals who had unilateral ACL rupture 23±2.4 years ago (33 received ACL reconstructive surgery, ACLR, and 37 had physiotherapy only, ACLPT) and 33 uninjured matched controls (CTRL) (mean age 46±5.3) stood quietly with eyes closed for 3min on a firm and on a compliant surface, respectively. Center of pressure (CoP) was registered with a force plate and postural sway was calculated from center of mass (CoM) derived from 3D kinematics. Sway density (SD) analyses of CoP assessed distance and duration of stable phases. The torque controlling postural sway was estimated from CoP-CoM. Comparisons across conditions to CTRL revealed larger CoP-CoM-area in ACLR (p=0.017, CI: 10.95, 143.10), but not in ACLPT. Mean distance between SD-peaks was greater for ACLR (p<0.001, CI: 1.73, 5.31) than for ACLPT (p=0.006, CI: 0.56, 4.12) relative to CTRL. Duration of SD-peaks was smaller for both ACLR and ACLPT (p<0.001, CI: -4.04, -1.23 and -3.82, -1.03, respectively) compared to CTRL. CoM-area in the ACL-groups did not differ from CTRL. ACL-injured subjects demonstrated greater postural control efforts than CTRL but without significant differences in postural sway. Control efforts were thus not directly associated with sway and further research should be focused on variance in postural control strategies. Copyright © 2016. Published by Elsevier B.V.

Fine-tuning synthesis of Yersinia pestis LcrV from runaway-like replication balanced-lethal plasmid in a Salmonella enterica serovar typhimurium vaccine induces protection against a lethal Y. pestis challenge in mice.

PubMed

Torres-Escobar, Ascención; Juárez-Rodríguez, María Dolores; Gunn, Bronwyn M; Branger, Christine G; Tinge, Steven A; Curtiss, Roy

2010-06-01

A balanced-lethal plasmid expression system that switches from low-copy-number to runaway-like high-copy-number replication (pYA4534) was constructed for the regulated delayed in vivo synthesis of heterologous antigens by vaccine strains. This is an antibiotic resistance-free maintenance system containing the asdA gene (essential for peptidoglycan synthesis) as a selectable marker to complement the lethal chromosomal DeltaasdA allele in live recombinant attenuated Salmonella vaccines (RASVs) such as Salmonella enterica serovar Typhimurium strain chi9447. pYA4534 harbors two origins of replication, pSC101 and pUC (low and high copy numbers, respectively). The pUC replication origin is controlled by a genetic switch formed by the operator/promoter of the P22 cro gene (O/P(cro)) (P(R)), which is negatively regulated by an arabinose-inducible P22 c2 gene located on both the plasmid and the chromosome (araC P(BAD) c2). The absence of arabinose, which is unavailable in vivo, triggers replication to a high-copy-number plasmid state. To validate these vector attributes, the Yersinia pestis virulence antigen LcrV was used to develop a vaccine against plague. An lcrV sequence encoding amino acids 131 to 326 (LcrV196) was optimized for expression in Salmonella, flanked with nucleotide sequences encoding the signal peptide (SS) and the carboxy-terminal domain (CT) of beta-lactamase, and cloned into pYA4534 under the control of the P(trc) promoter to generate plasmid pYA4535. Our results indicate that the live Salmonella vaccine strain chi9447 harboring pYA4535 efficiently stimulated a mixed Th1/Th2 immune response that protected mice against lethal challenge with Y. pestis strain CO92 introduced through either the intranasal or subcutaneous route.

Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans.

PubMed

Rhee, Mun Su; Kim, Jin-Woo; Qian, Yilei; Ingram, L O; Shanmugam, K T

2007-07-01

Bacillus coagulans is a sporogenic lactic acid bacterium that ferments glucose and xylose, major components of plant biomass, a potential feedstock for cellulosic ethanol. The temperature and pH for optimum rate of growth of B. coagulans (50 to 55 degrees C, pH 5.0) are very similar to that of commercially developed fungal cellulases (50 degrees C; pH 4.8). Due to this match, simultaneous saccharification and fermentation (SSF) of cellulose to products by B. coagulans is expected to require less cellulase than needed if the SSF is conducted at a sub-optimal temperature, such as 30 degrees C, the optimum for yeast, the main biocatalyst used by the ethanol industry. To fully exploit B. coagulans as a platform organism, we have developed an electroporation method to transfer plasmid DNA into this genetically recalcitrant bacterium. We also constructed a B. coagulans/E. coli shuttle vector, plasmid pMSR10 that contains the rep region from a native plasmid (pMSR0) present in B. coagulans strain P4-102B. The native plasmid, pMSR0 (6823bp), has 9 ORFs, and replicates by rolling-circle mode of replication. Plasmid pNW33N, developed for Geobacillus stearothermophilus, was also transformed into this host and stably maintained while several other Bacillus/Escherichia coli shuttle vector plasmids were not transformed into B. coagulans. The transformation efficiency of B. coagulans strain P4-102B using the plasmids pNW33N or pMSR10 was about 1.5x10(16) per mole of DNA. The availability of shuttle vectors and an electroporation method is expected to aid in genetic and metabolic engineering of B. coagulans.

Death-domain associated protein-6 (DAXX) mediated apoptosis in hantavirus infection is counter-balanced by activation of interferon-stimulated nuclear transcription factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khaiboullina, Svetlana F., E-mail: sv.khaiboullina@gmail.com; Morzunov, Sergey P.; Boichuk, Sergei V.

2013-09-01

Hantaviruses are negative strand RNA species that replicate predominantly in the cytoplasm. They also activate numerous cellular responses, but their involvement in nuclear processes is yet to be established. Using human umbilical vein endothelial cells (HUVECs), this study investigates the molecular finger-print of nuclear transcription factors during hantavirus infection. The viral-replication-dependent activation of pro-myelocytic leukemia protein (PML) was followed by subsequent localization in nuclear bodies (NBs). PML was also found in close proximity to activated Sp100 nuclear antigen and interferon-stimulated gene 20 kDa protein (ISG-20), but co-localization with death-domain associated protein-6 (DAXX) was not observed. These data demonstrate that hantavirusmore » triggers PML activation and localization in NBs in the absence of DAXX-PLM-NB co-localization. The results suggest that viral infection interferes with DAXX-mediated apoptosis, and expression of interferon-activated Sp100 and ISG-20 proteins may indicate intracellular intrinsic antiviral attempts.« less

Expression of the p12 subunit of human DNA polymerase δ (Pol δ), CDK inhibitor p21(WAF1), Cdt1, cyclin A, PCNA and Ki-67 in relation to DNA replication in individual cells.

PubMed

Zhao, Hong; Zhang, Sufang; Xu, Dazhong; Lee, Marietta Ywt; Zhang, Zhongtao; Lee, Ernest Yc; Darzynkiewicz, Zbigniew

2014-01-01

We recently reported that the p12 subunit of human DNA polymerase δ (Pol δ4) is degraded by CRL4(Cdt2) which regulates the licensing factor Cdt1 and p21(WAF1) during the G1 to S transition. Presently, we performed multiparameter laser scanning cytometric analyses of changes in levels of p12, Cdt1 and p21(WAF1), detected immunocytochemically in individual cells, vis-à-vis the initiation and completion of DNA replication. The latter was assessed by pulse-labeling A549 cells with the DNA precursor ethynyl-2'-deoxyribose (EdU). The loss of p12 preceded the initiation of DNA replication and essentially all cells incorporating EdU were p12 negative. Completion of DNA replication and transition to G2 phase coincided with the re-appearance and rapid rise of p12 levels. Similar to p12 a decline of p21(WAF1) and Cdt1 was seen at the end of G1 phase and all DNA replicating cells were p21(WAF1) and Cdt1 negative. The loss of p21(WAF1) preceded that of Cdt1 and p12 and the disappearance of the latter coincided with the onset of DNA replication. Loss of p12 leads to conversion of Pol δ4 to its trimeric form, Pol δ3, so that the results provide strong support to the notion that Pol δ3 is engaged in DNA replication during unperturbed progression through the S phase of cell cycle. Also assessed was a correlation between EdU incorporation, likely reflecting the rate of DNA replication in individual cells, and the level of expression of positive biomarkers of replication cyclin A, PCNA and Ki-67 in these cells. Of interest was the observation of stronger correlation between EdU incorporation and expression of PCNA (r = 0.73) than expression of cyclin A (r = 0.47) or Ki-67 (r = 0.47).

[Prospective study of prevalence hearing loss in preterm neonates in an intensive care unit].

PubMed

Tomasik, Tomasz

2002-01-01

The risk of hearing loss is higher in prematurely born infants compared with neonates born at term. It is due to unfinished development of auditory path and exposition to many harmful factors related to treatment in a neonatal intensive care unit. Assessment of hearing loss risk factors in preterm babies. 152 newborns with mean birth weight 1408 +/- 551 g and gestational age 30.3 +/- 3.2 weeks. After discharge follow-up (Me = 32 months) study of newborns born before 37 weeks of gestation age. The patients were assigned into two groups: A) with hearing loss (n = 9) and B) without hearing loss (n = 143) according to the results of clinical observation and audiological assessment after 6 months of life. The rate of hearing loss was higher in new-borns born between 24-28 weeks of gestation (6/50, 12%) than in those born between 29-32 (2/52.3%) and 33-36 (1/43, 2%, p = 0.03). Identified risk factors independent of gestational age were: Gram negative sepsis (OR = 6; 95%CI: 1.32-27.33) and hyperbilirubinemia > 340 mumol/l (OR = 40.5; 95%CI: 73.27-503). The other risk factors are: shock (OR = 6.65; 95%CI: 1.44-30.64), hypercarbia (pCO2 > 80 mmHg) (OR = 5.13; 95%CI: 1.29-20.37), severe anemia (Ht < 24%) (OR = 6.0; 95%CI: 1.32-27.33). Prolonged treatment with aminoglicosides (over 10 days) also increased hearing loss risk (OR = 10.4; 95%CI: 1.27-85.75). The risk of hearing loss is highest in the newborn born between 24-28 weeks of gestation. It can be further increased by shock, hypercapnia, severe anemia, prolonged treatment with aminoglicosides. Gestational age independent factors are: hyperbilirubinemia and Gram negative sepsis.

A biologically inspired two-species exclusion model: effects of RNA polymerase motor traffic on simultaneous DNA replication

NASA Astrophysics Data System (ADS)

Ghosh, Soumendu; Mishra, Bhavya; Patra, Shubhadeep; Schadschneider, Andreas; Chowdhury, Debashish

2018-04-01

We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles (P) represents RNAP motors while the other (R) represents the replication forks. Motivated by the biological phenomena that this model is intended to capture, a maximum of two R particles only are allowed to enter the lattice from two opposite ends whereas the unrestricted number of P particles constitutes a totally asymmetric simple exclusion process (TASEP) in a segment in the middle of the lattice. The model captures three distinct pathways for resolving the co-directional as well as head-on collision between the P and R particles. Using Monte Carlo simulations and heuristic analytical arguments that combine exact results for the TASEP with mean-field approximations, we predict the possible outcomes of the conflict between the traffic of RNAP motors (P particles engaged in transcription) and the replication forks (R particles). In principle, the model can be adapted to experimental conditions to account for the data quantitatively.

[The Efficacy of Rebamipide or Ecabet Sodium Supplementation for Helicobacter pylori Eradication Therapy Compared with Quadruple (Concomitant) Regimen].

PubMed

Kim, Joonhwan; Kim, Kyungwon; Lee, Jun Soo; Kim, Su Young; Kim, Kyung Oh; Kim, Yoon Jae; Kwon, Kwang An; Park, Dong Kyun; Chung, Jun Won

2018-04-25

Although some previous studies reported that a treatment combined with mucoprotective agent could improve the eradication rate in dual or triple therapy, there are other reports that question the efficacy of combining these drugs in concomitant therapy (CoCTx). The aim of this study was to investigate the effects of rebamipide or ecabet on the Helicobacter pylori ( H. pylori ) eradication combined with CoCTx. We retrospectively reviewed the medical records of 277 patients with proven H. pylori infection. They were assigned to one of 3 regimens for 10 days, twice daily: (a) CoCTx (n=118): lansoprazole 30 mg, amoxicillin 1 g, metronidazole 500 mg, and clarithromycin 500 mg; (b) CoCTx+rebamipide (100 mg) (n=85); (c) CoCTx+ecabet (1 g) (n=74). The baseline characteristics were not significantly different. H. pylori eradication rates were 82.2% (97/118) in CoCTx, 90.6% (77/85) in CoCTx+rebamipide, and 89.2% (66/74) in CoCTx+ecabet (p=0.17), which were statistically insignificant. Overall adverse events were more frequently reported in the CoCTx+rebamipide (50.6%. 43/85) and CoCTx+ecabet (44.6%, 33/74) groups than in the CoCTx (32.2%, 38/118) (p = 0.03) group. Drug compliances were not different between three groups (CoCTx: 95.8%, 113/118; CoCT+rebamipide: 92.9%, 79/85; CoCTx+ecabet 98.6%,73/74) (p=0.209). Multivariate analysis showed that the risk of eradication failure was significantly increased with decreased drug compliance (odds ratio 3.52, 95% confidence interval 1.00-12.32; p=0.05). Addition of these mucoprotective agent was not superior to CoCTx alone for eradicating H. pylori infection with frequent adverse events. Rather, drug compliance is the most related factor affecting the eradication rate. Our data suggest the importance of drug compliance over the drugs used.

Are Trends in Total Hip Arthroplasty Bearing Surface Continuing to Change? 2007-2015 Usage in a Large Database Cohort.

PubMed

Bedard, Nicholas A; Burnett, Robert A; DeMik, David E; Gao, Yubo; Liu, Steve S; Callaghan, John J

2017-12-01

Bearing surface issues related to trunnionosis or metal-on-metal (MoM) articulations have likely impacted recent trends in bearing surface choice. The purpose of this study is to evaluate trends in total hip arthroplasty (THA) bearing surface use, including 2015 data, with respect to the date of operation and patient demographics. The Humana dataset was reviewed from 2007 through 2015 to analyze bearing surface usage in primary THA. Four bearing surface types were identified by International Classification of Disease, 10th Revision codes and trended throughout the years: metal-on-polyethylene (MoP), ceramic-on-ceramic (CoC), ceramic-on-polyethylene (CoP), and MoM. Prevalence was analyzed as a function of age and sex. Of the 28,504 primary THA procedures, the most commonly used bearing was MoP (46.1%), followed by CoP (33.2%), MoM (17.1%), and ceramic-on-ceramic (3.6%). The use of CoP bearings significantly increased from 6.4% in 2007 to 52.0% in 2015, while MoM bearings decreased during this period. MoP bearings decreased over 2012-2015 (P < .001). CoP usage decreased with age, while MoP bearings increased with a transition occurring at 65-69 years of age. Women were more likely to receive MoP bearings (odds ratio [OR] 1.2), while men were more likely to receive MoM and CoP bearings (OR 1.1). Multivariate logistic regression showed age to be an independent predictor of bearing surface choice with patients 65 and older more likely to receive MoP bearings (OR 3.2). Bearing surface choice in primary THA has changed tremendously from 2007 to 2015. MoM bearing use has decreased as a result of adverse effects. Age continues to remain a significant factor in bearing surface choice. Copyright © 2017 Elsevier Inc. All rights reserved.

A survey of the interactome of Kaposi's sarcoma-associated herpesvirus ORF45 revealed its binding to viral ORF33 and cellular USP7, resulting in stabilization of ORF33 that is required for production of progeny viruses.

PubMed

Gillen, Joseph; Li, Wenwei; Liang, Qiming; Avey, Denis; Wu, Jianjun; Wu, Fayi; Myoung, JinJong; Zhu, Fanxiu

2015-05-01

The ORF45 protein of Kaposi's sarcoma-associated herpesvirus (KSHV) is a gammaherpesvirus-specific immediate-early tegument protein. Our previous studies have revealed its crucial roles in both early and late stages of KSHV infection. In this study, we surveyed the interactome of ORF45 using a panel of monoclonal antibodies. In addition to the previously identified extracellular regulated kinase (ERK) and p90 ribosomal S6 kinase (RSK) proteins, we found several other copurified proteins, including prominent ones of ∼38 kDa and ∼130 kDa. Mass spectrometry revealed that the 38-kDa protein is viral ORF33 and the 130-kDa protein is cellular USP7 (ubiquitin-specific protease 7). We mapped the ORF33-binding domain to the highly conserved carboxyl-terminal 19 amino acids (aa) of ORF45 and the USP7-binding domain to the reported consensus motif in the central region of ORF45. Using immunofluorescence staining, we observed colocalization of ORF45 with ORF33 or USP7 both under transfected conditions and in KSHV-infected cells. Moreover, we noticed ORF45-dependent relocalization of a portion of ORF33/USP7 from the nucleus to the cytoplasm. We found that ORF45 caused an increase in ORF33 protein accumulation that was abolished if either the ORF33- or USP7-binding domain in ORF45 was deleted. Furthermore, deletion of the conserved carboxyl terminus of ORF45 in the KSHV genome drastically reduced the level of ORF33 protein in KSHV-infected cells and abolished production of progeny virions. Collectively, our results not only reveal new components of the ORF45 interactome, but also demonstrate that the interactions among these proteins are crucial for KSHV lytic replication. Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of several human cancers. KSHV ORF45 is a multifunctional protein that is required for KSHV lytic replication, but the exact mechanisms by which ORF45 performs its critical functions are unclear. Our previous studies revealed that all ORF45 protein in cells exists in high-molecular-weight complexes. We therefore sought to characterize the interactome of ORF45 to provide insights into its roles during lytic replication. Using a panel of monoclonal antibodies, we surveyed the ORF45 interactome in KSHV-infected cells. We identified two new binding partners of ORF45: the viral protein ORF33 and cellular ubiquitin-specific protease 7 (USP7). We further demonstrate that the interaction between ORF45 and ORF33 is crucial for the efficient production of KSHV viral particles, suggesting that the targeted interference with this interaction may represent a novel strategy to inhibit KSHV lytic replication. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Domestication of Lambda Phage Genes into a Putative Third Type of Replicative Helicase Matchmaker

PubMed Central

Brézellec, Pierre; Petit, Marie-Agnès; Pasek, Sophie; Vallet-Gely, Isabelle; Possoz, Christophe

2017-01-01

Abstract At the onset of the initiation of chromosome replication, bacterial replicative helicases are recruited and loaded on the DnaA-oriC nucleoprotein platform, assisted by proteins like DnaC/DnaI or DciA. Two orders of bacteria appear, however, to lack either of these factors, raising the question of the essentiality of these factors in bacteria. Through a phylogenomic approach, we identified a pair of genes that could have substituted for dciA. The two domesticated genes are specific of the dnaC/dnaI- and dciA-lacking organisms and apparently domesticated from lambdoid phage genes. They derive from λO and λP and were renamed dopC and dopE, respectively. DopE is expected to bring the replicative helicase to the bacterial origin of replication, while DopC might assist DopE in this function. The confirmation of the implication of DopCE in the handling of the replicative helicase at the onset of replication in these organisms would generalize to all bacteria and therefore to all living organisms the need for specific factors dedicated to this function. PMID:28854626

MicroRNA-33 promotes the replicative senescence of mouse embryonic fibroblasts by suppressing CDK6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Shun; Huang, Haijiao; Li, Nanhong

2016-05-13

MicroRNAs are a large class of tiny noncoding RNAs, which have emerged as critical regulators of gene expression, and thus are involved in multiple cellular processes, including cellular senescence. MicroRNA-33 has previously been established to exert crucial effect on cell proliferation, lipid metabolism and cholesterol metabolism. Nonetheless, the association between microRNA-33 and cellular senescence and its underlying molecular mechanism are far to be elucidated. The present study has attempted to probe into the effect of microRNA-33 on MEFs senescence. Our data unveiled that microRNA-33 was dramatically down-regulated in senescent MEFs compared to the young MEFs, and ectopic expression of microRNA-33more » promoted MEFs senescence, while knock-down of microRNA-33 exhibited a protective effect against senescence phenotype. Moreover, we verified CDK6 as a direct target of microRNA-33 in mouse. Silencing of CDK6 induced the premature senescence phenotype of MEFs similarly as microRNA-33, while enforced expression of CDK6 significantly reverse the senescence-induction effect of microRNA-33. Taken together, our results suggested that microRNA-33 enhanced the replicative senescence of MEFs potentially by suppressing CDK6 expression. -- Highlights: •MicroRNA-33 was dramatically down-regulated in senescent MEF cells. •Altered expression of microRNA-33 exerted a critical role in MEFs senescence. •MicroRNA-33 promoted the replicative senescence of MEFs via targeting of CDK6.« less

Factors influencing the type, timing and severity of symptomatic responses to dietary gluten in patients with biopsy-proven coeliac disease.

PubMed

Barratt, Stephen M; Leeds, John S; Sanders, David S

2013-12-01

There is a paucity of data reflecting the symptomatic responses to dietary gluten (SRDG) in patients with Coeliac Disease (CD). We aimed to determine the type, timing and severity of SRDG with reference to a range of disease-related factors. Postal survey of 224 biopsy-proven patients including gluten-free diet (GFD) adherence, symptom checklist, ROME II criteria and The Hospital Anxiety & Depression Scale. Case-note review was also conducted. 26% of respondents were male. Full GFD adherence: n=159 (70%). Irritable bowel syndrome (IBS): n=50 (22%). Anxiety: n=30 (13%); Depression: n=33 (14%); Anxiety & Depression: n=72 (32%). Pruritus, fatigue and bloating were a more common SRDG in the partial/none GFD adherent group (p=ns). Co-existing IBS was associated with a greater prevalence of nausea and fatigue in response to gluten (p=<0.05). Fully GFD adherent patients are more likely to have SRDG <1hr than partial/none adherent (OR 4.8; p=0.004), as are a third of patients with co-existing IBS (OR 1.5; p=0.027) and those patients at risk of both anxiety and depression (OR 1.9; p=0.04). Inadvertent exposure to dietary gluten in the fully GFD adherent group is more likely to result in a severe SRDG in comparison to symptoms arising prior to consistent GFD adherence (OR 2.3; p=0.01). IBS sufferers are also more likely to rate their SRDG as severe in nature (OR 1.4; p=0.038). Patients with consistent GFD adherence experience a SRDG faster and more severe in comparison to prior gluten exposure possibly demonstrating an adept immunological response. Anxiety and depression also enhance the speed of symptom onset and co-existing visceral hypersensitivity is a risk factor for severe reactions to dietary gluten.

Potential sources of variability in mesocosm experiments on the response of phytoplankton to ocean acidification

NASA Astrophysics Data System (ADS)

Moreno de Castro, Maria; Schartau, Markus; Wirtz, Kai

2017-04-01

Mesocosm experiments on phytoplankton dynamics under high CO2 concentrations mimic the response of marine primary producers to future ocean acidification. However, potential acidification effects can be hindered by the high standard deviation typically found in the replicates of the same CO2 treatment level. In experiments with multiple unresolved factors and a sub-optimal number of replicates, post-processing statistical inference tools might fail to detect an effect that is present. We propose that in such cases, data-based model analyses might be suitable tools to unearth potential responses to the treatment and identify the uncertainties that could produce the observed variability. As test cases, we used data from two independent mesocosm experiments. Both experiments showed high standard deviations and, according to statistical inference tools, biomass appeared insensitive to changing CO2 conditions. Conversely, our simulations showed earlier and more intense phytoplankton blooms in modeled replicates at high CO2 concentrations and suggested that uncertainties in average cell size, phytoplankton biomass losses, and initial nutrient concentration potentially outweigh acidification effects by triggering strong variability during the bloom phase. We also estimated the thresholds below which uncertainties do not escalate to high variability. This information might help in designing future mesocosm experiments and interpreting controversial results on the effect of acidification or other pressures on ecosystem functions.

Lipopolysaccharide potentiates the effect of hepatocyte growth factor on hepatocyte replication in rats by augmenting AP-1 activity.

PubMed

Gao, C; Jokerst, R; Gondipalli, P; Cai, S R; Kennedy, S; Flye, M W; Ponder, K P

1999-12-01

The liver regenerates by replication of differentiated hepatocytes after damage or removal of part of the liver. Although several growth factors and signaling pathways are activated during regeneration, it is unclear as to which of these are essential for hepatocyte replication. We show here that low- (1 mg/kg) and high- (10 mg/kg) dose hepatocyte growth factor (HGF) induced replication of 2.1% and 11.1% of hepatocytes in rats, respectively. Lipopolysaccharide (LPS), an inducer of the acute phase response, augmented hepatocyte replication in response to low- and high-dose HGF by 4- and 2-fold, respectively. HGF alone induced moderate levels of c-Jun-N-terminal kinase (JNK) and p44/p42 mitogen-activated protein kinase (MAPK), resulting in moderate levels of AP-1-DNA binding activity. The combination of LPS + HGF increased JNK and AP-1-DNA binding activity more than levels seen with LPS or HGF alone. The activation of Stat3 that was observed after administration of LPS + HGF, but not HGF alone, could contribute to increased transcription of AP-1 components. Because phosphorylation of the c-Jun component of AP-1 by JNK increases its ability to activate transcription, the AP-1 in hepatocytes from animals treated with LPS + HGF may be more active than in rats treated with LPS or HGF alone. LPS may contribute to hepatocyte replication by potentiating the effect of HGF on the activation of both AP-1-DNA binding and transcriptional activity.

Poliovirus Replication Requires the N-terminus but not the Catalytic Sec7 Domain of ArfGEF GBF1

PubMed Central

Belov, George A.; Kovtunovych, Gennadiy; Jackson, Catherine L.; Ehrenfeld, Ellie

2010-01-01

Viruses are intracellular parasites whose reproduction relies on factors provided by the host. The cellular protein GBF1 is critical for poliovirus replication. Here we show that the contribution of GBF1 to virus replication is different from its known activities in uninfected cells. Normally GBF1 activates the Arf GTPases necessary for formation of COPI transport vesicles. GBF1 function is modulated by p115 and Rab1b. However, in polio-infected cells, p115 is degraded and neither p115 nor Rab1b knock-down affects virus replication. Poliovirus infection is very sensitive to BFA, an inhibitor of Arf activation by GBF1. BFA targets the catalytic Sec7 domain of GBF1. Nevertheless the BFA block of polio replication is rescued by expression of only the N-terminal region of GBF1 lacking the Sec7 domain. Replication of BFA-resistant poliovirus in the presence of BFA is uncoupled from Arf activation but is dependent on GBF1. Thus the function(s) of this protein essential for viral replication can be separated from those required for cellular metabolism. PMID:20497182

Detection and analysis of bovine foamy virus infection by an indicator cell line.

PubMed

Ma, Zhe; Qiao, Wen-tao; Xuan, Cheng-hao; Xie, Jin-hui; Chen, Qi-min; Geng, Yun-qi

2007-07-01

To determine the infectivity and replication strategy of bovine foamy virus (BFV) in different cultured cells using the BFV indicator cell line (BICL) system. BFV infection was induced by the co-culture method or the transient transfection of the infectious BFV plasmid [pCMV (cytomegalovirus) - BFV] clone. The infectivity of BFV was monitored by the percentage of green fluorescent protein-positive cells in the BICL. The effect of reverse transcriptase inhibitor zidovudine (AZT) on BFV replication was also evaluated in the BICL. The titer of BFV in fetal bovine lung cells was 4-5-folds more than that in either 293T or HeLa (Cells from Henrietta lacks) cells using the co-culture method, and in the meantime was significantly higher than that produced by the infectious clone pCMV-BFV in the same cells. AZT had only a minor effect on viral titers when added to cells prior to the virus infection. In contrast, viral titers reduced sharply to the level of the negative control when the virus was produced from cells in the presence of AZT. BICL can be used for the titration of the BFV viral infection in non-cytopathic condition. In addition, we provide important evidence to show that reverse transcription is essential for BFV replication at a late step of viral infection.

Stress-induced premature senescence (SIPS)--influence of SIPS on radiotherapy.

PubMed

Suzuki, Masatoshi; Boothman, David A

2008-03-01

Replicative senescence is a fundamental feature in normal human diploid cells and results from dysfunctional telomeres at the Hayflick cell division limit. Ionizing radiation (IR) prematurely induces the same phenotypes as replicative senescence prior to the Hayflick limit. This process is known as stress-induced premature senescence (SIPS). Since the cell cycle is irreversibly arrested in SIPS-induced cells, even if they are stimulated by various growth factors, it is thought that SIPS is a form of cell death, irreversibly eliminating replicating cells. IR-induced-focus formation of DNA repair proteins, a marker of DNA damage, is detected in SIPS as well as replicative senescent cells. Furthermore, both processes persistently induce cell cycle checkpoint mechanisms, indicating DNA damage created by ionizing radiation induces SIPS in normal cells, possibly by the same mechanisms as those occurring in replicative senescence. Interestingly, IR induces SIPS not only in normal cells, but also in tumor cells. Due to the expression of telomerase in tumor cells, telomere-dependent replicative senescence does not occur. However, SIPS is induced under certain conditions after IR exposure. Thus, cell death triggered by IR can be attributed to apoptosis or SIPS in tumor cells. However, metabolic function remains intact in SIPS-induced cancer cells, and recent studies show that senescence eliminate cells undergoing SIPS secrete various kinds of factors outside the cell, changing the microenvironment. Evidence using co-culture systems containing normal senescent stromal cells and epithelial tumor cells show that factors secreted from senescent stroma cells promote the growth of tumor epithelial cells both in vitro and in vivo. Thus, regulation of factors secreted from SIPS-induced stromal cells, as well as tumor cells, may affect radiotherapy.

[A model of multiple organ injury induced by Klebsiella pneumoniae pneumonia in aged rats].

PubMed

Li, Jian-sheng; Wang, Shou-fu; Qin, Jin-li; Zhang, Hui-jian; Li, Su-yun; Yu, Hai-bin; Wang, Feng; Liu, Si-hua; Li, Ya

2009-04-01

To reproduce a model of bacterial multiple organ injury (MOI) in aged rats. Male Sprague-Dawley (SD) rats were used. The young rats were divided into young control group (YCG, n=10) and young model group (YMG, n=15), and the elderly, aged control group (ACG, n=10) and aged model group (AMG, n=25). The model of rats with Klebsiella pneumoniae pneumonia was produced by tracheal instillation of the bacteria, and injury to various organs was observed and evaluated with changes in biochemical parameters, pathological pictures and mortality. Between YMG and AMG, the mortality rates were 33.33% (5/15) and 60.00% (15/25), respectively, at 24 hours after instillation of the bacteria. Compared with YCG and ACG, the neutrophil percentage and white blood cell (WBC) counts in peripheral blood increased significantly in YMG and AMG groups (all P<0.01), the rates of dysfunction of the lungs, the heart and the liver, were 60%-100%. The respiratory dysfunction was evidenced by an increase in the arterial partial pressure of carbon dioxide (PaCO(2), P<0.01), and a decrease in the arterial partial pressure of oxygen (PaO(2), P<0.05 or P<0.01). Myocardial dysfunction was shown by a the sharp increase in creatine kinase (CK), creatine kinase isoenzyme MB (CK-MB) and lactate dehydrogenase (LDH), and that of the liver by changes in alanine aminotransferase (ALT) and aspartate aminotransferase (AST, P<0.05 or P<0.01). The pathological changes under light and electronic microscopy were obvious, and the main feature was infiltration of the inflammatory cells. Compared with YMG, PaO(2) in AMG dropped significantly, PaCO(2) increased, CK, CK-MB, LDH, ALT and AST also increased significantly (P<0.05 or P<0.01). The scores of pathological injury in the lungs, the heart and the small intestine in the AMG were obviously higher than that in YMG group (all P<0.05), and the same was trend in the liver and the kidney. The model of bacterial MOI in aged rats is reproduced successfully, and it mimics the pathogenesis of multiple organ dysfunction syndrome (MODS) which initiates from infection in the lungs. The model is simple and convenient to replicate with a high success rate. The MOI in the aged rats is characterized by the severity of the organ injury and a high mortality rate.

Synthesis and characterization of sulfur-voided cubanes. Structural analogues for the MoFe(3)S(3) subunit in the nitrogenase cofactor.

PubMed

Coucouvanis, Dimitri; Han, Jaehong; Moon, Namdoo

2002-01-16

A new class of Mo/Fe/S clusters with the MoFe(3)S(3) core has been synthesized in attempts to model the FeMo-cofactor in nitrogenase. These clusters are obtained in reactions of the (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et (I), (n)Pr (II)] clusters with CO. The new clusters include those preliminarily reported: (Cl(4)-cat)MoFe(3)S(3)(PEt(3))(2)(CO)(6) (III), (Cl(4)-cat)(O)MoFe(3)S(3)(PEt(3))(3)(CO)(5) (IV), (Cl(4)-cat)(Pyr)MoFe(3)S(3)(PEt(3))(2)(CO)(6) (VI), and (Cl(4)-cat)(Pyr)MoFe(3)S(3)(P(n)Pr(3))(3)(CO)(4) (VIII). In addition the new (Cl(4)-cat)(O)MoFe(3)S(3)(P(n)Pr(3))(3)(CO)(5) cluster (IVa), the (Cl(4)-cat)(O)MoFe(3)S(3)(PEt(3))(2)(CO)(6)cluster (V), the (Cl(4)-cat)(O)MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (Va), the (Cl(4)-cat)(Pyr)MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (VIa), and the (Cl(4)-cat)(P(n)Pr(3))MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (VII) also are reported. Clusters III-VIII have been structurally and spectroscopically characterized. EPR, zero-field (57)Fe-Mössbauer spectroscopic characterizations, and magnetic susceptibility measurements have been used for a tentative assignment of the electronic and oxidation states of the MoFe(3)S(3) sulfur-voided cuboidal clusters. A structural comparison of the clusters with the MoFe(3)S(3) subunit of the FeMo-cofactor has led to the suggestion that the storage of reducing equivalents into M-M bonds, and their use in the reduction of substrates, may occur with the FeMo-cofactor, which also appears to have M-M bonding. On the basis of this argument, a possible N(2)-binding and reduction mechanism on the FeMoco-cofactor is proposed.

Environmental market factors associated with electronic health record adoption among cancer hospitals.

PubMed

Tarver, Will L; Menachemi, Nir

2017-02-22

Although recent literature has explored the relationship between various environmental market characteristics and the adoption of electronic health records (EHRs) among general, acute care hospitals, no such research currently exists for specialty hospitals, including those providing cancer care. The aim of the study was to examine the relationship between market characteristics and the adoption of EHRs among Commission on Cancer (CoC)-accredited hospitals. Secondary data on EHR adoption combined with hospital and environmental market characteristics were analyzed using logistic regression. Using the resource dependence theory, we examined how measures of munificence, complexity, and dynamism are related to the adoption of EHRs among CoC-accredited hospitals and, separately, hospitals not CoC-accredited. In a sample of 2,670 hospitals, 141 (0.05%) were academic-based CoC-accredited hospitals and 562 (21%) were community-based CoC-accredited hospitals. Measures of munificence such as cancer incidence rates (OR = 0.99, CI [0.99, 1.00], p = .020) and percentage population aged 65+ (OR = 0.99, CI [0.99, 1.00], p = .001) were negatively associated with basic EHR adoption, whereas urban location was positively associated with comprehensive EHR adoption (OR = 3.07, CI [0.89, 10.61], p = .076) for community-based CoC-accredited hospitals. Measures of complexity such as hospitals in areas with less competition were less likely to adopt a basic EHR (OR = 0.33, CI [0.19, 0.96], p = .005), whereas Medicare Managed Care penetration was positively associated with comprehensive EHR adoption (OR = 1.02, CI [1.00, 1.05], p = .070) among community-based CoC-accredited hospitals. Lastly, dynamism, measured as population change, was negatively associated with the adoption of comprehensive EHRs (OR = 0.99, CI [0.99, 1.00], p = .070) among academic-based CoC-accredited hospitals. A greater understanding of the environment's relationship to health information technology adoption in cancer hospitals will help stakeholders in these institutions make informed strategic decisions about information technology investments guided by their facilities' respective environmental factors. The results of this study may also be useful to hospital chief information officers and chief executive officers seeking to either improve their quality of care or achieve and maintain accreditation in providing cancer care.

Formation of ternary CaUO2(CO3)3(2-) and Ca2UO2(CO3)3(aq) complexes under neutral to weakly alkaline conditions.

PubMed

Lee, Jun-Yeop; Yun, Jong-Il

2013-07-21

The chemical behavior of ternary Ca-UO2-CO3 complexes was investigated by using time-resolved laser fluorescence spectroscopy (TRLFS) in combination with EDTA complexation at pH 7-9. A novel TRLFS revealed two distinct fluorescence lifetimes of 12.7 ± 0.2 ns and 29.2 ± 0.4 ns for uranyl complexes which were formed increasingly dependent upon the calcium ion concentration, even though nearly indistinguishable fluorescence peak shapes and positions were measured for both Ca-UO2-CO3 complexes. For identifying the stoichiometric number of complexed calcium ions, slope analysis in terms of relative fluorescence intensity versus calcium concentration was employed in a combination with the complexation reaction of CaEDTA(2-) by adding EDTA. The formation of CaUO2(CO3)3(2-) and Ca2UO2(CO3)3(aq) was identified under given conditions and their formation constants were determined at I = 0.1 M Na/HClO4 medium, and extrapolated to infinitely dilute solution using specific ion interaction theory (SIT). As a result, the formation constants for CaUO2(CO3)3(2-) and Ca2UO2(CO3)3(aq) were found to be log β113(0) = 27.27 ± 0.14 and log β213(0) = 29.81 ± 0.19, respectively, providing that the ternary Ca-UO2-CO3 complexes were predominant uranium(vi) species at neutral to weakly alkaline pH in the presence of Ca(2+) and CO3(2-) ions.

Evidence for possible biological advantages of the newly emerging HIV-1 circulating recombinant form from Malaysia - CRF33_01B in comparison to its progenitors - CRF01_AE and subtype B.

PubMed

Lau, Katherine A; Wang, Bin; Miranda-Saksena, Monica; Boadle, Ross; Kamarulzaman, Adeeba; Ng, Kee-Peng; Saksena, Nitin K

2010-04-01

In Malaysia, co-circulation of CRF01_AE and subtype B has resulted in the emergence of the second generation derivative; CRF33_01B in approximately 20% of its HIV-1 infected individuals. Our objective was to identify possible biological advantages that CRF33_01B possesses over its progenitors. Biological and molecular comparisons of CRF33_01B against its parental subtypes clearly show that CRF33_01B replicated better in activated whole peripheral blood mononuclear cells (PBMCs) and CD4+ T-lymphocytes, but not monocyte-derived macrophages (MDMs). Also, its acquired fitness was greater than CRF01_AE but not subtype B. Moreover, CRF33_01B has higher rate of apoptotic cell death and syncytia induction compared to subtype B. These adaptive and survival abilities could have been acquired by CRF33_01B due to the incorporation of subtype B fragments into the gag-RT region of its full-length genome. Our studies confirm the previously held belief that HIV-1 strains may harbor enhanced biological fitness upon recombination. We therefore estimate a possible gradual replacement of the current predominance of CRF01_AE, as well as wider dissemination of CRF33_01B, together with the identification of other new CRF01_AE/B inter-subtype recombinants in Malaysia.

The Gag Cleavage Product, p12, is a Functional Constituent of the Murine Leukemia Virus Pre-Integration Complex

PubMed Central

Laham-Karam, Nihay; Selig, Sara; Ehrlich, Marcelo; Bacharach, Eran

2010-01-01

The p12 protein is a cleavage product of the Gag precursor of the murine leukemia virus (MLV). Specific mutations in p12 have been described that affect early stages of infection, rendering the virus replication-defective. Such mutants showed normal generation of genomic DNA but no formation of circular forms, which are markers of nuclear entry by the viral DNA. This suggested that p12 may function in early stages of infection but the precise mechanism of p12 action is not known. To address the function and follow the intracellular localization of the wt p12 protein, we generated tagged p12 proteins in the context of a replication-competent virus, which allowed for the detection of p12 at early stages of infection by immunofluorescence. p12 was found to be distributed to discrete puncta, indicative of macromolecular complexes. These complexes were localized to the cytoplasm early after infection, and thereafter accumulated adjacent to mitotic chromosomes. This chromosomal accumulation was impaired for p12 proteins with a mutation that rendered the virus integration-defective. Immunofluorescence demonstrated that intracellular p12 complexes co-localized with capsid, a known constituent of the MLV pre-integration complex (PIC), and immunofluorescence combined with fluorescent in situ hybridization (FISH) revealed co-localization of the p12 proteins with the incoming reverse transcribed viral DNA. Interactions of p12 with the capsid and with the viral DNA were also demonstrated by co-immunoprecipitation. These results imply that p12 proteins are components of the MLV PIC. Furthermore, a large excess of wt PICs did not rescue the defect in integration of PICs derived from mutant p12 particles, demonstrating that p12 exerts its function as part of this complex. Altogether, these results imply that p12 proteins are constituent of the MLV PIC and function in directing the PIC from the cytoplasm towards integration. PMID:21085616

Enhancement of the infectivity of SARS-CoV in BALB/c mice by IMP dehydrogenase inhibitors, including ribavirin.

PubMed

Barnard, Dale L; Day, Craig W; Bailey, Kevin; Heiner, Matthew; Montgomery, Robert; Lauridsen, Larry; Winslow, Scott; Hoopes, Justin; Li, Joseph K-K; Lee, Jongdae; Carson, Dennis A; Cottam, Howard B; Sidwell, Robert W

2006-08-01

Because of the conflicting data concerning the SARS-CoV inhibitory efficacy of ribavirin, an inosine monophosphate (IMP) dehydrogenase inhibitor, studies were done to evaluate the efficacy of ribavirin and other IMP dehydrogenase inhibitors (5-ethynyl-1-beta-D-ribofuranosylimidazole-4-carboxamide (EICAR), mizoribine, and mycophenolic acid) in preventing viral replication in the lungs of BALB/c mice, a replication model for severe acute respiratory syndrome (SARS) infections (Subbarao, K., McAuliffe, J., Vogel, L., Fahle, G., Fischer, S., Tatti, K., Packard, M., Shieh, W.J., Zaki, S., Murphy, B., 2004. Prior infection and passive transfer of neutralizing antibody prevent replication of severe acute respiratory syndrome coronavirus (SARS-CoV) in the respiratory tract of mice. J. Virol. 78, 3572-3577). Ribavirin given at 75 mg/kg 4 h prior to virus exposure and then given twice daily for 3 days beginning at day 0 was found to increase virus lung titers and extend the length of time that virus could be detected in the lungs of mice. Other IMP dehydrogenase inhibitors administered near maximum tolerated doses using the same dosing regimen as for ribavirin were found to slightly enhance virus replication in the lungs. In addition, ribavirin treatment seemed also to promote the production of pro-inflammatory cytokines 4 days after cessation of treatment, although after 3 days of treatment ribavirin inhibited pro-inflammatory cytokine production in infected mice, significantly reducing the levels of the cytokines IL-1alpha, interleukin-5 (IL-5), monocyte chemotactic protein-1 (MCP-1), and granulocyte-macrophage colony stimulating factor (GM-CSF). These findings suggest that ribavirin may actually contribute to the pathogenesis of SARS-CoV by prolonging and/or enhancing viral replication in the lungs. By not inhibiting viral replication in the lungs of infected mice, ribavirin treatment may have provided a continual source of stimulation for the inflammatory response thought to contribute to the pathogenesis of the infection. Our data do not support the use of ribavirin or other IMP dehydrogenase inhibitors for treating SARS infections in humans.

Influence of common mucosal co-factors on HIV infection in the female genital tract.

PubMed

Ferreira, Victor H; Kafka, Jessica K; Kaushic, Charu

2014-06-01

Women constitute almost half of HIV-infected population globally, and the female genital tract (FGT) accounts for approximately 40% of all new HIV infections worldwide. The FGT is composed of upper and lower parts, distinct in their morphological and functional characteristics. Co-factors in the genital microenvironment, such as presence of hormones, semen, and other sexually transmitted infections, can facilitate or deter HIV infection and play a critical role in determining susceptibility to HIV. In this review, we examine some of these co-factors and their potential influence. Presence of physical and chemical barriers such as epithelial tight junctions, mucus, and anti-microbial peptides can actively block and inhibit viral replication, presenting a significant deterrent to HIV. Upon exposure, HIV and other pathogens first encounter the genital epithelium: cells that express a wide repertoire of pattern recognition receptors that can recognize and directly initiate innate immune responses. These and other interactions in the genital tract can lead to direct and indirect inflammation and enhance the number of local target cells, immune activation, and microbial translocation, all of which promote HIV infection and replication. Better understanding of the dynamics of HIV transmission in the female genital tract would be invaluable for improving the design of prophylactic strategies against HIV. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Rev-binding aptamer and CMV promoter act as decoys to inhibit HIV replication.

PubMed

Konopka, K; Lee, N S; Rossi, J; Düzgüneş, N

2000-09-19

We examined whether the antiviral effect of an HIV-1 Rev-binding aptamer [RBE(apt)] could be enhanced by a ribozyme directed against the HIV-1 env gene, and whether the antiviral activity was affected by different promoters. The efficacy of the aptamer and ribozyme DNAs was tested in HeLa cells co-transfected with the HIV-1 proviral clones, HXBDeltaBgl or pNL4-3, using transferrin-lipoplexes. The RBE(apt) and anti-env ribozyme genes were inserted into the pTZU6+27 plasmid, or constructed under the control of the human cytomegalovirus (CMV) or Rous sarcoma virus (RSV) promoters. The parental vector plasmids were used as controls. Co-transfection of the pTZU6+27 RBE(apt) plasmid with HXBDeltaBgl, or pNL4-3, at a weight ratio of 5:1, inhibited p24 production by 70 and 45%, respectively. The RSV RBE(apt) plasmid co-transfected with either HIV clone, at the same weight ratio, reduced viral production by 88%. The addition of the anti-env ribozyme to the RSV RBE(apt) did not enhance its antiviral activity. When the constructs were under the control of the CMV promoter, the expression of the HIV plasmids was very low and was independent of the presence of the RBE(apt). Thus, the effect of the RBE(apt) was strongly dependent on the promoter of the tested construct. The anti-HIV activity of the CMV RBE(apt) construct was non-specific, because co-transfection with either pCMV. SPORT-betagal or pCMVlacZ significantly suppressed HIV production from the HIV proviral clones. The reduction in p24 could not be attributed to the non-specific toxicity of the transfection procedure. Transfection of acutely HIV-infected HeLa-CD4 cells with pCMV.SPORT-betagal reduced the p24 level by 35%, while the expression of the U6 RBE(apt) did not affect p24 production. The suppression of HIV production from the HIV proviral clones by the CMV promoter constructs in the co-transfection assays may be explained by competition for transcription factors (TFs) between HIV and CMV promoters. This observation points to the potential for misleading results in co-transfections involving CMV constructs and HIV.

The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes.

PubMed

Beattie, Thomas R; Bell, Stephen D

2011-01-01

Efficient processing of Okazaki fragments generated during discontinuous lagging-strand DNA replication is critical for the maintenance of genome integrity. In eukaryotes, a number of enzymes co-ordinate to ensure the removal of initiating primers from the 5'-end of each fragment and the generation of a covalently linked daughter strand. Studies in eukaryotic systems have revealed that the co-ordination of DNA polymerase δ and FEN-1 (Flap Endonuclease 1) is sufficient to remove the majority of primers. Other pathways such as that involving Dna2 also operate under certain conditions, although, notably, Dna2 is not universally conserved between eukaryotes and archaea, unlike the other core factors. In addition to the catalytic components, the DNA sliding clamp, PCNA (proliferating-cell nuclear antigen), plays a pivotal role in binding and co-ordinating these enzymes at sites of lagging-strand replication. Structural studies in eukaryotic and archaeal systems have revealed that PCNA-binding proteins can adopt different conformations when binding PCNA. This conformational malleability may be key to the co-ordination of these enzymes' activities.

Running Economy: Neuromuscular and Joint Stiffness Contributions in Trained Runners.

PubMed

Tam, Nicholas; Tucker, Ross; Santos-Concejero, Jordan; Prins, Danielle; Lamberts, Robert P

2018-05-29

It is debated whether running biomechanics make good predictors of running economy, with little known information about the neuromuscular and joint stiffness contributions to economical running gait. The aim of this study was to understand the relationship between certain neuromuscular and spatiotemporal biomechanical factors associated with running economy. Thirty trained runners performed a 6-minute constant-speed running set at 3.3 m∙s -1 , where oxygen consumption was assessed. Overground running trials were also performed at 3.3 m∙s -1 to assess kinematics, kinetics and muscle activity. Spatiotemporal gait variables, joint stiffness, pre-activation and stance phase muscle activity (gluteus medius; rectus femoris (RF); biceps femoris(BF); peroneus longus (PL); tibialis anterior (TA); gastrocnemius lateralis and medius (LG and MG) were variables of specific interest and thus determined. Additionally, pre-activation and ground contact of agonist:antagonist co-activation were calculated. More economical runners presented with short ground contact times (r=0.639, p<0.001) and greater strides frequencies (r=-0.630, p<0.001). Lower ankle and greater knee stiffness were associated with lower oxygen consumption (r=0.527, p=0.007 & r=0.384, p=0.043, respectively). Only LG:TA co-activation during stance were associated with lower oxygen cost of transport (r=0.672, p<0.0001). Greater muscle pre-activation and bi-articular muscle activity during stance were associated with more economical runners. Consequently, trained runners who exhibit greater neuromuscular activation prior to and during ground contact, in turn optimise spatiotemporal variables and joint stiffness, will be the most economical runners.

Fine-Tuning Synthesis of Yersinia pestis LcrV from Runaway-Like Replication Balanced-Lethal Plasmid in a Salmonella enterica Serovar Typhimurium Vaccine Induces Protection against a Lethal Y. pestis Challenge in Mice▿

PubMed Central

Torres-Escobar, Ascención; Juárez-Rodríguez, María Dolores; Gunn, Bronwyn M.; Branger, Christine G.; Tinge, Steven A.; Curtiss, Roy

2010-01-01

A balanced-lethal plasmid expression system that switches from low-copy-number to runaway-like high-copy-number replication (pYA4534) was constructed for the regulated delayed in vivo synthesis of heterologous antigens by vaccine strains. This is an antibiotic resistance-free maintenance system containing the asdA gene (essential for peptidoglycan synthesis) as a selectable marker to complement the lethal chromosomal ΔasdA allele in live recombinant attenuated Salmonella vaccines (RASVs) such as Salmonella enterica serovar Typhimurium strain χ9447. pYA4534 harbors two origins of replication, pSC101 and pUC (low and high copy numbers, respectively). The pUC replication origin is controlled by a genetic switch formed by the operator/promoter of the P22 cro gene (O/Pcro) (PR), which is negatively regulated by an arabinose-inducible P22 c2 gene located on both the plasmid and the chromosome (araC PBAD c2). The absence of arabinose, which is unavailable in vivo, triggers replication to a high-copy-number plasmid state. To validate these vector attributes, the Yersinia pestis virulence antigen LcrV was used to develop a vaccine against plague. An lcrV sequence encoding amino acids 131 to 326 (LcrV196) was optimized for expression in Salmonella, flanked with nucleotide sequences encoding the signal peptide (SS) and the carboxy-terminal domain (CT) of β-lactamase, and cloned into pYA4534 under the control of the Ptrc promoter to generate plasmid pYA4535. Our results indicate that the live Salmonella vaccine strain χ9447 harboring pYA4535 efficiently stimulated a mixed Th1/Th2 immune response that protected mice against lethal challenge with Y. pestis strain CO92 introduced through either the intranasal or subcutaneous route. PMID:20308296

BiP: Master Regulator of the Unfolded Protein Response and Crucial Factor in Flavivirus Biology


PubMed Central

Lewy, Tyler G.; Grabowski, Jeffrey M.; Bloom, Marshall E.

2017-01-01

Flaviviruses have an intimate relationship with their host cells, utilizing host proteins during replication. Much of viral genome replication and virion assembly occurs on and within the endoplasmic reticulum (ER). As a cellular protein folding hub, the ER provides an ideal environment for flaviviruses to replicate. Flaviviruses can interact with several ER processes, including the unfolded protein response (UPR), a cellular stress mechanism responsible for managing unfolded protein accumulation and ER stress. The UPR can alter the ER environment in several ways, including increasing ER volume and quantity of available chaperones, both of which can favor viral replication. BiP, a chaperone and master regulator of the UPR, has been demonstrated to play a key role in several flavivirus infections. Here we describe what is known in regard to BiP, its implicated role with flavivirus infection, and what remains to be discovered. PMID:28656015

BiP: Master Regulator of the Unfolded Protein Response and Crucial Factor in Flavivirus Biology
.

PubMed

Lewy, Tyler G; Grabowski, Jeffrey M; Bloom, Marshall E

2017-06-01

Flaviviruses have an intimate relationship with their host cells, utilizing host proteins during replication. Much of viral genome replication and virion assembly occurs on and within the endoplasmic reticulum (ER). As a cellular protein folding hub, the ER provides an ideal environment for flaviviruses to replicate. Flaviviruses can interact with several ER processes, including the unfolded protein response (UPR), a cellular stress mechanism responsible for managing unfolded protein accumulation and ER stress. The UPR can alter the ER environment in several ways, including increasing ER volume and quantity of available chaperones, both of which can favor viral replication. BiP, a chaperone and master regulator of the UPR, has been demonstrated to play a key role in several flavivirus infections. Here we describe what is known in regard to BiP, its implicated role with flavivirus infection, and what remains to be discovered.

Co-occurrence of IBS and symptoms of anxiety or depression, among Norwegian twins, is influenced by both heredity and intrauterine growth.

PubMed

Bengtson, May-Bente; Aamodt, Geir; Vatn, Morten H; Harris, Jennifer R

2015-02-05

Environmental and genetic factors contribute to variation in irritable bowel syndrome (IBS), anxiety and depression. Comorbidity between these disorders is high. A previous investigation of our population-based twin cohort revealed that low birth weight increased the risk for development of IBS, with environmental influences in utero as the most relevant contributing factor. We hypothesise that both intrauterine and genetic factors influence the co-occurrence of IBS and symptoms of anxiety and depression. A postal questionnaire sent to 12700 Norwegian twins born between 1967 and 1979 comprised a checklist of 31 illnesses and symptoms, including IBS and symptoms of anxiety and depression. The influence of genetic factors and intrauterine growth on comorbidity between these disorders were analysed in the full sample and compared to those based on only monozygotic (MZ) twin pairs discordant for IBS (95 pairs) in birth weight group < 2500 g and ≥ 2500 g. In the co-twin analyses restricted growth (birth weight < 2500 g) was significantly associated with anxiety and depression (average birth weight difference of 181.0 g (p <0.0001) and 249.9 g (p < 0.0001), respectively). The analysis of the full sample revealed that IBS was significantly associated with symptoms of anxiety (adjusted OR = 2.5, 95% CI: 1.9, 3.3) and depression (adjusted OR = 2.3. 95% CI: 1.8, 3.0). Analyses of MZ pairs discordant for IBS indicated significant associations between IBS and symptoms of anxiety (OR = 3.7, 95% CI: 1.3, 10.5) and between IBS and symptoms of depression (OR = 4.2, 95% CI: 1.7, 9.9) only in the birth weight group below 2500 g. Our findings suggest that genetic factors partly explain the association between IBS and symptoms of anxiety and depression. In the low range of birth weight (<2500 g), restricted fetal growth seems to be a common contributing factor to the co-occurrence between these disorders.

Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake.

PubMed

Tanaka, Toshiko; Ngwa, Julius S; van Rooij, Frank J A; Zillikens, M Carola; Wojczynski, Mary K; Frazier-Wood, Alexis C; Houston, Denise K; Kanoni, Stavroula; Lemaitre, Rozenn N; Luan, Jian'an; Mikkilä, Vera; Renstrom, Frida; Sonestedt, Emily; Zhao, Jing Hua; Chu, Audrey Y; Qi, Lu; Chasman, Daniel I; de Oliveira Otto, Marcia C; Dhurandhar, Emily J; Feitosa, Mary F; Johansson, Ingegerd; Khaw, Kay-Tee; Lohman, Kurt K; Manichaikul, Ani; McKeown, Nicola M; Mozaffarian, Dariush; Singleton, Andrew; Stirrups, Kathleen; Viikari, Jorma; Ye, Zheng; Bandinelli, Stefania; Barroso, Inês; Deloukas, Panos; Forouhi, Nita G; Hofman, Albert; Liu, Yongmei; Lyytikäinen, Leo-Pekka; North, Kari E; Dimitriou, Maria; Hallmans, Goran; Kähönen, Mika; Langenberg, Claudia; Ordovas, Jose M; Uitterlinden, André G; Hu, Frank B; Kalafati, Ioanna-Panagiota; Raitakari, Olli; Franco, Oscar H; Johnson, Andrew; Emilsson, Valur; Schrack, Jennifer A; Semba, Richard D; Siscovick, David S; Arnett, Donna K; Borecki, Ingrid B; Franks, Paul W; Kritchevsky, Stephen B; Lehtimäki, Terho; Loos, Ruth J F; Orho-Melander, Marju; Rotter, Jerome I; Wareham, Nicholas J; Witteman, Jacqueline C M; Ferrucci, Luigi; Dedoussis, George; Cupples, L Adrienne; Nettleton, Jennifer A

2013-06-01

Macronutrient intake varies substantially between individuals, and there is evidence that this variation is partly accounted for by genetic variants. The objective of the study was to identify common genetic variants that are associated with macronutrient intake. We performed 2-stage genome-wide association (GWA) meta-analysis of macronutrient intake in populations of European descent. Macronutrients were assessed by using food-frequency questionnaires and analyzed as percentages of total energy consumption from total fat, protein, and carbohydrate. From the discovery GWA (n = 38,360), 35 independent loci associated with macronutrient intake at P < 5 × 10(-6) were identified and taken forward to replication in 3 additional cohorts (n = 33,533) from the DietGen Consortium. For one locus, fat mass obesity-associated protein (FTO), cohorts with Illumina MetaboChip genotype data (n = 7724) provided additional replication data. A variant in the chromosome 19 locus (rs838145) was associated with higher carbohydrate (β ± SE: 0.25 ± 0.04%; P = 1.68 × 10(-8)) and lower fat (β ± SE: -0.21 ± 0.04%; P = 1.57 × 10(-9)) consumption. A candidate gene in this region, fibroblast growth factor 21 (FGF21), encodes a fibroblast growth factor involved in glucose and lipid metabolism. The variants in this locus were associated with circulating FGF21 protein concentrations (P < 0.05) but not mRNA concentrations in blood or brain. The body mass index (BMI)-increasing allele of the FTO variant (rs1421085) was associated with higher protein intake (β ± SE: 0.10 ± 0.02%; P = 9.96 × 10(-10)), independent of BMI (after adjustment for BMI, β ± SE: 0.08 ± 0.02%; P = 3.15 × 10(-7)). Our results indicate that variants in genes involved in nutrient metabolism and obesity are associated with macronutrient consumption in humans. Trials related to this study were registered at clinicaltrials.gov as NCT00005131 (Atherosclerosis Risk in Communities), NCT00005133 (Cardiovascular Health Study), NCT00005136 (Family Heart Study), NCT00005121 (Framingham Heart Study), NCT00083369 (Genetic and Environmental Determinants of Triglycerides), NCT01331512 (InCHIANTI Study), and NCT00005487 (Multi-Ethnic Study of Atherosclerosis).

Indicators of replicative damage in equine tendon fibroblast monolayers

PubMed Central

2013-01-01

Background Superficial digital flexor tendon (SDFT) injuries of horses usually follow cumulative matrix microdamage; it is not known why the reparative abilities of tendon fibroblasts are overwhelmed or subverted. Relevant in vitro studies of this process require fibroblasts not already responding to stresses caused by the cell culture protocols. We investigated indicators of replicative damage in SDFT fibroblast monolayers, effects of this on their reparative ability, and measures that can be taken to reduce it. Results We found significant evidence of replicative stress, initially observing consistently large numbers of binucleate (BN) cells. A more variable but prominent feature was the presence of numerous gammaH2AX (γH2AX) puncta in nuclei, this being a histone protein that is phosphorylated in response to DNA double-stranded breaks (DSBs). Enrichment for injury detection and cell cycle arrest factors (p53 (ser15) and p21) occurred most frequently in BN cells; however, their numbers did not correlate with DNA damage levels and it is likely that the two processes have different causative mechanisms. Such remarkable levels of injury and binucleation are usually associated with irradiation, or treatment with cytoskeletal-disrupting agents. Both DSBs and BN cells were greatest in subconfluent (replicating) monolayers. The DNA-damaged cells co-expressed the replication markers TPX2/repp86 and centromere protein F. Once damaged in the early stages of culture establishment, fibroblasts continued to express DNA breaks with each replicative cycle. However, significant levels of cell death were not measured, suggesting that DNA repair was occurring. Comet assays showed that DNA repair was delayed in proportion to levels of genotoxic stress. Conclusions Researchers using tendon fibroblast monolayers should assess their “health” using γH2AX labelling. Continued use of early passage cultures expressing initially high levels of γH2AX puncta should be avoided for mechanistic studies and ex-vivo therapeutic applications, as this will not be resolved with further replicative cycling. Low density cell culture should be avoided as it enriches for both DNA damage and mitotic defects (polyploidy). As monolayers differing only slightly in baseline DNA damage levels showed markedly variable responses to a further injury, studies of effects of various stressors on tendon cells must be very carefully controlled. PMID:24025445

Interrelationships of metal transfer factor under wastewater reuse and soil pollution.

PubMed

Papaioannou, D; Kalavrouziotis, I K; Koukoulakis, P H; Papadopoulos, F; Psoma, P

2018-06-15

The transfer of heavy metals under soil pollution wastewater reuse was studied in a Greenhouse experiment using a randomized block design, including 6 treatments of heavy metals mixtures composed of Zn, Mn, Cd, Co, Cu, Cr, Ni, and Pb, where each metal was taking part in the mixture with 0, 10, 20, 30, 40, 50 mg/kg respectively, in four replications. The Beta vulgaris L (beet) was used as a test plant. It was found that the metal transfer factors were statistically significantly related to the: (i) DTPA extractable soil metals, (ii) the soil pollution level as assessed by the pollution indices, (iii) the soil pH, (iv) the beet dry matter yield and (v) the interactions between the heavy metals in the soil. It was concluded that the Transfer Factor is subjected to multifactor effects and its real nature is complex, and there is a strong need for further study for the understanding of its role in metal-plant relationships. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of obesity on IL-33/ST2 system in heart, adipose tissue and liver: study in the experimental model of Zucker rats.

PubMed

Ragusa, Rosetta; Cabiati, Manuela; Guzzardi, Maria Angela; D'Amico, Andrea; Giannessi, Daniela; Del Ry, Silvia; Caselli, Chiara

2017-04-01

Suppression of tumorigenicity 2 (ST2) mediates the effect of Interleukin-33 (IL-33). Few data are reported on the relationship between IL-33/ST2 and obesity. We aimed to investigate effects of obesity on IL-33/ST2 system in heart, adipose tissue and liver in a rodent model of obesity. The relationship of cardiac expression of IL-33/ST2 system with natriuretic peptides (NPs) system and inflammatory mediators was also studied. mRNA expression of IL-33/ST2 system was evaluated in cardiac, adipose and hepatic biopsies from obese Zucker rats (O) and controls (CO). Expression levels of sST2 was significantly lower in O rats compared with CO (p<0.05) in all tissues. Besides, the mRNA levels of IL-33 decreased significant in fat of O respect to CO, while, expression levels of ST2L was significantly higher in liver of CO than in O. A strong relationship of IL-33/ST2 with NPs and classical inflammatory mediators was observed in cardiac tissue. Expression of sST2 in cardiac, adipose and liver tissue decreased in O compared with controls, suggesting an involvement for IL-33/ST2 system in molecular mechanisms of obesity. The strong relationships with NP systems and inflammatory mediators could suggest an involvement for IL-33/ST2 in molecular pathways leading to cardiac dysfunction and inflammation associated with obesity. Copyright © 2017 Elsevier Inc. All rights reserved.

Initiation and termination of DNA replication during S phase in relation to cyclins D1, E and A, p21WAF1, Cdt1 and the p12 subunit of DNA polymerase δ revealed in individual cells by cytometry

PubMed Central

Darzynkiewicz, Zbigniew; Zhao, Hong; Zhang, Sufang; Marietta, Y.W.T. Lee; Ernest, Y.C. Lee; Zhang, Zhongtao

2015-01-01

During our recent studies on mechanism of the regulation of human DNA polymerase δ in preparation for DNA replication or repair, multiparameter imaging cytometry as exemplified by laser scanning cytometry (LSC) has been used to assess changes in expression of the following nuclear proteins associated with initiation of DNA replication: cyclin A, PCNA, Ki-67, p21WAF1, DNA replication factor Cdt1 and the smallest subunit of DNA polymerase δ, p12. In the present review, rather than focusing on Pol δ, we emphasize the application of LSC in these studies and outline possibilities offered by the concurrent differential analysis of DNA replication in conjunction with expression of the nuclear proteins. A more extensive analysis of the data on a correlation between rates of EdU incorporation, likely reporting DNA replication, and expression of these proteins, is presently provided. New data, specifically on the expression of cyclin D1 and cyclin E with respect to EdU incorporation as well as on a relationship between expression of cyclin A vs. p21WAF1 and Ki-67 vs. Cdt1, are also reported. Of particular interest is the observation that this approach makes it possible to assess the temporal sequence of degradation of cyclin D1, p21WAF1, Cdt1 and p12, each with respect to initiation of DNA replication and with respect to each other. Also the sequence or reappearance of these proteins in G2 after termination of DNA replication is assessed. The reviewed data provide a more comprehensive presentation of potential markers, whose presence or absence marks the DNA replicating cells. Discussed is also usefulness of these markers as indicators of proliferative activity in cancer tissues that may bear information on tumor progression and have a prognostic value. PMID:26059433

Initiation and termination of DNA replication during S phase in relation to cyclins D1, E and A, p21WAF1, Cdt1 and the p12 subunit of DNA polymerase δ revealed in individual cells by cytometry.

PubMed

Darzynkiewicz, Zbigniew; Zhao, Hong; Zhang, Sufang; Lee, Marietta Y W T; Lee, Ernest Y C; Zhang, Zhongtao

2015-05-20

During our recent studies on mechanism of the regulation of human DNA polymerase δ in preparation for DNA replication or repair, multiparameter imaging cytometry as exemplified by laser scanning cytometry (LSC) has been used to assess changes in expression of the following nuclear proteins associated with initiation of DNA replication: cyclin A, PCNA, Ki-67, p21(WAF1), DNA replication factor Cdt1 and the smallest subunit of DNA polymerase δ, p12. In the present review, rather than focusing on Pol δ, we emphasize the application of LSC in these studies and outline possibilities offered by the concurrent differential analysis of DNA replication in conjunction with expression of the nuclear proteins. A more extensive analysis of the data on a correlation between rates of EdU incorporation, likely reporting DNA replication, and expression of these proteins, is presently provided. New data, specifically on the expression of cyclin D1 and cyclin E with respect to EdU incorporation as well as on a relationship between expression of cyclin A vs. p21(WAF1) and Ki-67 vs. Cdt1, are also reported. Of particular interest is the observation that this approach makes it possible to assess the temporal sequence of degradation of cyclin D1, p21(WAF1), Cdt1 and p12, each with respect to initiation of DNA replication and with respect to each other. Also the sequence or reappearance of these proteins in G2 after termination of DNA replication is assessed. The reviewed data provide a more comprehensive presentation of potential markers, whose presence or absence marks the DNA replicating cells. Discussed is also usefulness of these markers as indicators of proliferative activity in cancer tissues that may bear information on tumor progression and have a prognostic value.

Cardiovascular Risk Factor Burden in Veterans and Non-Veterans with Parkinson Disease

PubMed Central

Kotagal, Vikas; Albin, Roger L.; Müller, Martijn L.T.M; Bohnen, Nicolaas I.

2018-01-01

Background Medical comorbidities, including cardiovascular risk factors such as hypertension and diabetes, influence disease progression in Parkinson disease (PD) and may be variably present in different clinical populations. Objective/Methods We conducted a retrospective nested case-control study of 29 Veterans with PD and 29 non-Veteran PD controls. The groups were matched for age, gender, and disease duration. Both groups underwent clinical and imaging testing as part of their participation in a larger cross-sectional PD observational study at our research center. Veterans were recruited primarily from movement disorders neurology clinics at the Ann Arbor Veterans Affairs (VA) Health System. Non-Veterans were recruited primarily from analogous clinics at the University of Michigan Health System. We explored differences in cardiovascular risks factor burden between the groups. Results Veterans with PD showed higher scores on the simplified Framingham 10-year general cardiovascular disease risk calculator (FR score; 27.3% (11.5) vs. 20.7% (6.8); t = −2.66, p = 0.011) and fewer years of self-reported education (14.5 (2.5) vs. 16.7 (2.6); t = 3.33, p = 0.002). After adjusting for age, disease duration, education, and the use of antihypertensive medications, Veterans showed higher FR scores (t = 2.95, p = 0.005) and a higher intra-subject ratio of FR score to age-and-gender normalized FR score (t = 2.49, p = 0.016), representing an elevated component of modifiable cardiovascular risk factor burden. Conclusion Cardiovascular comorbidities are common in Veterans with PD and may be more severe than in non-Veteran PD populations. These findings merit replication in other representative cohorts. Veterans may be a preferred population for clinical trials evaluating cardiovascular risk factor management on PD progression. PMID:29480230

Induction of necrosis via mitochondrial targeting of Melon necrotic spot virus replication protein p29 by its second transmembrane domain.

PubMed

Mochizuki, Tomofumi; Hirai, Katsuyuki; Kanda, Ayami; Ohnishi, Jun; Ohki, Takehiro; Tsuda, Shinya

2009-08-01

The virulence factor of Melon necrotic spot virus (MNSV), a virus that induces systemic necrotic spot disease on melon plants, was investigated. When the replication protein p29 was expressed in N. benthamiana using a Cucumber mosaic virus vector, necrotic spots appeared on the leaf tissue. Transmission electron microscopy revealed abnormal mitochondrial aggregation in these tissues. Fractionation of tissues expressing p29 and confocal imaging using GFP-tagged p29 revealed that p29 associated with the mitochondrial membrane as an integral membrane protein. Expression analysis of p29 deletion fragments and prediction of hydrophobic transmembrane domains (TMDs) in p29 showed that deletion of the second putative TMD from p29 led to deficiencies in both the mitochondrial localization and virulence of p29. Taken together, these results indicated that MNSV p29 interacts with the mitochondrial membrane and that p29 may be a virulence factor causing the observed necrosis.

Induction of necrosis via mitochondrial targeting of Melon necrotic spot virus replication protein p29 by its second transmembrane domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mochizuki, Tomofumi; Hirai, Katsuyuki; Kanda, Ayami

2009-08-01

The virulence factor of Melon necrotic spot virus (MNSV), a virus that induces systemic necrotic spot disease on melon plants, was investigated. When the replication protein p29 was expressed in N. benthamiana using a Cucumber mosaic virus vector, necrotic spots appeared on the leaf tissue. Transmission electron microscopy revealed abnormal mitochondrial aggregation in these tissues. Fractionation of tissues expressing p29 and confocal imaging using GFP-tagged p29 revealed that p29 associated with the mitochondrial membrane as an integral membrane protein. Expression analysis of p29 deletion fragments and prediction of hydrophobic transmembrane domains (TMDs) in p29 showed that deletion of the secondmore » putative TMD from p29 led to deficiencies in both the mitochondrial localization and virulence of p29. Taken together, these results indicated that MNSV p29 interacts with the mitochondrial membrane and that p29 may be a virulence factor causing the observed necrosis.« less

Amino Acids 257 to 288 of Mouse p48 Control the Cooperation of Polyomavirus Large T Antigen, Replication Protein A, and DNA Polymerase α-Primase To Synthesize DNA In Vitro

PubMed Central

Kautz, Armin R.; Weisshart, Klaus; Schneider, Annerose; Grosse, Frank; Nasheuer, Heinz-Peter

2001-01-01

Although p48 is the most conserved subunit of mammalian DNA polymerase α-primase (pol-prim), the polypeptide is the major species-specific factor for mouse polyomavirus (PyV) DNA replication. Human and murine p48 contain two regions (A and B) that show significantly lower homology than the rest of the protein. Chimerical human-murine p48 was prepared and coexpressed with three wild-type subunits of pol-prim, and four subunit protein complexes were purified. All enzyme complexes synthesized DNA on single-stranded (ss) DNA and replicated simian virus 40 DNA. Although the recombinant protein complexes physically interacted with PyV T antigen (Tag), we determined that the murine region A mediates the species specificity of PyV DNA replication in vitro. More precisely, the nonconserved phenylalanine 262 of mouse p48 is crucial for this activity, and pol-prim with mutant p48, h-S262F, supports PyV DNA replication in vitro. DNA synthesis on RPA-bound ssDNA revealed that amino acid (aa) 262, aa 266, and aa 273 to 288 are involved in the functional cooperation of RPA, pol-prim, and PyV Tag. PMID:11507202

Matrix Conditions and KLF2-Dependent Induction of Heme Oxygenase-1 Modulate Inhibition of HCV Replication by Fluvastatin

PubMed Central

Singethan, Katrin; Sirma, Hüseyin; Keller, Amelie Dorothea; Rosal, Sergio René Perez; Schrader, Jörg; Loscher, Christine; Volz, Tassilo; Bartenschlager, Ralf; Lohmann, Volker; Protzer, Ulrike; Dandri, Maura; Lohse, Ansgar W.; Tiegs, Gisa; Sass, Gabriele

2014-01-01

Background & Aims HMG-CoA-reductase-inhibitors (statins) have been shown to interfere with HCV replication in vitro. We investigated the mechanism, requirements and contribution of heme oxygenase-1(HO-1)-induction by statins to interference with HCV replication. Methods HO-1-induction by fluva-, simva-, rosuva-, atorva- or pravastatin was correlated to HCV replication, using non-infectious replicon systems as well as the infectious cell culture system. The mechanism of HO-1-induction by statins as well as its relevance for interference with HCV replication was investigated using transient or permanent knockdown cell lines. Polyacrylamide(PAA) gels of different density degrees or the Rho-kinase-inhibitor Hydroxyfasudil were used in order to mimic matrix conditions corresponding to normal versus fibrotic liver tissue. Results All statins used, except pravastatin, decreased HCV replication and induced HO-1 expression, as well as interferon response in vitro. HO-1-induction was mediated by reduction of Bach1 expression and induction of the Nuclear factor (erythroid-derived 2)-like 2 (NRF2) cofactor Krueppel-like factor 2 (KLF2). Knockdown of KLF2 or HO-1 abrogated effects of statins on HCV replication. HO-1-induction and anti-viral effects of statins were more pronounced under cell culture conditions mimicking advanced stages of liver disease. Conclusions Statin-mediated effects on HCV replication seem to require HO-1-induction, which is more pronounced in a microenvironment resembling fibrotic liver tissue. This implicates that certain statins might be especially useful to support HCV therapy of patients at advanced stages of liver disease. PMID:24801208

EFFECT OF LOW LEVEL CARBON MONOXIDE ON COMPENSATORY TRACKING AND EVENT MONITORING

EPA Science Inventory

Experiments by Putz et al. concerning the effect of carbon monoxide (CO) exposure on compensatory tracking and monitoring in healthy young men were replicated. Task and procedural variables were reproduced as closely as practical. Subjects were exposed to either room air or 100 p...

Ultrahigh Piezoelectric Properties in Textured (K,Na)NbO3 -Based Lead-Free Ceramics.

PubMed

Li, Peng; Zhai, Jiwei; Shen, Bo; Zhang, Shujun; Li, Xiaolong; Zhu, Fangyuan; Zhang, Xingmin

2018-02-01

High-performance lead-free piezoelectric materials are in great demand for next-generation electronic devices to meet the requirement of environmentally sustainable society. Here, ultrahigh piezoelectric properties with piezoelectric coefficients (d 33 ≈700 pC N -1 , d 33 * ≈980 pm V -1 ) and planar electromechanical coupling factor (k p ≈76%) are achieved in highly textured (K,Na)NbO 3 (KNN)-based ceramics. The excellent piezoelectric properties can be explained by the strong anisotropic feature, optimized engineered domain configuration in the textured ceramics, and facilitated polarization rotation induced by the intermediate phase. In addition, the nanodomain structures with decreased domain wall energy and increased domain wall mobility also contribute to the ultrahigh piezoelectric properties. This work not only demonstrates the tremendous potential of KNN-based ceramics to replace lead-based piezoelectrics but also provides a good strategy to design high-performance piezoelectrics by controlling appropriate phase and crystallographic orientation. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sociodemographic, clinical, and psychosocial factors associated with depression among type 2 diabetic outpatients in Black Lion General Specialized Hospital, Addis Ababa, Ethiopia: a cross-sectional study.

PubMed

Habtewold, Tesfa Dejenie; Alemu, Sisay Mulugeta; Haile, Yohannes Gebreegziabhere

2016-04-15

Depression is a common comorbidity among patients with type 2 diabetes. There are several reports supporting a bidirectional association between depression and type 2 diabetes. However, there is limited data from non-western countries. Therefore, the aim of this study was to assess the sociodemographic, clinical, and psychosocial factors associated with co-morbid depression among type 2 diabetic outpatients presenting to Black Lion General Specialized Hospital, Addis Ababa, Ethiopia. This institution based cross-sectional study design was conducted on a random sample of 276 type 2 diabetic outpatients. Type 2 diabetes patients were evaluated for depression by administering a validated nine-item Patient Health Questionnaire (PHQ-9). Risk factors for depression among type 2 diabetes patients were identified using multiple logistic regression analysis. In total, 264 study participants were interviewed with a response rate of 95.6%. The prevalence of depression was 44.7%. In the multivariate analysis, the statistically significant risk factors for depression were monthly family income ≤ 650 (p-value = 0.056; OR = 2.0; 95% CI = 1.01, 4.2), presence of ≥3 diabetic complications (p-value = 0.03; OR = 3.3; 95% CI = 1.1, 10.0), diabetic nephropathy (p-value = 0.01; OR = 2.9; 95% CI = 1.2, 6.7), negative life events (p-value = 0.01; OR = 2.4; 95% CI = 1.2, 4.5), and poor social support (p-value = 0.001; OR = 2.7; 95% CI = 1.5, 5.0). This study demonstrated that depression is a common co-morbid health problem with a prevalence rate of 44.7%. The presence of diabetic complications, low monthly family income, diabetic nephropathy, negative life event, and poor social support were the statistically significant risk factors associated with depression. We presume that the burden of mental health especially depression is high in the population with type 2 diabetes mellitus co-morbidity. Therefore, specific attention is needed to diagnose early and treat promptly.

The evolution of the Antarctic ice sheet at the Eocene-Oligocene Transition.

NASA Astrophysics Data System (ADS)

Ladant, Jean-Baptiste; Donnadieu, Yannick; Dumas, Christophe

2017-04-01

An increasing number of studies suggest that the Middle to Late Eocene has witnessed the waxing and waning of relatively small ephemeral ice sheets. These alternating episodes culminated in the Eocene-Oligocene transition (34 - 33.5 Ma) during which a sudden and massive glaciation occurred over Antarctica. Data studies have demonstrated that this glacial event is constituted of two 50 kyr-long steps, the first of modest (10 - 30 m of equivalent sea level) and the second of major (50 - 90 m esl) glacial amplitude, and separated by 200 kyrs. Since a decade, modeling studies have put forward the primary role of CO2 in the initiation of this glaciation, in doing so marginalizing the original "gateway hypothesis". Here, we investigate the impacts of CO2 and orbital parameters on the evolution of the ice sheet during the 500 kyrs of the EO transition using a tri-dimensional interpolation method. The latter allows precise orbital variations, CO2 evolution and ice sheet feedbacks (including the albedo) to be accounted for. Our results show that orbital variations are instrumental in initiating the first step of the EO glaciation but that the primary driver of the major second step is the atmospheric pCO2 crossing a modelled glacial threshold of 900 ppm. Although model-dependant, this higher glacial threshold makes a stronger case for ephemeral Middle-Late Eocene ice sheets. In addition, sensitivity tests demonstrate that the small first step only exists if the absolute pCO2 value remains within 100 ppm higher than the glacial threshold during the first 250 kyrs of the transition. Thereby, the pCO2 sufficiently counterbalances the strong insolation minima occurring at 33.9 and 33.8 Ma but is low enough to allow the ice sheet to nucleate. Nevertheless, questions remain as to what may cause this pCO2 drop.

Histone acetylation regulates the time of replication origin firing.

PubMed

Vogelauer, Maria; Rubbi, Liudmilla; Lucas, Isabelle; Brewer, Bonita J; Grunstein, Michael

2002-11-01

The temporal firing of replication origins throughout S phase in yeast depends on unknown determinants within the adjacent chromosomal environment. We demonstrate here that the state of histone acetylation of surrounding chromatin is an important regulator of temporal firing. Deletion of RPD3 histone deacetylase causes earlier origin firing and concurrent binding of the replication factor Cdc45p to origins. In addition, increased acetylation of histones in the vicinity of the late origin ARS1412 by recruitment of the histone acetyltransferase Gcn5p causes ARS1412 alone to fire earlier. These data indicate that histone acetylation is a direct determinant of the timing of origin firing.

The synthesis and structure of a chiral 1D aluminophosphate chain compound: d-Co(en) 3[AlP 2O 8]·6.5H 2O

NASA Astrophysics Data System (ADS)

Chen, Peng; Li, Jiyang; Yu, Jihong; Wang, Yu; Pan, Qinhe; Xu, Ruren

2005-06-01

A new chiral one-dimensional (1D) aluminophosphate chain compound [ d-Co(en) 3][AlP 2O 8]·6.5H 2O (designated AlPO-CJ22) has been hydrothermally synthesized by using the optically pure d-Co(en) 3I 3 complex as the template. Single-crystal structural analysis reveals that its structure is built up from alternating connection of AlO 4 and PO 2(=O 2) tetrahedra to form corner-shared Al 2P 2 four-membered ring (4-MR) chains. The d-Co(en) 33+ complex cations extended along the 2 1 screw axis interact with the inorganic chains through hydrogen-bonds of N⋯O atoms in a helical fashion. Optical rotation measurement shows that AlPO-CJ22 is chiral as with d-Co(en) 33+ complex cations. Crystal data: orthorhombic, I2 12 12 1, a=8.5573(8) Å, b=22.613(2) Å, c=22.605(2) Å, Z=8, R1=0.067, wR2=0.1291, and Flack parameter: -0.02(3). CCDC number: 254179.

Utilization of tigernut (Cyperus rotundus, L.) meal in diets for cockerel starters.

PubMed

Bamgbose, A M; Eruvbetine, Daisy; Dada, W

2003-09-01

The effect of feeding graded levels of tigernut meal (TGN) as a replacement for maize in the diets of cockerel starters on carcass characteristics and economics of feed conversion was assessed for 70 days. Tigernut replaced maize at 0%, 33.33%, 66.67% and 100% levels. A total of 120 day-old chicks were randomly allotted to four experimental diets such that each dietary treatment had three replicates of ten birds. Inclusion of TGN at 33.33% in cockerel diets supported better carcass yield in terms of high plucked, eviscerated, drumstick, thigh, neck, wing, heads, shanks, livers, hearts and lung weights without significant differences (P>0.05) in values obtained. However, there were significant difference (P<0.05) in back, breast, abdominal fat, gizzard, spleen, kidney and intestinal weights and lengths. Inclusion of TGN 100% level significantly depressed parameters assessed. The optimum replacement level of maize with TGN was 33.33% as this gave no significant reduction in carcass yield of the birds but a significant reduction in the cost of feed consumed. It required a feed cost of 42.90 ( 0.31 US dollars) to produce one kilogram weight gain on diet 2 (33.33%). Inclusion of TNG in the diets resulted in feed cost savings of 4.88% (D2), 8.17 (D3) and 8.90% (D4) respectively.

Crimean-Congo haemorrhagic fever virus replication in adult Hyalomma truncatum and Amblyomma variegatum ticks.

PubMed

Gonzalez, J P; Cornet, J P; Wilson, M L; Camicas, J L

1991-01-01

The kinetics of the replication of the Crimean-Congo haemorrhagic fever virus (CCHFV) was studied in intra-anally inoculated adult Hyalomma truncatum and Amblyomma variegatum ticks. The virus was re-isolated by suckling mouse inoculation and revealed by antigen capture with ground ticks and indirect immunofluorescence of haemolymph. The virus was detected in ticks in the first hours post-inoculation (p.i.) and its replication was observed from 36 h p.i. onwards. Virus titre reached a maximum within 3-5 days then decreased slowly to a level of at 2 log LD50/ml for several months until the end of observations. Several specific, non-identified factors seem to favour CCHFV replication in H. truncatum. Long-term virus persistence seems to occur in CCHFV-infected adult ticks.

[Effects of ciclosporin and tacrolimus on replication of hepatitis B virus in vitro: a comparative study].

PubMed

Xia, Wei-liang; Xie, Hai-yang; Shen, Yan; Wu, Li-ming; Zhang, Feng; Zheng, Shu-sen

2006-01-10

To investigate the effects of ciclosporin (CsA) and tacrolimus (FK506) on replication of hepatitis B virus (HBV) in vitro. HBV genome permanently transfected human liver cancer cells of the line HepG2.2.15 were cultured. CsA and FK506 at different concentrations were added into the culture fluid so as to identify the nontoxic concentrations by MTT method. Then the HepG2.2.15 cells were treated by CsA and FK506 at different nontoxic concentrations respectively for 4 days. ELISA was used to detect the HB surface antigen (HBsAg) and HB e antigen (HBeAg) in the supernatant. The relative replication level of HBV DNA was detected by slot blot analysis. MTT method confirmed that the nontoxic concentrations of CsA and FK506 were 0-40.0 microg/ml and 0-400 ng/ml respectively. After the treatment of CsA at the concentration of 1.3, 2.5, and 5.0 microg/ml, in comparison to the control group, the suppression rates of HBsAg expression in the HepG2.2.15 cells were 16.5% +/- 9.4%, 21.5% +/- 8.9%, and 33.1% +/- 5.3% respectively (all P < 0.05); the suppression rates of HBeAg expression in the HepG2.2.15 cells were 7.8% +/- 2.2%, 11.0% +/- 2.3%, and 20.8% +/- 1.5% respectively (all P < 0.05); and the HBV DNA replication levels were 56 +/- 16, 42 +/- 11, and 40 +/- 10 respectively (P > 0.05, P < 0.05, and P > 0.05). However, FK506 at different nontoxic concentrations showed no significant inhibitory effect on the levels of HBsAg, HBeAg, and HBV DNA. CsA dose-dependently inhibits the HBV replication in vitro, and FK506 does not exercise similar effects.

Induction of the tumor-suppressor p16(INK4a) within regenerative epithelial crypts in ulcerative colitis.

PubMed

Furth, Emma E; Gustafson, Karen S; Dai, Charlotte Y; Gibson, Steven L; Menard-Katcher, Paul; Chen, Tina; Koh, Jim; Enders, Greg H

2006-06-01

p16(INK4a) is a major tumor-suppressor protein, but its regulation and settings of fuction remain poorly understood. To explore the notion that p16 is induced in vivo in response to replicative stress, we examined p16 expression in tissues from human ulcerative colitis (UC; n = 25) and normal controls (n = 20). p16 was expressed strongly in UC-associated neoplasms (n = 17), as seen previously in sporadic colonic neoplasms. In non-neoplastic UC epithelium, p16 was expressed in 33% of crypts (the proliferative compartment) compared to < 1% of normal controls. p16 expression did not correlate with degree of inflammation but did correlate with the degree of crypt architecture distortion (P = .002)-a reflection of epithelial regeneration. In coimmunofluorescence studies with Ki67, p16 expression was associated with cell cycle arrest (P < .001). Both UC and normal crypts displayed evidence for the activation of the DNA damage checkpoint pathway, and p16 was induced in primary cultures of normal epithelial cells by ionizing irradiation (IR). However, induction by IR displayed delayed kinetics, implying that p16 is not an immediate target of the checkpoint pathway. These findings support a model in which p16 is induced as an "emergency brake" in cells experiencing sustained replicative stress.

Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium

PubMed Central

Moayyeri, Alireza; Hsu, Yi-Hsiang; Karasik, David; Estrada, Karol; Xiao, Su-Mei; Nielson, Carrie; Srikanth, Priya; Giroux, Sylvie; Wilson, Scott G.; Zheng, Hou-Feng; Smith, Albert V.; Pye, Stephen R.; Leo, Paul J.; Teumer, Alexander; Hwang, Joo-Yeon; Ohlsson, Claes; McGuigan, Fiona; Minster, Ryan L.; Hayward, Caroline; Olmos, José M.; Lyytikäinen, Leo-Pekka; Lewis, Joshua R.; Swart, Karin M.A.; Masi, Laura; Oldmeadow, Chris; Holliday, Elizabeth G.; Cheng, Sulin; van Schoor, Natasja M.; Harvey, Nicholas C.; Kruk, Marcin; del Greco M, Fabiola; Igl, Wilmar; Trummer, Olivia; Grigoriou, Efi; Luben, Robert; Liu, Ching-Ti; Zhou, Yanhua; Oei, Ling; Medina-Gomez, Carolina; Zmuda, Joseph; Tranah, Greg; Brown, Suzanne J.; Williams, Frances M.; Soranzo, Nicole; Jakobsdottir, Johanna; Siggeirsdottir, Kristin; Holliday, Kate L.; Hannemann, Anke; Go, Min Jin; Garcia, Melissa; Polasek, Ozren; Laaksonen, Marika; Zhu, Kun; Enneman, Anke W.; McEvoy, Mark; Peel, Roseanne; Sham, Pak Chung; Jaworski, Maciej; Johansson, Åsa; Hicks, Andrew A.; Pludowski, Pawel; Scott, Rodney; Dhonukshe-Rutten, Rosalie A.M.; van der Velde, Nathalie; Kähönen, Mika; Viikari, Jorma S.; Sievänen, Harri; Raitakari, Olli T.; González-Macías, Jesús; Hernández, Jose L.; Mellström, Dan; Ljunggren, Östen; Cho, Yoon Shin; Völker, Uwe; Nauck, Matthias; Homuth, Georg; Völzke, Henry; Haring, Robin; Brown, Matthew A.; McCloskey, Eugene; Nicholson, Geoffrey C.; Eastell, Richard; Eisman, John A.; Jones, Graeme; Reid, Ian R.; Dennison, Elaine M.; Wark, John; Boonen, Steven; Vanderschueren, Dirk; Wu, Frederick C.W.; Aspelund, Thor; Richards, J. Brent; Bauer, Doug; Hofman, Albert; Khaw, Kay-Tee; Dedoussis, George; Obermayer-Pietsch, Barbara; Gyllensten, Ulf; Pramstaller, Peter P.; Lorenc, Roman S.; Cooper, Cyrus; Kung, Annie Wai Chee; Lips, Paul; Alen, Markku; Attia, John; Brandi, Maria Luisa; de Groot, Lisette C.P.G.M.; Lehtimäki, Terho; Riancho, José A.; Campbell, Harry; Liu, Yongmei; Harris, Tamara B.; Akesson, Kristina; Karlsson, Magnus; Lee, Jong-Young; Wallaschofski, Henri; Duncan, Emma L.; O'Neill, Terence W.; Gudnason, Vilmundur; Spector, Timothy D.; Rousseau, François; Orwoll, Eric; Cummings, Steven R.; Wareham, Nick J.; Rivadeneira, Fernando; Uitterlinden, Andre G.; Prince, Richard L.; Kiel, Douglas P.; Reeve, Jonathan; Kaptoge, Stephen K.

2014-01-01

Quantitative ultrasound of the heel captures heel bone properties that independently predict fracture risk and, with bone mineral density (BMD) assessed by X-ray (DXA), may be convenient alternatives for evaluating osteoporosis and fracture risk. We performed a meta-analysis of genome-wide association (GWA) studies to assess the genetic determinants of heel broadband ultrasound attenuation (BUA; n = 14 260), velocity of sound (VOS; n = 15 514) and BMD (n = 4566) in 13 discovery cohorts. Independent replication involved seven cohorts with GWA data (in silico n = 11 452) and new genotyping in 15 cohorts (de novo n = 24 902). In combined random effects, meta-analysis of the discovery and replication cohorts, nine single nucleotide polymorphisms (SNPs) had genome-wide significant (P < 5 × 10−8) associations with heel bone properties. Alongside SNPs within or near previously identified osteoporosis susceptibility genes including ESR1 (6q25.1: rs4869739, rs3020331, rs2982552), SPTBN1 (2p16.2: rs11898505), RSPO3 (6q22.33: rs7741021), WNT16 (7q31.31: rs2908007), DKK1 (10q21.1: rs7902708) and GPATCH1 (19q13.11: rs10416265), we identified a new locus on chromosome 11q14.2 (rs597319 close to TMEM135, a gene recently linked to osteoblastogenesis and longevity) significantly associated with both BUA and VOS (P < 8.23 × 10−14). In meta-analyses involving 25 cohorts with up to 14 985 fracture cases, six of 10 SNPs associated with heel bone properties at P < 5 × 10−6 also had the expected direction of association with any fracture (P < 0.05), including three SNPs with P < 0.005: 6q22.33 (rs7741021), 7q31.31 (rs2908007) and 10q21.1 (rs7902708). In conclusion, this GWA study reveals the effect of several genes common to central DXA-derived BMD and heel ultrasound/DXA measures and points to a new genetic locus with potential implications for better understanding of osteoporosis pathophysiology. PMID:24430505

Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium.

PubMed

Moayyeri, Alireza; Hsu, Yi-Hsiang; Karasik, David; Estrada, Karol; Xiao, Su-Mei; Nielson, Carrie; Srikanth, Priya; Giroux, Sylvie; Wilson, Scott G; Zheng, Hou-Feng; Smith, Albert V; Pye, Stephen R; Leo, Paul J; Teumer, Alexander; Hwang, Joo-Yeon; Ohlsson, Claes; McGuigan, Fiona; Minster, Ryan L; Hayward, Caroline; Olmos, José M; Lyytikäinen, Leo-Pekka; Lewis, Joshua R; Swart, Karin M A; Masi, Laura; Oldmeadow, Chris; Holliday, Elizabeth G; Cheng, Sulin; van Schoor, Natasja M; Harvey, Nicholas C; Kruk, Marcin; del Greco M, Fabiola; Igl, Wilmar; Trummer, Olivia; Grigoriou, Efi; Luben, Robert; Liu, Ching-Ti; Zhou, Yanhua; Oei, Ling; Medina-Gomez, Carolina; Zmuda, Joseph; Tranah, Greg; Brown, Suzanne J; Williams, Frances M; Soranzo, Nicole; Jakobsdottir, Johanna; Siggeirsdottir, Kristin; Holliday, Kate L; Hannemann, Anke; Go, Min Jin; Garcia, Melissa; Polasek, Ozren; Laaksonen, Marika; Zhu, Kun; Enneman, Anke W; McEvoy, Mark; Peel, Roseanne; Sham, Pak Chung; Jaworski, Maciej; Johansson, Åsa; Hicks, Andrew A; Pludowski, Pawel; Scott, Rodney; Dhonukshe-Rutten, Rosalie A M; van der Velde, Nathalie; Kähönen, Mika; Viikari, Jorma S; Sievänen, Harri; Raitakari, Olli T; González-Macías, Jesús; Hernández, Jose L; Mellström, Dan; Ljunggren, Osten; Cho, Yoon Shin; Völker, Uwe; Nauck, Matthias; Homuth, Georg; Völzke, Henry; Haring, Robin; Brown, Matthew A; McCloskey, Eugene; Nicholson, Geoffrey C; Eastell, Richard; Eisman, John A; Jones, Graeme; Reid, Ian R; Dennison, Elaine M; Wark, John; Boonen, Steven; Vanderschueren, Dirk; Wu, Frederick C W; Aspelund, Thor; Richards, J Brent; Bauer, Doug; Hofman, Albert; Khaw, Kay-Tee; Dedoussis, George; Obermayer-Pietsch, Barbara; Gyllensten, Ulf; Pramstaller, Peter P; Lorenc, Roman S; Cooper, Cyrus; Kung, Annie Wai Chee; Lips, Paul; Alen, Markku; Attia, John; Brandi, Maria Luisa; de Groot, Lisette C P G M; Lehtimäki, Terho; Riancho, José A; Campbell, Harry; Liu, Yongmei; Harris, Tamara B; Akesson, Kristina; Karlsson, Magnus; Lee, Jong-Young; Wallaschofski, Henri; Duncan, Emma L; O'Neill, Terence W; Gudnason, Vilmundur; Spector, Timothy D; Rousseau, François; Orwoll, Eric; Cummings, Steven R; Wareham, Nick J; Rivadeneira, Fernando; Uitterlinden, Andre G; Prince, Richard L; Kiel, Douglas P; Reeve, Jonathan; Kaptoge, Stephen K

2014-06-01

Quantitative ultrasound of the heel captures heel bone properties that independently predict fracture risk and, with bone mineral density (BMD) assessed by X-ray (DXA), may be convenient alternatives for evaluating osteoporosis and fracture risk. We performed a meta-analysis of genome-wide association (GWA) studies to assess the genetic determinants of heel broadband ultrasound attenuation (BUA; n = 14 260), velocity of sound (VOS; n = 15 514) and BMD (n = 4566) in 13 discovery cohorts. Independent replication involved seven cohorts with GWA data (in silico n = 11 452) and new genotyping in 15 cohorts (de novo n = 24 902). In combined random effects, meta-analysis of the discovery and replication cohorts, nine single nucleotide polymorphisms (SNPs) had genome-wide significant (P < 5 × 10(-8)) associations with heel bone properties. Alongside SNPs within or near previously identified osteoporosis susceptibility genes including ESR1 (6q25.1: rs4869739, rs3020331, rs2982552), SPTBN1 (2p16.2: rs11898505), RSPO3 (6q22.33: rs7741021), WNT16 (7q31.31: rs2908007), DKK1 (10q21.1: rs7902708) and GPATCH1 (19q13.11: rs10416265), we identified a new locus on chromosome 11q14.2 (rs597319 close to TMEM135, a gene recently linked to osteoblastogenesis and longevity) significantly associated with both BUA and VOS (P < 8.23 × 10(-14)). In meta-analyses involving 25 cohorts with up to 14 985 fracture cases, six of 10 SNPs associated with heel bone properties at P < 5 × 10(-6) also had the expected direction of association with any fracture (P < 0.05), including three SNPs with P < 0.005: 6q22.33 (rs7741021), 7q31.31 (rs2908007) and 10q21.1 (rs7902708). In conclusion, this GWA study reveals the effect of several genes common to central DXA-derived BMD and heel ultrasound/DXA measures and points to a new genetic locus with potential implications for better understanding of osteoporosis pathophysiology.

Association of RANTES with the replication of severe acute respiratory syndrome coronavirus in THP-1 cells.

PubMed

Li, D; Wu, N; Yao, H; Bader, A; Brockmeyer, Norbert H; Altmeyer, P

2005-03-29

Severe acute respiratory syndrome (SARS) is a novel infectious disease which is characterized by an overaggressive immune response. Chemokines are important inflammatory mediators and regulate disease due to viral infection. In previous study, we found that SARS-CoV has the ability to replicate in mononuclear cells. In present work, we sought to characterize the replication of SARS-CoV at the presence of RANTES in THP-1 cells. To determine whether RANTES play an role in the process of SARS, THP-1 cells were incubated with heat-inactivated SARS-CoV and ELISA was used to test RANTES levels in the supernatants; Then the effect of dexamethasone on the induced secretion was evaluated. Real-time PCR was used to investigate the effort of RANTES on the replication of SARS-CoV in vitro. Macrophages, induced by THP-1 cells, were used as cell model. Inactive SARS-CoV could induce THP-1 cells secret RANTES and this increase effect could not be suppressed by DXM. RANTES itself could inhibit the replication of SARS-CoV in THP-1 cells when it was added into the culture before or at the same time with the virus; No inhibition effect was shown when RANTES were added into the culture after SARS-CoV infected the cells.

Emodin inhibits coxsackievirus B3 replication via multiple signalling cascades leading to suppression of translation.

PubMed

Zhang, Huifang M; Wang, Fengping; Qiu, Ye; Ye, Xin; Hanson, Paul; Shen, Hongxing; Yang, Decheng

2016-02-15

CVB3 (coxsackievirus 3) is a primary causal agent of viral myocarditis. Emodin is a natural compound isolated from certain plant roots. In the present study, we found that emodin inhibited CVB3 replication in vitro and in mice, and now we report an unrecognized mechanism by which emodin inhibits CVB3 replication through suppression of viral protein translation via multiple pathways. On one hand, emodin treatment inhibited Akt/mTOR (mammalian target of rapamycin) signalling and activated 4EBP1 (eukaryotic initiation factor 4R-binding protein 1), leading to suppression of translation initiation of ribosomal protein L32 encoded by a 5'-TOP (terminal oligopyrimidine) mRNA. On the other hand, emodin treatment differentially regulated multiple signal cascades, including Akt/mTORC1/p70(S6K) (p70 S6 kinase), ERK1/2 (extracellular-signal-regulated kinase 1/2)/p90(RSK) (p90 ribosomal S6 kinase) and Ca(2+)/calmodulin, leading to activation of eEF2K (eukaryotic elongation factor 2 kinase) and subsequent inactivation of eEF2 (eukaryotic elongation factor 2), resulting in inhibition of CVB3 VP1 (viral protein 1) synthesis. These data imply that eEF2K is a major factor mediating cross-talk of different arms of signalling cascades in this signal network. This notion was verified by either overexpressing eEF2K or treating the cells with siRNAs or eEF2K inhibitor A484954. We showed further that the emodin-induced decrease in p70(S6K) phosphorylation plays a dominant positive role in activation of eEF2K and in turn in conferring the antiviral effect of emodin. This finding was further solidified by expressing constitutively active and dominant-negative Akt. Collectively, our data reveal that emodin inhibits viral replication through impairing translational machinery and suppression of viral translation elongation. © 2016 Authors; published by Portland Press Limited.

Physical properties of inorganic PMW-PNN-PZT ceramics

NASA Astrophysics Data System (ADS)

Sin, Sang-Hoon; Yoo, Ju-hyun; Kim, Yong-Jin; Baek, Sam-ki; Ha, Jun-Soo; No, Chung-Han; Song, Hyun-Seon; Shin, Dong-Chan

2015-07-01

In this work, inorganic Pb(Mg1/2W1/2)0.03(Ni1/3Nb2/3)x(Zr0.5Ti0.5)0.97-xO3 (x = 0.02 ∼ 0.12) composition ceramics were fabricated by the conventional solid state reaction method. And then their micro structure and ferroelectric properties were investigated according to the amount of PNN substitution. Small amounts of Li2CO3 and CaCO3 were used in order to decrease the sintering temperature of the ceramics. The 0.10 mol PNN-substituted PMW-PNN- PZT ceramics sintered at 920°C showed the excellent physical properties of piezoelectric constant (d33), electromechanical coupling factor (kp), mechanical quality coefficient (Qm), and dielectric constant of 566 pC/N, 0.61, 73, and 2183, respectively.

Responses of the Emiliania huxleyi proteome to ocean acidification.

PubMed

Jones, Bethan M; Iglesias-Rodriguez, M Debora; Skipp, Paul J; Edwards, Richard J; Greaves, Mervyn J; Young, Jeremy R; Elderfield, Henry; O'Connor, C David

2013-01-01

Ocean acidification due to rising atmospheric CO2 is expected to affect the physiology of important calcifying marine organisms, but the nature and magnitude of change is yet to be established. In coccolithophores, different species and strains display varying calcification responses to ocean acidification, but the underlying biochemical properties remain unknown. We employed an approach combining tandem mass-spectrometry with isobaric tagging (iTRAQ) and multiple database searching to identify proteins that were differentially expressed in cells of the marine coccolithophore species Emiliania huxleyi (strain NZEH) between two CO2 conditions: 395 (∼current day) and ∼1340 p.p.m.v. CO2. Cells exposed to the higher CO2 condition contained more cellular particulate inorganic carbon (CaCO3) and particulate organic nitrogen and carbon than those maintained in present-day conditions. These results are linked with the observation that cells grew slower under elevated CO2, indicating cell cycle disruption. Under high CO2 conditions, coccospheres were larger and cells possessed bigger coccoliths that did not show any signs of malformation compared to those from cells grown under present-day CO2 levels. No differences in calcification rate, particulate organic carbon production or cellular organic carbon: nitrogen ratios were observed. Results were not related to nutrient limitation or acclimation status of cells. At least 46 homologous protein groups from a variety of functional processes were quantified in these experiments, of which four (histones H2A, H3, H4 and a chloroplastic 30S ribosomal protein S7) showed down-regulation in all replicates exposed to high CO2, perhaps reflecting the decrease in growth rate. We present evidence of cellular stress responses but proteins associated with many key metabolic processes remained unaltered. Our results therefore suggest that this E. huxleyi strain possesses some acclimation mechanisms to tolerate future CO2 scenarios, although the observed decline in growth rate may be an overriding factor affecting the success of this ecotype in future oceans.

Responses of the Emiliania huxleyi Proteome to Ocean Acidification

PubMed Central

Jones, Bethan M.; Iglesias-Rodriguez, M. Debora; Skipp, Paul J.; Edwards, Richard J.; Greaves, Mervyn J.; Young, Jeremy R.; Elderfield, Henry; O'Connor, C. David

2013-01-01

Ocean acidification due to rising atmospheric CO2 is expected to affect the physiology of important calcifying marine organisms, but the nature and magnitude of change is yet to be established. In coccolithophores, different species and strains display varying calcification responses to ocean acidification, but the underlying biochemical properties remain unknown. We employed an approach combining tandem mass-spectrometry with isobaric tagging (iTRAQ) and multiple database searching to identify proteins that were differentially expressed in cells of the marine coccolithophore species Emiliania huxleyi (strain NZEH) between two CO2 conditions: 395 (∼current day) and ∼1340 p.p.m.v. CO2. Cells exposed to the higher CO2 condition contained more cellular particulate inorganic carbon (CaCO3) and particulate organic nitrogen and carbon than those maintained in present-day conditions. These results are linked with the observation that cells grew slower under elevated CO2, indicating cell cycle disruption. Under high CO2 conditions, coccospheres were larger and cells possessed bigger coccoliths that did not show any signs of malformation compared to those from cells grown under present-day CO2 levels. No differences in calcification rate, particulate organic carbon production or cellular organic carbon: nitrogen ratios were observed. Results were not related to nutrient limitation or acclimation status of cells. At least 46 homologous protein groups from a variety of functional processes were quantified in these experiments, of which four (histones H2A, H3, H4 and a chloroplastic 30S ribosomal protein S7) showed down-regulation in all replicates exposed to high CO2, perhaps reflecting the decrease in growth rate. We present evidence of cellular stress responses but proteins associated with many key metabolic processes remained unaltered. Our results therefore suggest that this E. huxleyi strain possesses some acclimation mechanisms to tolerate future CO2 scenarios, although the observed decline in growth rate may be an overriding factor affecting the success of this ecotype in future oceans. PMID:23593500

Monitoring for HHV-6 infection after renal transplantation: evaluation of risk factors for sustained viral replication.

PubMed

Luiz, Claudia R; Machado, Clarisse M; Canto, Cynthia L M; Christ, Silvia C C; Pestana, Jose O M; Kotton, Camille N; Camargo, Luis F A

2013-03-27

Human herpesvirus-6 (HHV-6) is known to reactivate after renal transplantation and has been associated with several clinical manifestations. Risk factors for sustained viral replication, however, remain unclear. Thirty consecutive kidney transplant patients were prospectively followed for HHV-6 replication between February 2007 and February 2008. Plasma samples for DNA detection were collected from the donor and the recipient before transplantation and from the recipient weekly for the first 2 months after transplantation and then every 2 weeks for 2 additional months. HHV-6 active infection was defined as detection of viral DNA in plasma, by polymerase chain reaction, in at least two consecutive samples over an interval of at least 1 week. Active viral infection was detected in 25% of the recipients before transplantation and 27% (8 of 30) of the patients after transplantation. The mean time to onset of viral replication was 28.1 days after transplantation and 7 of 8 (87.5%) were asymptomatic. Risk factors associated with active HHV-6 infection were receiving an organ from a living donor (P=0.028), recipients with IgM antibodies detected before transplantation (P=0.005), and pretransplantation recipient HHV-6 viral load more than 10,000 copies/mL plasma (P=0.034). Active HHV-6 infection occurs early after renal transplantation and is mostly asymptomatic. Donor or recipient infection may occur at the time of transplantation and are related to higher rates of posttransplantation infections.

Hypercapnia Response in Patients with Obesity-Hypoventilation Syndrome Treated with Non-Invasive Ventilation at Home.

PubMed

Fernández Álvarez, Ramón; Rubinos Cuadrado, Gemma; Ruiz Alvarez, Ines; Hermida Valverde, Tamara; Iscar Urrutia, Marta; Vázquez Lopez, María José; Casan Clara, Pere

2018-06-02

Respiratory center (RC) dysfunction has been implicated in the pathogenesis of obesity-hypoventilation syndrome (OHS), and often requires treatment with home non-invasive ventilation (NIV). Our objective was to measure the effect of NIV on RC function in patients with OHS, and the factors that determine such an effect. We performed a prospective, repeated measures study to evaluate hypercapnia response (HR) by determining the p01/pEtCO 2 ratio slope at baseline and after 6months of treatment with NIV in a group of OHS patients. A threshold of 0.22cmH 2 O/mmHg had previously been established in a control group, in order to differentiate optimal RC response from suboptimal RC response. A total of 36 cases were included, 19 men (52%) aged 65 (SD 9) years, 63% of whom had p01/pEtCO 2 below the reference value. Baseline p01/pEtCO 2 was 0.17 (SD: 0.14) cmH 2 O/mmHg and, after 6 months of NIV, 0.30 (SD: 0.22) cmH 2 O/mmHg (p=0.011). After 6months of treatment with NIV, depressed RC function persisted in 12 cases (33%). In total, 63% of OHS patients had RC dysfunction. The application of NIV improves RC function but not in all cases. Copyright © 2018 SEPAR. Publicado por Elsevier España, S.L.U. All rights reserved.

When a Social Experimenter Overwrites Effects of Salient Objects in an Individual Go/No-Go Simon Task - An ERP Study.

PubMed

Michel, René; Bölte, Jens; Liepelt, Roman

2018-01-01

When two persons share a Simon task, a joint Simon effect occurs. The task co-representation account assumes that the joint Simon effect is the product of a vicarious representation of the co-actor's task. In contrast, recent studies show that even (non-human) event-producing objects could elicit a Simon effect in an individual go/no-go Simon task arguing in favor of the referential coding account. For the human-induced Simon effect, a modulation of the P300 component in Electroencephalography (EEG) is typically considered as a neural indicator of the joint Simon effect and task co-representation. Showing that the object-induced Simon effects also modulates the P300 would lead to a re-evaluation of the interpretation of the P300 in individual go/no-go and joint Simon task contexts. To do so, the present study conceptually replicated Experiment 1 from Dolk et al. (2013a) adding EEG recordings and an experimenter controlling the EEG computer to test whether a modulation of the P300 can also be elicited by adding a Japanese waving cat to the task context. Subjects performed an individual go/no-go Simon task with or without a cat placed next to them. Results show an overall Simon effect regardless of the cat's presence and no modulatory influence of the cat on the P300 (Experiment 1), even when conceivably interfering context factors are diminished (Experiment 2). These findings may suggest that the presence of a spatially aligned experimenter in the laboratory may produce an overall Simon effect overwriting a possible modulation of the Japanese waving cat.

Nutritional and metabolic implications of replacing cornstarch with D-xylose in broiler chickens fed corn and soybean meal-based diet.

PubMed

Regassa, A; Kiarie, E; Sands, J S; Walsh, M C; Kim, W K; Nyachoti, C M

2017-02-01

Effects of substituting cornstarch with D-xylose on growth performance, nutrients digestibility, serum metabolites, and expression of select hepatic genes involved in glucose and lipid metabolism were investigated in broiler chickens. A total of 360 one-day-old male Ross chicks were fed 3 diets (n = 24; 5 chicks/cage) for 21 days. A control corn-soybean meal-based diet with 25% cornstarch was formulated to meet specifications. Two additional diets were formulated by substituting cornstarch with 5 or 15% D-xylose w/w. Growth performance and digestibility by index method were determined in 12 replicate cages. Birds in these replicates had free access to feed and water, the BW and feed intake (FI) were monitored weekly and the excreta samples were collected on d 18 to 20. The other 12 replicates were used for blood and liver sampling by serial slaughter. On d 18, baseline (t0) birds were sampled following a 12 h overnight fasting and birds allowed 30 min access to the feed; samples were subsequently taken at 60, 120, 180, 240, and 300 min post feeding. Serum metabolites (glucose, xylose, and insulin) were assayed at all time points, whereas expression of hepatic transcripts was evaluated at zero, 180 and 300 min. Xylose linearly reduced (P < 0.05) FI, BWG, gross energy digestibility, and feed conversion ratio (FCR) but increased (P < 0.05) serum xylose level. Serum glucose and insulin levels were higher (P < 0.05) in the post-fed state compared with baseline, irrespective of treatments. There was an interaction (P < 0.05) between diet and sampling time on the expression of hepatic genes. At t0, xylose linearly increased (P < 0.05) the expression of pyruvate carboxylase, Acetyl Co-A acethyltransferase 2 (ACAT2), and glucose transporter 2. Xylose linearly reduced (P < 0.05) the expression of ACAT2 at 300 min post feeding. In conclusion, 5% or more xylose reduced growth performance and utilization of nutrients linked to hepatic enzymes and transcription factors involved in glucose and lipid metabolism. © 2016 Poultry Science Association Inc.

Feeling the future: A meta-analysis of 90 experiments on the anomalous anticipation of random future events

PubMed Central

Bem, Daryl; Tressoldi, Patrizio; Rabeyron, Thomas; Duggan, Michael

2016-01-01

In 2011, one of the authors (DJB) published a report of nine experiments in the Journal of Personality and Social Psychology purporting to demonstrate that an individual’s cognitive and affective responses can be influenced by randomly selected stimulus events that do not occur until after his or her responses have already been made and recorded, a generalized variant of the phenomenon traditionally denoted by the term precognition. To encourage replications, all materials needed to conduct them were made available on request. We here report a meta-analysis of 90 experiments from 33 laboratories in 14 countries which yielded an overall effect greater than 6 sigma, z = 6.40, p = 1.2 × 10 -10  with an effect size (Hedges’ g) of 0.09. A Bayesian analysis yielded a Bayes Factor of 5.1 × 10 9, greatly exceeding the criterion value of 100 for “decisive evidence” in support of the experimental hypothesis. When DJB’s original experiments are excluded, the combined effect size for replications by independent investigators is 0.06, z = 4.16, p = 1.1 × 10 -5, and the BF value is 3,853, again exceeding the criterion for “decisive evidence.” The number of potentially unretrieved experiments required to reduce the overall effect size of the complete database to a trivial value of 0.01 is 544, and seven of eight additional statistical tests support the conclusion that the database is not significantly compromised by either selection bias or by intense “ p-hacking”—the selective suppression of findings or analyses that failed to yield statistical significance. P-curve analysis, a recently introduced statistical technique, estimates the true effect size of the experiments to be 0.20 for the complete database and 0.24 for the independent replications, virtually identical to the effect size of DJB’s original experiments (0.22) and the closely related “presentiment” experiments (0.21). We discuss the controversial status of precognition and other anomalous effects collectively known as psi. PMID:26834996

Predation of freshwater fish in environments with elevated carbon dioxide

USGS Publications Warehouse

Midway, Stephen R.; Hasler, Caleb T.; Wagner, Tyler; Suski, Cory D.

2017-01-01

Carbon dioxide (CO2) in fresh-water environments is poorly understood, yet in marine environments CO2 can affect fish behaviour, including predator–prey relationships. To examine changes in predator success in elevated CO2, we experimented with predatory Micropterus salmoides and Pimephales promelas prey. We used a two-factor fully crossed experimental design; one factor was 4-day (acclimation) CO2 concentration and the second factor CO2 concentration during 20-min predation experiments. Both factors had three treatment levels, including ambient partial pressure of CO2(pCO2; 0–1000 μatm), low pCO2 (4000–5000 μatm) and high pCO2 (8000–10 000 μatm). Micropterus salmoides was exposed to both factors, whereas P. promelas was not exposed to the acclimation factor. In total, 83 of the 96 P. promelas were consumed (n = 96 trials) and we saw no discernible effect of CO2 on predator success or time to predation. Failed strikes and time between failed strikes were too infrequent to model. Compared with marine systems, our findings are unique in that we not only saw no changes in prey capture success with increasing CO2, but we also used CO2 treatments that were substantially higher than those in past experiments. Our work demonstrated a pronounced resiliency of freshwater predators to elevated CO2 exposure, and a starting point for future work in this area.

Transferability of genome-wide associated loci for asthma in African Americans.

PubMed

Faruque, Mezbah U; Chen, Guanjie; Doumatey, Ayo P; Zhou, Jie; Huang, Hanxia; Shriner, Daniel; Adeyemo, Adebowale A; Rotimi, Charles N; Dunston, Georgia M

2017-01-02

Transferability of significantly associated loci or GWAS "hits" adds credibility to genotype-disease associations and provides evidence for generalizability across different ancestral populations. We sought evidence of association of known asthma-associated single nucleotide polymorphisms (SNPs) in an African American population. Subjects comprised 661 participants (261 asthma cases and 400 controls) from the Howard University Family Study. Forty-eight SNPs previously reported to be associated with asthma by GWAS were selected for testing. We adopted a combined strategy by first adopting an "exact" approach where we looked-up only the reported index SNP. For those index SNPs missing form our dataset, we used a "local" approach that examined all the regional SNPs in LD with the index SNP. Out of the 48 SNPs, our cohort had genotype data available for 27, which were examined for exact replication. Of these, two SNPs were found positively associated with asthma. These included: rs10508372 (OR = 1.567 [95%CI, 1.133-2.167], P = 0.0066) and rs2378383 (OR = 2.147 [95%CI, 1.149-4.013], P = 0.0166), located on chromosomal bands 10p14 and 9q21.31, respectively. Local replication of the remaining 21 loci showed association at two chromosomal loci (9p24.1-rs2381413 and 6p21.32-rs3132947; Bonferroni-corrected P values: 0.0033 and 0.0197, respectively). Of note, multiple SNPs in LD with rs2381413 located upstream of IL33 were significantly associated with asthma. This study has successfully transferred four reported asthma-associated loci in an independent African American population. Identification of several asthma-associated SNPs in the upstream of the IL33, a gene previously implicated in allergic inflammation of asthmatic airway, supports the generalizability of this finding.

Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis.

PubMed

Washington, Tracy A; Smith, Janet L; Grossman, Alan D

2017-10-01

DnaA is the widely conserved bacterial AAA+ ATPase that functions as both the replication initiator and a transcription factor. In many organisms, DnaA controls expression of its own gene and likely several others during growth and in response to replication stress. To evaluate the effects of DnaA on gene expression, separate from its role in replication initiation, we analyzed changes in mRNA levels in Bacillus subtilis cells with and without dnaA, using engineered strains in which dnaA is not essential. We found that dnaA was required for many of the changes in gene expression in response to replication stress. We also found that dnaA indirectly affected expression of several regulons during growth, including those controlled by the transcription factors Spo0A, AbrB, PhoP, SinR, RemA, Rok and YvrH. These effects were largely mediated by the effects of DnaA on expression of sda. DnaA activates transcription of sda, and Sda inhibits histidine protein kinases required for activation of the transcription factor Spo0A. We also found that loss of dnaA caused a decrease in the development of genetic competence. Together, our results indicate that DnaA plays an important role in modulating cell physiology, separate from its role in replication initiation. © 2017 John Wiley & Sons Ltd.

Parvovirus Minute Virus of Mice Induces a DNA Damage Response That Facilitates Viral Replication

PubMed Central

Adeyemi, Richard O.; Landry, Sebastien; Davis, Meredith E.; Weitzman, Matthew D.; Pintel, David J.

2010-01-01

Infection by DNA viruses can elicit DNA damage responses (DDRs) in host cells. In some cases the DDR presents a block to viral replication that must be overcome, and in other cases the infecting agent exploits the DDR to facilitate replication. We find that low multiplicity infection with the autonomous parvovirus minute virus of mice (MVM) results in the activation of a DDR, characterized by the phosphorylation of H2AX, Nbs1, RPA32, Chk2 and p53. These proteins are recruited to MVM replication centers, where they co-localize with the main viral replication protein, NS1. The response is seen in both human and murine cell lines following infection with either the MVMp or MVMi strains. Replication of the virus is required for DNA damage signaling. Damage response proteins, including the ATM kinase, accumulate in viral-induced replication centers. Using mutant cell lines and specific kinase inhibitors, we show that ATM is the main transducer of the signaling events in the normal murine host. ATM inhibitors restrict MVM replication and ameliorate virus-induced cell cycle arrest, suggesting that DNA damage signaling facilitates virus replication, perhaps in part by promoting cell cycle arrest. Thus it appears that MVM exploits the cellular DNA damage response machinery early in infection to enhance its replication in host cells. PMID:20949077

Differences in quality of life of women and men with drug-resistant epilepsy in Poland.

PubMed

Bala, Aleksandra; Szantroch, Marta; Gleinert, Alicja; Rysz, Andrzej; Marchel, Andrzej

2016-07-01

The aim of the study was to assess the differences in health-related quality of life in groups of men and women suffering with drug-resistant epilepsy and to determine which factors influence quality of life. The examined group consisted of 64 subjects with drug-resistant epilepsy - 31 men and 33 women. The mean duration of epilepsy was 17.56±8.92 and 19±9.56years, respectively. The following diagnostic tools were used: QOLIE-31-P, Wechsler Adult Intelligence Scale - Revised (WAIS-R (PL)), and Hamilton Rating Scale for Depression (HRSD). Scores in QOLIE-31-P did not differ significantly between groups of men and women with drug-resistant epilepsy; however, a more detailed analysis revealed certain disparities. Multiple regression analyses indicated that some distinct factors were associated with quality of life in each sex. In the group of women, there were no significant predictors of their quality of life. Among the group of men, depression intensity was the only statistically significant QoL predictor, explaining 16% of the variance (adjusted R(2)=0.16, F(6, 24)=19.7, p<0.01). Moreover, patients with depression had lowered scores in the Emotional Well-Being and Energy/Fatigue subscales, regardless of the sex. The study revealed that, despite similar scores in QOLIE-31-P, specific factors may differentially affect the quality of life of men and women with drug-resistant epilepsy in Poland. Nevertheless, replication of these results with a larger number of participants is needed for a more definitive conclusion. Copyright © 2016 Elsevier Inc. All rights reserved.

Dimensions of self-leadership: a German replication and extension.

PubMed

Müller, Güonter F

2006-10-01

In a sample of 167 German students three dimensions of self-leadership, i.e., constructive thoughts, natural reward creation, and proactive behavior, were replicated as when scale values of a German self-leadership questionnaire were subjected to confirmatory factor analysis very satisfactory fit-indices were obtained. In addition, dimensions of self-leadership correlated with entrepreneurial trait disposition (multiple R=0.46, p < .01), and entrepreneurial job orientation (multiple R=0.23, p < .05). Conclusions for further research and practical applications are discussed.

Effect of substituting increasing levels of organic Zn for inorganic Zn on performance, hematological and serum biochemical constituents, antioxidant status and immune response in rat.

PubMed

Nagalakshmi, D; Sridhar, K; Swain, P S; Reddy, A G

2016-01-01

The effect of replacing dietary Zn supplemented from inorganic (ZnCO 3 ) source with organic Zn (Zn methionine; Zn-met) was investigated in 72 rats (98.42 ± 1.483 g) by randomly allotting to 4 diets (6 replicates/diet, 3 rats/replicate). Basal diet was prepared with purified ingredients without Zn. The control diet (AIN-76A) contained 12 ppm of Zn from ZnCO 3 (100-I). In the other diets ZnCO 3 was replaced with Zn-met at the rates of 50 (50I:50O), 75 (25I:75O) or 100% (100-O). Weekly body weight and daily feed intake were recorded for 14 weeks. Blood was collected by retro-orbital puncture on the 70th and 80th day to determine haematological and various serum biochemical constituents, and antioxidant enzyme activities in haemolysate, respectively. Rats were antigenically challenged with sheep RBC on day 73 to assess humoral immune response (HIR), and on day 95 for cell mediated immune response (CMIR) and rats were sacrificed at the end of rearing period to collect liver, muscle, pancreas and kidneys for Zn estimation and oxidative stress markers in liver. The data were analysed using completely randomized design. Weight gain and feed intake, hematological and serum biochemical constituents, Zn content in organs (except liver) were not influenced by replacing ZnCO 3 with Zn-met. Zinc concentrations in the serum and liver were higher (P<0.05) with 50% replacement of ZnCO 3 with Zn-met compared to 0 or 100% replacement. Lower (P<0.05) lipid peroxidation and higher (P<0.05) glutathione peroxidase and glutathione reductase activities were observed with 50 and 75% replacement of ZnCO 3 with Zn-met compared to 0 or 100% replacement. Protein carbonyls and reduced glutathione in liver were not affected, while TBARS decreased (P<0.05) with substituting Zn-met (50-100%) for ZnCO 3 . The HIR and CMIR increased with increasing Zn-met supplementation and the highest response was observed with 75-100% replacement of ZnCO 3 with Zn-met. It is concluded that replacement of 50 or 75% of ZnCO 3 with Zn-met increased antioxidant and immune response in rats with no effect on growth.

Validation of the Self-Beliefs Related to Social Anxiety Scale

PubMed Central

Moulds, Michelle L.; Rapee, Ronald M.

2014-01-01

The importance of self-beliefs in prominent models of social phobia has led to the development of measures that tap this cognitive construct. The Self-Beliefs Related to Social Anxiety (SBSA) Scale is one such measure and taps the three maladaptive belief types proposed in Clark and Wells’s model of social phobia. This study aimed to replicate and extend previous research on the psychometric properties of the SBSA. Replicating previous research, in an (undiagnosed) undergraduate sample (n = 235), the SBSA was found to have a correlated three-factor structure using confirmatory factor analyses, and the SBSA and its subscales demonstrated good internal consistency and test–retest reliability. The SBSA and its subscales also had unique relationships with social anxiety and depression, the majority of which replicated previous research. Extending previous research, the SBSA and its subscales showed good incremental validity in the undergraduate sample and good discriminative validity using the undergraduate sample and a sample of individuals with social phobia (n = 33). The SBSA’s strong theoretical basis and the findings of this study suggest that the SBSA is an ideal research and clinical tool to assess the cognitions characteristic of social phobia. PMID:23575344

Chloroquine inhibits lytic replication of Kaposi's sarcoma-associated herpesvirus by disrupting mTOR and p38-MAPK activation.

PubMed

Yang, Mengtian; Huang, Lu; Li, Xiaojuan; Kuang, Ersheng

2016-09-01

Lytic infection is essential for the persistent infection and pathogenesis of Kaposi's sarcoma-associated herpesvirus (KSHV), and inhibiting KSHV lytic replication may effectively prevent the occurrence of KSHV-related diseases. Chloroquine (CQ), a well-known antimalarial drug and autophagy inhibitor, exerts broad-spectrum antiviral effects and shows anti-cancer therapeutic potential. However, the ability of CQ and its derivatives to control infection of oncogenic γ-herpesvirus remains undefined. Here we reveal that CQ suppresses KSHV lytic gene expression and virion production, and shows cytotoxicity toward KSHV lytically infected B cells at clinically acceptable doses. CQ suppresses mTOR and p38-MAPK pathway activation during KSHV lytic replication but not latent infection. Furthermore, CQ blocks Epstein-Barr virus (EBV) lytic replication via a distinct mechanism that is invoked to block virion production but does not affect viral gene expression. These results suggest that CQ is an effective antiviral drug against KSHV lytic infection. Our findings indicate that CQ treatment should be considered for controlling KSHV-related diseases, particularly for primary use in co-infection of KSHV with malaria. Copyright © 2016 Elsevier B.V. All rights reserved.

Replication of TPMT and ABCC3 genetic variants highly associated with cisplatin-induced hearing loss in children.

PubMed

Pussegoda, K; Ross, C J; Visscher, H; Yazdanpanah, M; Brooks, B; Rassekh, S R; Zada, Y F; Dubé, M-P; Carleton, B C; Hayden, M R

2013-08-01

Cisplatin is a widely used chemotherapeutic agent for the treatment of solid tumors. A serious complication of cisplatin treatment is permanent hearing loss. The aim of this study was to replicate previous genetic findings in an independent cohort of 155 pediatric patients. Associations were replicated for genetic variants in TPMT (rs12201199, P = 0.0013, odds ratio (OR) 6.1) and ABCC3 (rs1051640, P = 0.036, OR 1.8). A predictive model combining variants in TPMT, ABCC3, and COMT with clinical variables (patient age, vincristine treatment, germ-cell tumor, and cranial irradiation) significantly improved the prediction of hearing-loss development as compared with using clinical risk factors alone (area under the curve (AUC) 0.786 vs. 0.708, P = 0.00048). The novel combination of genetic and clinical factors predicted the risk of hearing loss with a sensitivity of 50.3% and a specificity of 92.7%. These findings provide evidence to support the importance of TPMT, COMT, and ABCC3 in the prediction of cisplatin-induced hearing loss in children.

Replication of TPMT and ABCC3 Genetic Variants Highly Associated With Cisplatin-Induced Hearing Loss in Children

PubMed Central

Pussegoda, K; Ross, CJ; Visscher, H; Yazdanpanah, M; Brooks, B; Rassekh, SR; Zada, YF; Dubé, M-P; Carleton, BC; Hayden, MR

2014-01-01

Cisplatin is a widely used chemotherapeutic agent for the treatment of solid tumors. A serious complication of cisplatin treatment is permanent hearing loss. The aim of this study was to replicate previous genetic findings in an independent cohort of 155 pediatric patients. Associations were replicated for genetic variants in TPMT (rs12201199, P = 0.0013, odds ratio (OR) 6.1) and ABCC3 (rs1051640, P = 0.036, OR 1.8). A predictive model combining variants in TPMT, ABCC3, and COMT with clinical variables (patient age, vincristine treatment, germ-cell tumor, and cranial irradiation) significantly improved the prediction of hearing-loss development as compared with using clinical risk factors alone (area under the curve (AUC) 0.786 vs. 0.708, P = 0.00048). The novel combination of genetic and clinical factors predicted the risk of hearing loss with a sensitivity of 50.3% and a specificity of 92.7%. These findings provide evidence to support the importance of TPMT, COMT, and ABCC3 in the prediction of cisplatin-induced hearing loss in children. PMID:23588304

Non-invasive ventilation in acute respiratory failure in children

PubMed Central

Abadesso, Clara; Nunes, Pedro; Silvestre, Catarina; Matias, Ester; Loureiro, Helena; Almeida, Helena

2012-01-01

The aim of this paper is to assess the clinical efficacy of non-invasive ventilation (NIV) in avoiding endotracheal intubation (ETI), to demonstrate clinical and gasometric improvement and to identify predictive risk factors associated with NIV failure. An observational prospective clinical study was carried out. Included Patients with acute respiratory disease (ARD) treated with NIV, from November 2006 to January 2010 in a Pediatric Intensive Care Unit (PICU). NIV was used in 151 patients with acute respiratory failure (ARF). Patients were divided in two groups: NIV success and NIV failure, if ETI was required. Mean age was 7.2±20.3 months (median: 1 min: 0,3 max.: 156). Main diagnoses were bronchiolitis in 102 (67.5%), and pneumonia in 44 (29%) patients. There was a significant improvement in respiratory rate (RR), heart rate (HR), pH, and pCO2 at 2, 6, 12 and 24 hours after NIV onset (P<0.05) in both groups. Improvement in pulse oximetric saturation/fraction of inspired oxygen (SpO2/FiO2) was verified at 2, 4, 6, 12 and 24 hours after NIV onset in the success group (P<0.001). In the failure group, significant SpO2/FiO2 improvement was only observed in the first 4 hours. NIV failure occurred in 34 patients (22.5%). Risk factors for NIV failure were apnea, prematurity, pneumonia, and bacterial co-infection (P<0.05). Independent risk factors for NIV failure were apneia (P<0.001; odds ratio 15.8; 95% confidence interval: 3.42–71.4) and pneumonia (P<0.001, odds ratio 31.25; 95% confidence interval: 8.33–111.11). There were no major complications related with NIV. In conclusion this study demonstrates the efficacy of NIV as a form of respiratory support for children and infants with ARF, preventing clinical deterioration and avoiding ETI in most of the patients. Risk factors for failure were related with immaturity and severe infection. PMID:22802994

Non-invasive ventilation in acute respiratory failure in children.

PubMed

Abadesso, Clara; Nunes, Pedro; Silvestre, Catarina; Matias, Ester; Loureiro, Helena; Almeida, Helena

2012-04-02

The aim of this paper is to assess the clinical efficacy of non-invasive ventilation (NIV) in avoiding endotracheal intubation (ETI), to demonstrate clinical and gasometric improvement and to identify predictive risk factors associated with NIV failure. An observational prospective clinical study was carried out. Included Patients with acute respiratory disease (ARD) treated with NIV, from November 2006 to January 2010 in a Pediatric Intensive Care Unit (PICU). NIV was used in 151 patients with acute respiratory failure (ARF). Patients were divided in two groups: NIV success and NIV failure, if ETI was required. Mean age was 7.2±20.3 months (median: 1 min: 0,3 max.: 156). Main diagnoses were bronchiolitis in 102 (67.5%), and pneumonia in 44 (29%) patients. There was a significant improvement in respiratory rate (RR), heart rate (HR), pH, and pCO(2) at 2, 6, 12 and 24 hours after NIV onset (P<0.05) in both groups. Improvement in pulse oximetric saturation/fraction of inspired oxygen (SpO(2)/FiO(2)) was verified at 2, 4, 6, 12 and 24 hours after NIV onset in the success group (P<0.001). In the failure group, significant SpO(2)/FiO(2) improvement was only observed in the first 4 hours. NIV failure occurred in 34 patients (22.5%). Risk factors for NIV failure were apnea, prematurity, pneumonia, and bacterial co-infection (P<0.05). Independent risk factors for NIV failure were apneia (P<0.001; odds ratio 15.8; 95% confidence interval: 3.42-71.4) and pneumonia (P<0.001, odds ratio 31.25; 95% confidence interval: 8.33-111.11). There were no major complications related with NIV. In conclusion this study demonstrates the efficacy of NIV as a form of respiratory support for children and infants with ARF, preventing clinical deterioration and avoiding ETI in most of the patients. Risk factors for failure were related with immaturity and severe infection.

Experimental determination of pCo perturbation factors for plane-parallel chambers

NASA Astrophysics Data System (ADS)

Kapsch, R. P.; Bruggmoser, G.; Christ, G.; Dohm, O. S.; Hartmann, G. H.; Schüle, E.

2007-12-01

For plane-parallel chambers used in electron dosimetry, modern dosimetry protocols recommend a cross-calibration against a calibrated cylindrical chamber. The rationale for this is the unacceptably large (up to 3-4%) chamber-to-chamber variations of the perturbation factors (pwall)Co, which have been reported for plane-parallel chambers of a given type. In some recent publications, it was shown that this is no longer the case for modern plane-parallel chambers. The aims of the present study are to obtain reliable information about the variation of the perturbation factors for modern types of plane-parallel chambers, and—if this variation is found to be acceptably small—to determine type-specific mean values for these perturbation factors which can be used for absorbed dose measurements in electron beams using plane-parallel chambers. In an extensive multi-center study, the individual perturbation factors pCo (which are usually assumed to be equal to (pwall)Co) for a total of 35 plane-parallel chambers of the Roos type, 15 chambers of the Markus type and 12 chambers of the Advanced Markus type were determined. From a total of 188 cross-calibration measurements, variations of the pCo values for different chambers of the same type of at most 1.0%, 0.9% and 0.6% were found for the chambers of the Roos, Markus and Advanced Markus types, respectively. The mean pCo values obtained from all measurements are \\bar{p}^Roos_Co = 1.0198, \\bar{p}^Markus_Co = 1.0175 and \\bar{p}^Advanced_Co = 1.0155 ; the relative experimental standard deviation of the individual pCo values is less than 0.24% for all chamber types; the relative standard uncertainty of the mean pCo values is 1.1%.

Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India.

PubMed

Saxena, Richa; Saleheen, Danish; Been, Latonya F; Garavito, Martha L; Braun, Timothy; Bjonnes, Andrew; Young, Robin; Ho, Weang Kee; Rasheed, Asif; Frossard, Philippe; Sim, Xueling; Hassanali, Neelam; Radha, Venkatesan; Chidambaram, Manickam; Liju, Samuel; Rees, Simon D; Ng, Daniel Peng-Keat; Wong, Tien-Yin; Yamauchi, Toshimasa; Hara, Kazuo; Tanaka, Yasushi; Hirose, Hiroshi; McCarthy, Mark I; Morris, Andrew P; Basit, Abdul; Barnett, Anthony H; Katulanda, Prasad; Matthews, David; Mohan, Viswanathan; Wander, Gurpreet S; Singh, Jai Rup; Mehra, Narinder K; Ralhan, Sarju; Kamboh, M Ilyas; Mulvihill, John J; Maegawa, Hiroshi; Tobe, Kazuyuki; Maeda, Shiro; Cho, Yoon S; Tai, E Shyong; Kelly, M Ann; Chambers, John C; Kooner, Jaspal S; Kadowaki, Takashi; Deloukas, Panos; Rader, Daniel J; Danesh, John; Sanghera, Dharambir K

2013-05-01

We performed a genome-wide association study (GWAS) and a multistage meta-analysis of type 2 diabetes (T2D) in Punjabi Sikhs from India. Our discovery GWAS in 1,616 individuals (842 case subjects) was followed by in silico replication of the top 513 independent single nucleotide polymorphisms (SNPs) (P < 10⁻³) in Punjabi Sikhs (n = 2,819; 801 case subjects). We further replicated 66 SNPs (P < 10⁻⁴) through genotyping in a Punjabi Sikh sample (n = 2,894; 1,711 case subjects). On combined meta-analysis in Sikh populations (n = 7,329; 3,354 case subjects), we identified a novel locus in association with T2D at 13q12 represented by a directly genotyped intronic SNP (rs9552911, P = 1.82 × 10⁻⁸) in the SGCG gene. Next, we undertook in silico replication (stage 2b) of the top 513 signals (P < 10⁻³) in 29,157 non-Sikh South Asians (10,971 case subjects) and de novo genotyping of up to 31 top signals (P < 10⁻⁴) in 10,817 South Asians (5,157 case subjects) (stage 3b). In combined South Asian meta-analysis, we observed six suggestive associations (P < 10⁻⁵ to < 10⁻⁷), including SNPs at HMG1L1/CTCFL, PLXNA4, SCAP, and chr5p11. Further evaluation of 31 top SNPs in 33,707 East Asians (16,746 case subjects) (stage 3c) and 47,117 Europeans (8,130 case subjects) (stage 3d), and joint meta-analysis of 128,127 individuals (44,358 case subjects) from 27 multiethnic studies, did not reveal any additional loci nor was there any evidence of replication for the new variant. Our findings provide new evidence on the presence of a population-specific signal in relation to T2D, which may provide additional insights into T2D pathogenesis.

Statistical evaluation of nutritional components impacting phycocyanin production Synechocystis SP.

PubMed Central

Deshmukh, Devendra V.; Puranik, Pravin R.

2012-01-01

Alkaliphilic cyanobacterial cultures were isolated from Lonar lake (MS, India). Among the set of cultures, Synechocystis sp, was studied for phycocyanin production. A maximum yield was obtained in BG-11 medium at optimized conditions (pH 10 and 16 h light). In order to increase the phycocyanin yield media optimization based on the eight media components a Plackett-Burman design of the 12 experimental trials was used. As per the analysis CaCl2, 2H2O and Na2CO3 have been found to be the most influencing media components at 95% significance. Further the optimum concentrations of these components were estimated following a Box Wilson Central Composite Design (CCD) with four star points and five replicates at the center points for each of two factors was adopted for optimization of these two media components. The results indicated that there was an interlinked influence of CaCl2, 2H2O and Na2CO3 on 98% significance. The maximum yield of phycocyanin (12% of dry wt) could be obtained at 0.058 g/l and 0.115 g/l of CaCl2, 2H2O and Na2CO3, respectively. PMID:24031838

The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome.

PubMed

van Bel, Nikki; van der Velden, Yme; Bonnard, Damien; Le Rouzic, Erwann; Das, Atze T; Benarous, Richard; Berkhout, Ben

2014-01-01

The viral integrase (IN) is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs). Although designed to interfere with the IN-LEDGF/p75 interaction to block HIV DNA integration during the early phase of HIV-1 replication, the major impact was surprisingly found on the process of virus maturation during the late phase, causing a reverse transcription defect upon infection of target cells. Virus particles produced in the presence of an ALLINI are misformed with the ribonucleoprotein located outside the virus core. Virus assembly and maturation are highly orchestrated and regulated processes in which several viral proteins and RNA molecules closely interact. It is therefore of interest to study whether ALLINIs have unpredicted pleiotropic effects on these RNA-related processes. We confirm that the ALLINI BI-D inhibits virus replication and that the produced virus is non-infectious. Furthermore, we show that the wild-type level of HIV-1 genomic RNA is packaged in virions and these genomes are in a dimeric state. The tRNAlys3 primer for reverse transcription was properly placed on this genomic RNA and could be extended ex vivo. In addition, the packaged reverse transcriptase enzyme was fully active when extracted from virions. As the RNA and enzyme components for reverse transcription are properly present in virions produced in the presence of BI-D, the inhibition of reverse transcription is likely to reflect the mislocalization of the components in the aberrant virus particle.

Predominant Non-additive Effects of Multiple Stressors on Autotroph C:N:P Ratios Propagate in Freshwater and Marine Food Webs

PubMed Central

Villar-Argaiz, Manuel; Medina-Sánchez, Juan M.; Biddanda, Bopaiah A.; Carrillo, Presentación

2018-01-01

A continuing challenge for scientists is to understand how multiple interactive stressor factors affect biological interactions, and subsequently, ecosystems–in ways not easily predicted by single factor studies. In this review, we have compiled and analyzed available research on how multiple stressor pairs composed of temperature (T), light (L), ultraviolet radiation (UVR), nutrients (Nut), carbon dioxide (CO2), dissolved organic carbon (DOC), and salinity (S) impact the stoichiometry of autotrophs which in turn shapes the nature of their ecological interactions within lower trophic levels in streams, lakes and oceans. Our analysis from 66 studies with 320 observations of 11 stressor pairs, demonstrated that non-additive responses predominate across aquatic ecosystems and their net interactive effect depends on the stressor pair at play. Across systems, there was a prevalence of antagonism in freshwater (60–67% vs. 47% in marine systems) compared to marine systems where synergism was more common (49% vs. 33–40% in freshwaters). While the lack of data impeded comparisons among all of the paired stressors, we found pronounced system differences for the L × Nut interactions. For this interaction, our data for C:P and N:P is consistent with the initial hypothesis that the interaction was primarily synergistic in the oceans, but not for C:N. Our study found a wide range of variability in the net effects of the interactions in freshwater systems, with some observations supporting antagonism, and others synergism. Our results suggest that the nature of the stressor pairs interactions on C:N:P ratios regulates the “continuum” commensalistic-competitive-predatory relationship between algae and bacteria and the food chain efficiency at the algae-herbivore interface. Overall, the scarce number of studies with even more fewer replications in each study that are available for freshwater systems have prevented a more detailed, insightful analysis. Our findings highlighting the preponderance of antagonistic and synergistic effects of stressor interactions in aquatic ecosystems—effects that play key roles in the functioning of feedback loops in the biosphere—also stress the need for further studies evaluating the interactive effects of multiple stressors in a rapidly changing world facing a confluence of tipping points. PMID:29441051

Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis)

PubMed Central

Munster, Vincent J.; Adney, Danielle R.; van Doremalen, Neeltje; Brown, Vienna R.; Miazgowicz, Kerri L.; Milne-Price, Shauna; Bushmaker, Trenton; Rosenke, Rebecca; Scott, Dana; Hawkinson, Ann; de Wit, Emmie; Schountz, Tony; Bowen, Richard A.

2016-01-01

The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) highlights the zoonotic potential of Betacoronaviruses. Investigations into the origin of MERS-CoV have focused on two potential reservoirs: bats and camels. Here, we investigated the role of bats as a potential reservoir for MERS-CoV. In vitro, the MERS-CoV spike glycoprotein interacted with Jamaican fruit bat (Artibeus jamaicensis) dipeptidyl peptidase 4 (DPP4) receptor and MERS-CoV replicated efficiently in Jamaican fruit bat cells, suggesting there is no restriction at the receptor or cellular level for MERS-CoV. To shed light on the intrinsic host-virus relationship, we inoculated 10 Jamaican fruit bats with MERS-CoV. Although all bats showed evidence of infection, none of the bats showed clinical signs of disease. Virus shedding was detected in the respiratory and intestinal tract for up to 9 days. MERS-CoV replicated transiently in the respiratory and, to a lesser extent, the intestinal tracts and internal organs; with limited histopathological changes observed only in the lungs. Analysis of the innate gene expression in the lungs showed a moderate, transient induction of expression. Our results indicate that MERS-CoV maintains the ability to replicate in bats without clinical signs of disease, supporting the general hypothesis of bats as ancestral reservoirs for MERS-CoV. PMID:26899616

Analysis of DNA replication associated chromatin decondensation: in vivo assay for understanding chromatin remodeling mechanisms of selected proteins.

PubMed

Borysov, Sergiy; Bryant, Victoria L; Alexandrow, Mark G

2015-01-01

Of critical importance to many of the events underlying transcriptional control of gene expression are modifications to core and linker histones that regulate the accessibility of trans-acting factors to the DNA substrate within the context of chromatin. Likewise, control over the initiation of DNA replication, as well as the ability of the replication machinery to proceed during elongation through the multiple levels of chromatin condensation that are likely to be encountered, is known to involve the creation of chromatin accessibility. In the latter case, chromatin access will likely need to be a transient event so as to prevent total genomic unraveling of the chromatin that would be deleterious to cells. While there are many molecular and biochemical approaches in use to study histone changes and their relationship to transcription and chromatin accessibility, few techniques exist that allow a molecular dissection of the events underlying DNA replication control as it pertains to chromatin changes and accessibility. Here, we outline a novel experimental strategy for addressing the ability of specific proteins to induce large-scale chromatin unfolding (decondensation) in vivo upon site-specific targeting to an engineered locus. Our laboratory has used this powerful system in novel ways to directly address the ability of DNA replication proteins to create chromatin accessibility, and have incorporated modifications to the basic approach that allow for a molecular genetic analysis of the mechanisms and associated factors involved in causing chromatin decondensation by a protein of interest. Alternative approaches involving co-expression of other proteins (competitors or stimulators), concurrent drug treatments, and analysis of co-localizing histone modifications are also addressed, all of which are illustrative of the utility of this experimental system for extending basic findings to physiologically relevant mechanisms. Although used by our group to analyze mechanisms underlying DNA replication associated chromatin accessibility, this unique and powerful experimental system has the propensity to be a valuable tool for understanding chromatin remodeling mechanisms orchestrated by other cellular processes such as DNA repair, recombination, mitotic chromosome condensation, or other chromosome dynamics involving chromatin alterations and accessibility.

Sensitivity towards elevated pCO2 in great scallop (Pecten maximus Lamarck) embryos and fed larvae

NASA Astrophysics Data System (ADS)

Andersen, Sissel; Grefsrud, Ellen S.; Harboe, Torstein

2017-02-01

The increasing amount of dissolved anthropogenic CO2 has caused a drop in pH values in the open ocean known as ocean acidification. This change in seawater carbonate chemistry has been shown to have a negative effect on a number of marine organisms. Early life stages are the most vulnerable, and especially the organisms that produce calcified structures in the phylum Mollusca. Few studies have looked at effects on scallops, and this is the first study presented including fed larvae of the great scallop (Pecten maximus) followed until day 14 post-fertilization. Fertilized eggs from unexposed parents were exposed to three levels of pCO2 using four replicate units: 465 (ambient), 768 and 1294 µatm, corresponding to pHNIST of 7.94, 7.75 (-0.19 units) and 7.54 (-0.40 units), respectively. All of the observed parameters were negatively affected by elevated pCO2: survival, larval development, shell growth and normal shell development. The latter was observed to be affected only 2 days after fertilization. Negative effects on the fed larvae at day 7 were similar to what was shown earlier for unfed P. maximus larvae. Growth rate in the group at 768 µatm seemed to decline after day 7, indicating that the ability to overcome the environmental change at moderately elevated pCO2 was lost over time. The present study shows that food availability does not decrease the sensitivity to elevated pCO2 in P. maximus larvae. Unless genetic adaptation and acclimatization counteract the negative effects of long term elevated pCO2, recruitment in populations of P. maximus will most likely be negatively affected by the projected drop of 0.06-0.32 units in pH within year 2100.

IRF4 Variants Have Age-Specific Effects on Nevus Count and Predispose to Melanoma

PubMed Central

Duffy, David L.; Iles, Mark M.; Glass, Dan; Zhu, Gu; Barrett, Jennifer H.; Höiom, Veronica; Zhao, Zhen Z.; Sturm, Richard A.; Soranzo, Nicole; Hammond, Chris; Kvaskoff, Marina; Whiteman, David C.; Mangino, Massimo; Hansson, Johan; Newton-Bishop, Julia A.; Bataille, Veronique; Hayward, Nicholas K.; Martin, Nicholas G.; Bishop, D. Timothy; Spector, Timothy D.; Montgomery, Grant W.

2010-01-01

High melanocytic nevus count is a strong predictor of melanoma risk. A GWAS of nevus count in Australian adolescent twins identified an association of nevus count with the interferon regulatory factor 4 gene (IRF4 [p = 6 × 10−9]). There was a strong genotype-by-age interaction, which was replicated in independent UK samples of adolescents and adults. The rs12203592∗T allele was associated with high nevus counts and high freckling scores in adolescents, but with low nevus counts and high freckling scores in adults. The rs12203592∗T increased counts of flat (compound and junctional) nevi in Australian adolescent twins, but decreased counts of raised (intradermal) nevi. In combined analysis of melanoma case-control data from Australia, the UK, and Sweden, the rs12203592∗C allele was associated with melanoma (odds ratio [OR] 1.15, p = 4 × 10−3), most significantly on the trunk (OR = 1.33, p = 2.5 × 10−5). The melanoma association was corroborated in a GWAS performed by the GenoMEL consortium for an adjacent SNP, rs872071 (rs872071∗T: OR 1.14, p = 0.0035; excluding Australian, the UK, and Swedish samples typed at rs12203592: OR 1.08, p = 0.08). PMID:20602913

Association of GWAS Top Genes With Late-Onset Alzheimer's Disease in Colombian Population.

PubMed

Moreno, Diana Jennifer; Ruiz, Susana; Ríos, Ángela; Lopera, Francisco; Ostos, Henry; Via, Marc; Bedoya, Gabriel

2017-02-01

The association of variants in CLU, CR1, PICALM, BIN1, ABCA7, and CD33 genes with late-onset Alzheimer's disease (LOAD) was evaluated and confirmed through genome-wide association study. However, it is unknown whether these associations can be replicated in admixed populations. The association of 14 single-nucleotide polymorphisms in those genes was evaluated in 280 LOAD cases and 357 controls from the Colombian population. In a multivariate analysis using age, gender, APOE∊4 status, and admixture covariates, significant associations were obtained ( P < .05) for variants in BIN1 (rs744373, odds ratio [OR]: 1.42), CLU (rs11136000, OR: 0.66), PICALM (rs541458, OR: 0.69), ABCA7 (rs3764650, OR: 1.7), and CD33 (rs3865444, OR: 1.12). Likewise, a significant interaction effect was observed between CLU and CR1 variants with APOE. This study replicated the associations previously reported in populations of European ancestry and shows that APOE variants have a regulatory role on the effect that variants in other loci have on LOAD, reflecting the importance of gene-gene interactions in the etiology of neurodegenerative diseases.

The High-Risk Human Papillomavirus E6 Oncogene Exacerbates the Negative Effect of Tryptophan Starvation on the Development of Chlamydia trachomatis

PubMed Central

Sherchand, Shardulendra P.; Ibana, Joyce A.; Zea, Arnold H.; Quayle, Alison J.; Aiyar, Ashok

2016-01-01

Chlamydia trachomatis is an obligate intracellular pathogen that requires specific essential nutrients from the host cell, one of which is the amino acid tryptophan. In this context interferon gamma (IFNγ) is the major host protective cytokine against chlamydial infections because it induces the expression of the host enzyme, indoleamine 2,3-dioxygenase 1, that degrades tryptophan, thereby restricting bacterial replication. The mechanism by which IFNγ acts has been dissected in vitro using epithelial cell-lines such as HeLa, HEp-2, or the primary-like endocervical cell-line A2EN. All these cell-lines express the high-risk human papillomavirus oncogenes E6 & E7. While screening cell-lines to identify those suitable for C. trachomatis co-infections with other genital pathogens, we unexpectedly found that tryptophan starvation did not completely block chlamydial development in cell-lines that were HR-HPV negative, such as C33A and 293. Therefore, we tested the hypothesis that HR-HPV oncogenes modulate the effect of tryptophan starvation on chlamydial development by comparing chlamydial development in HeLa and C33A cell-lines that were both derived from cervical carcinomas. Our results indicate that during tryptophan depletion, unlike HeLa, C33A cells generate sufficient intracellular tryptophan via proteasomal activity to permit C. trachomatis replication. By generating stable derivatives of C33A that expressed HPV16 E6, E7 or E6 & E7, we found that E6 expression alone was sufficient to convert C33A cells to behave like HeLa during tryptophan starvation. The reduced tryptophan levels in HeLa cells have a biological consequence; akin to the previously described effect of IFNγ, tryptophan starvation protects C. trachomatis from clearance by doxycycline in HeLa but not C33A cells. Curiously, when compared to the known Homo sapiens proteome, the representation of tryptophan in the HR-HPV E6 & E6AP degradome is substantially lower, possibly providing a mechanism that underlies the lowered intracellular free tryptophan levels in E6-expressing cells during starvation. PMID:27658027

Elements in the transcriptional regulatory region flanking herpes simplex virus type 1 oriS stimulate origin function.

PubMed

Wong, S W; Schaffer, P A

1991-05-01

Like other DNA-containing viruses, the three origins of herpes simplex virus type 1 (HSV-1) DNA replication are flanked by sequences containing transcriptional regulatory elements. In a transient plasmid replication assay, deletion of sequences comprising the transcriptional regulatory elements of ICP4 and ICP22/47, which flank oriS, resulted in a greater than 80-fold decrease in origin function compared with a plasmid, pOS-822, which retains these sequences. In an effort to identify specific cis-acting elements responsible for this effect, we conducted systematic deletion analysis of the flanking region with plasmid pOS-822 and tested the resulting mutant plasmids for origin function. Stimulation by cis-acting elements was shown to be both distance and orientation dependent, as changes in either parameter resulted in a decrease in oriS function. Additional evidence for the stimulatory effect of flanking sequences on origin function was demonstrated by replacement of these sequences with the cytomegalovirus immediate-early promoter, resulting in nearly wild-type levels of oriS function. In competition experiments, cotransfection of cells with the test plasmid, pOS-822, and increasing molar concentrations of a competitor plasmid which contained the ICP4 and ICP22/47 transcriptional regulatory regions but lacked core origin sequences resulted in a significant reduction in the replication efficiency of pOS-822, demonstrating that factors which bind specifically to the oriS-flanking sequences are likely involved as auxiliary proteins in oriS function. Together, these studies demonstrate that trans-acting factors and the sites to which they bind play a critical role in the efficiency of HSV-1 DNA replication from oriS in transient-replication assays.

Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: Implications for replication and genome packaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaturvedi, Sonali; Rao, A.L.N., E-mail: arao@ucr.edu

2014-09-15

In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein–protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase.more » Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. - Highlights: • YFP fusion proteins of BMV p1a and p2a are biologically active. • Self-interaction was observed for p1a, p2a and CP. • CP interacts with p2a but not p1a. • Majority of reconstituted YFP resulting from bona fide fusion protein partners localized on ER.« less

Ring opening and carbonylation of 3,3-dimethylthietane ligands in ruthenium carbonyl cluster complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, R.D.; Belinski, J.A.; Yamamoto, J.H.

1992-10-01

When heated to 97{degrees}C, the complex Ru{sub 4}(CO){sub 12}[{mu}-SCH{sub 2}CMe{sub 2}CH{sub 2}]2 (1) was transformed into two new hexaruthenium cluster complexes, Ru{sub 6}(CO){sub 13}({mu}{sub 3}-SCH{sub 2}CMe{sub 2}CH{sub 2}){sub 4} (2) and Ru{sub 6}(CO){sub 12}({mu}-SCH{sub 2}CMe{sub 2}CH{sub 2})({mu}{sub 3}-SCH{sub 2}CMe{sub 2}CH{sub 2}){sub 3}[{mu}{sub 3}-SCH{sub 2}C(Me)(CH{sub 2})CH{sub 2}] ({mu}-H) (3), that contain four and five ring-opened 3,3-dimethylthietane (3,3-DMT) ligands, respectively. In compound 3 one of the ring-opened DMT ligands has also undergone a CH activation on one of the methyl groups. Compound 2 reacts with additional 3,3-DMT at 97{degrees}C to form 3 in 18% yield. When treated with CO at 95{degrees}C (500more » psi), compound 2 yielded 4,4-dimethylthiobutyrolactone and Ru{sub 3}(CO){sub 12}. It was also found that the complex Os{sub 3}(CO){sub 11-}(SCH{sub 2}CMe{sub 2}CH{sub 2}C{double_bond}O) (4) yields 4,4-dimethylthiobutyrolactone when treated with CO at 120{degrees}C (1200 psi). Crystal data for 2: space group P2{sub 1}/n, {alpha} = 22.652 (7) A, {beta} = 11.712 (2) A, c = 19.965 (6) A, {Beta} = 115.75 (2){degrees} Z = 4, 3665 reflections, R = 0.021. Crystal data for 3: space group P2{sub 1}/c, {alpha} = 17.332 (8) A, {Beta} = 14.668 (9) A, c = 19.823 (9) A, {Beta} = 91.27 (4){degrees}, Z = 4, 1875 reflections, R = 0.050. 13 refs., 2 figs., 13 refs.« less

Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method.

PubMed

Dou, Dan; Hernández-Neuta, Iván; Wang, Hao; Östbye, Henrik; Qian, Xiaoyan; Thiele, Swantje; Resa-Infante, Patricia; Kouassi, Nancy Mounogou; Sender, Vicky; Hentrich, Karina; Mellroth, Peter; Henriques-Normark, Birgitta; Gabriel, Gülsah; Nilsson, Mats; Daniels, Robert

2017-07-05

Genome delivery to the proper cellular compartment for transcription and replication is a primary goal of viruses. However, methods for analyzing viral genome localization and differentiating genomes with high identity are lacking, making it difficult to investigate entry-related processes and co-examine heterogeneous RNA viral populations. Here, we present an RNA labeling approach for single-cell analysis of RNA viral replication and co-infection dynamics in situ, which uses the versatility of padlock probes. We applied this method to identify influenza A virus (IAV) infections in cells and lung tissue with single-nucleotide specificity and to classify entry and replication stages by gene segment localization. Extending the classification strategy to co-infections of IAVs with single-nucleotide variations, we found that the dependence on intracellular trafficking places a time restriction on secondary co-infections necessary for genome reassortment. Altogether, these data demonstrate how RNA viral genome labeling can help dissect entry and co-infections. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Evaluation of Intestinal Absorption and Bioavailability of a Bergenin-Phospholipid Complex Solid Dispersion in Rats.

PubMed

Gao, Haoshi; Wei, Yue; Xi, Long; Sun, Yuanyuan; Zhang, Tianhong

2018-05-01

Bergenin (BN) is a Biopharmaceutics Classification System class IV (BCS IV) drug with poor hydrophilicity and lipophilicity and is potentially eliminated by the efflux function of P-glycoprotein (P-gp). These factors may explain its low oral bioavailability. In the present study, a BN-phospholipid complex solid dispersion (BNPC-SD) was prepared by solvent evaporation and characterized based on differential scanning calorimetry, powder X-ray diffraction, scanning electron microscopy, infrared diffraction, solubility, octanol-water partition coefficient, and in vitro dissolution. To investigate how P-gp can inhibit BN absorption in vivo, the P-gp inhibitor verapamil was co-administered with BNPC-SD to Sprague Dawley rats. By in situ single-pass intestinal perfusion, the membrane permeability of BN from BNPC-SD was higher than that of BN given alone and was improved further by co-administered verapamil. A pharmacokinetics study was done in Sprague Dawley rats, with plasma BN levels estimated by high-performance liquid chromatography. C max and AUC 0 → t values for BN were significantly higher for BNPC-SD than for BN given alone and were increased further by verapamil. Thus, the relative oral bioavailability of BNPC-SD as well as BNPC-SD co-administered with verapamil was 156.33 and 202.46%, respectively, compared with the value for BN given alone. These results showed that BNPC-SD can increase the oral bioavailability of BCS IV drugs.

Prevalence of hepatitis B virus co-infection among HIV-seropositive persons attending antiretroviral clinics in the Eastern Region of Ghana.

PubMed

Kye-Duodu, Gideon; Nortey, Priscillia; Malm, Keziah; Nyarko, Kofi Mensah; Sackey, Samuel Oko; Ofori, Sampson; Afari, Edwin Andrews

2016-01-01

Hepatitis B and HIV infections are endemic in sub-Saharan Africa including Ghana. Understanding the extent of the co-infection is critical to the optimal care of persons living with HIV and AIDS (PLHIV). We determined the prevalence and risk factors of HBV co-infection in PLHIV and assessed the knowledge of health care workers (HCW) in Antiretroviral Therapy (ART) clinics regarding the co-infection. A cross sectional study was conducted in five ART clinics to obtain data from a systematic random sample of PLHIV in the Eastern region of Ghana from March to June 2012. We used self-administered questionnaires to assess knowledge of HCW on knowledge and management of the co-infection. Descriptive statistics and logistic regression models were used for analysis at 5% significance level. Of 320 PLHIV recruited into study, with median age of 40 years (IQR: 33-50 years), 28 tested positive for HBsAg giving an overall prevalence of 8.8%. There were significant associations between HBV infection and being an adult (p=0.004), increasing serum ALT levels (p=0.002) and partner with history of HBV infection (p=0.010). HCW obtained 84.2% (SD± 20.53; 95% CI: 89-98.1) and 53.1% (SD± 35.06; 95% CI: 13.0-88.9) in the "general knowledge" and "management practice" indexes respectively. Prevalence of HBV-HIV co-infection was relatively high among PLHIV in Eastern region. Knowledge of HCW on management practices of HBV-HIV co-infection and HBV vaccination coverage among PLHIV were found to be relatively low. Regular trainings of HCW and a HBV vaccination programme targeted at PLHIV should be considered.

Common variants at the promoter region of the APOM confer a risk of rheumatoid arthritis

PubMed Central

Hu, Hae-Jin; Jin, Eun-Heui; Yim, Seon-Hee; Yang, So-Young; Jung, Seung-Hyun; Shin, Seung-Hun; Kim, Wan-Uk; Shim, Seung-Cheol; Kim, Tai-Gyu

2011-01-01

Although the genetic component in the etiology of rheumatoid arthritis (RA) has been consistently suggested, many novel genetic loci remain to uncover. To identify RA risk loci, we performed a genome-wide association study (GWAS) with 100 RA cases and 600 controls using Affymetrix SNP array 5.0. The candidate risk locus (APOM gene) was re-sequenced to discover novel promoter and coding variants in a group of the subjects. Replication was performed with the independent case-control set comprising of 578 RAs and 711 controls. Through GWAS, we identified a novel SNP associated with RA at the APOM gene in the MHC class III region on 6p21.33 (rs805297, odds ratio (OR) = 2.28, P = 5.20 × 10-7). Three more polymorphisms were identified at the promoter region of the APOM by the re-sequencing. For the replication, we genotyped the four SNP loci in the independent case-control set. The association of rs805297 identified by GWAS was successfully replicated (OR = 1.40, P = 6.65 × 10-5). The association became more significant in the combined analysis of discovery and replication sets (OR = 1.56, P = 2.73 ± 10-10). The individuals with the rs805297 risk allele (A) at the promoter region showed a significantly lower level of APOM expression compared with those with the protective allele (C) homozygote. In the logistic regressions by the phenotype status, the homozygote risk genotype (A/A) consistently showed higher ORs than the heterozygote one (A/C) for the phenotype-positive RAs. These results indicate that APOM promoter polymorphisms are significantly associated with the susceptibility to RA. PMID:21844665

Human Immunodeficiency Virus Type-1 Elite Controllers Maintain Low Co-Expression of Inhibitory Receptors on CD4+ T Cells.

PubMed

Noyan, Kajsa; Nguyen, Son; Betts, Michael R; Sönnerborg, Anders; Buggert, Marcus

2018-01-01

Human immunodeficiency virus type-1 (HIV-1) elite controllers (ELCs) represent a unique population that control viral replication in the absence of antiretroviral therapy (cART). It is well established that expression of multiple inhibitory receptors on CD8+ T cells is associated with HIV-1 disease progression. However, whether reduced co-expression of inhibitory receptors on CD4+ T cells is linked to natural viral control and slow HIV-1 disease progression remains undefined. Here, we report on the expression pattern of numerous measurable inhibitory receptors, associated with T cell exhaustion (programmed cell death-1, CTLA-4, and TIGIT), on different CD4+ T cell memory populations in ELCs and HIV-infected subjects with or without long-term cART. We found that the co-expression pattern of inhibitory receptors was significantly reduced in ELCs compared with HIV-1 cART-treated and viremic subjects, and similar to healthy controls. Markers associated with T cell exhaustion varied among different memory CD4+ T cell subsets and highest levels were found mainly on transitional memory T cells. CD4+ T cells co-expressing all inhibitory markers were positively correlated to T cell activation (CD38+ HLA-DR+) as well as the transcription factors Helios and FoxP3. Finally, clinical parameters such as CD4 count, HIV-1 viral load, and the CD4/CD8 ratio all showed significant associations with CD4+ T cell exhaustion. We demonstrate that ELCs are able to maintain lower levels of CD4+ T cell exhaustion despite years of ongoing viral replication compared with successfully cART-treated subjects. Our findings suggest that ELCs harbor a "healthy" state of inhibitory receptor expression on CD4+ T cells that might play part in maintenance of their control status.

Cord blood level of insulin-like growth factor-1 and IGF binding protein-3 in monochorionic twins.

PubMed

Teng, Ru-Jeng; Wu, Tzong-Jin; Hsieh, Fon-Jou

2015-04-01

Insulin-like growth factors (IGFs) and their binding proteins (IGFBPs) are known to modulate fetal growth but their role in intrauterine growth of monochorionic twins (MCT) has not been studied. Cord venous blood was collected directly after birth. IGF-1 and IGFBP-3 in the cord venous blood were quantified by radioimmunoassay. Birth weights (BWs) were obtained electronically. Placentas were examined for chorionicity. Cord blood was collected in 37 pairs of MCT (15 pairs were males). BWs ranged from 564 to 3240 g, and gestational ages (GAs) were between 24 weeks and 39 weeks. There was a correlation between BW and cord venous blood IGFBP-3 concentration (r = 0.28, p = 0.015), but not between BW and cord venous blood IGF-1 level. There was no difference in IGF-1 between the heavier twins (30.8 ± 61.8 ng/mL) and lighter twins (33.2 ± 63.7 ng/mL), but a trend (p = 0.096) of higher IGFBP-3 level was demonstrated in heavier twins (3.14 ± 1.23 μg/mL) than in lighter twins (2.71 ± 1.19 μg/mL). The IGFBP-3 levels were higher (p = 0.042) in female twins (3.20 ± 1.33 μg/mL) than in male twins (2.64 ± 1.04 μg/mL). The IGF-1 level of the heavier twins correlated significantly to their lighter co-twin (r = 0.73, p < 0.001). Our data showed that cord venous blood IGF-1 level might be controlled mainly by genetic factors. IGFBP-3 might play an important role in fetal growth. Copyright © 2013. Published by Elsevier B.V.

Radiation resistance and loss of crystal violet binding activity in Yersinia enterocolitica suspended in raw ground pork exposed to gamma radiation and modified atmosphere.

PubMed

Bhaduri, Saumya; Sheen, Shiowshuh; Sommers, Christopher H

2014-05-01

Virulence of many foodborne pathogens is directly linked to genes carried on self-replicating extra-chromosomal elements, which can transfer genetic material, both vertically and horizontally, between bacteria of the same and different species. Pathogenic Yersinia enterocolitica harbors a 70-kb virulence plasmid (pYV) that encodes genes for low calcium response, crystal violet (CV) binding, Congo red uptake, autoagglutination (AA), hydrophobicity (HP), type III secretion channels, host immune suppression factors, and biofilm formation. Ionizing radiation and modified atmosphere packaging (MAP) are used to control foodborne pathogens and meat spoilage. In this study, the effect of gamma radiation and modified atmosphere (air, 100% N2 , 75% N2 : 25% CO2 , 50% N2 : 50% CO2 , 25% N2 : 75% CO2 , 100% CO2 ) were examined by using the CV binding phenotype, for the presence or absence of pYV in Y. enterocolitica, suspended in raw ground pork. All Y. enterocolitica serovars used (O:3, O:8, and O5,27) were more sensitive to radiation as the CO2 concentration increased above 50%. Crystal violet binding following a radiation dose of 1.0 kGy, which reduced the Y. enterocolitica serovars >5 log, was greatest in the presence of air (ca. 8%), but was not affected by N2 or CO2 concentration (ca. 5%). Following release from modified atmosphere after irradiation, the loss of CV binding rose from 5% to 8% immediately following irradiation to >30% after outgrowth at 25 °C for 24 h. These results, using Y. enterocolitica as a model system, indicate that the risk of foodborne illness could be affected by the loss of virulence factors when postprocess intervention technologies are used. Provides gamma radiation D10 data for inactivation data for Y. enterocolitica irradiated under modified atmosphere and information to risk assessors regarding the difference between pathogen presence versus actual virulence. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Interactive effect of elevated CO2 and temperature on coral physiology

NASA Astrophysics Data System (ADS)

Grottoli, A. G.; Cai, W.; Warner, M.; Melman, T.; Schoepf, V.; Baumann, J.; Matsui, Y.; Pettay, D. T.; Hoadley, K.; Xu, H.; Wang, Y.; Li, Q.; Hu, X.

2011-12-01

Increases in ocean acidification and temperature threaten coral reefs globally. However, the interactive effect of both lower pH and higher temperature on coral physiology and growth are poorly understood. Here, we present preliminary findings from a replicated controlled experiment where four species of corals (Acorpora millepora, Pocillopora damicornis, Montipora monasteriata, Turbinaria reniformis) were reared under the following six treatments for three weeks: 1) 400ppm CO2 and ambient temperature, 2) 400ppm CO2 and elevated temperature, 3) 650ppm CO2 and ambient temperature, 4) 650ppm CO2 and elevated temperature, 5) 800ppm CO2 and ambient temperature, 6) 800ppm CO2 and elevated temperature. Initial findings of photophysiological health (Fv/Fm), calcification rates (as measured by both buoyant weight and the total alkalinity methods), and energy reserves will be presented.

Induction of the Tumor-Suppressor p16INK4a within Regenerative Epithelial Crypts in Ulcerative Colitis1

PubMed Central

Furth, Emma E; Gustafson, Karen S; Dai, Charlotte Y; Gibson, Steven L; Menard-Katcher, Paul; Chen, Tina; Koh, Jim; Enders, Greg H

2006-01-01

Abstract p16INK4a is a major tumor-suppressor protein, but its regulation and settings of fuction remain poorly understood. To explore the notion that p16 is induced in vivo in response to replicative stress, we examined p16 expression in tissues from human ulcerative colitis (UC; n = 25) and normal controls (n = 20). p16 was expressed strongly in UC-associated neoplasms (n = 17), as seen previously in sporadic colonic neoplasms. In non-neoplastic UC epithelium, p16 was expressed in 33% of crypts (the proliferative compartment) compared to < 1% of normal controls. p16 expression did not correlate with degree of inflammation but did correlate with the degree of crypt architecture distortion (P = .002)—a reflection of epithelial regeneration. In coimmunofluorescence studies with Ki67, p16 expression was associated with cell cycle arrest (P < .001). Both UC and normal crypts displayed evidence for the activation of the DNA damage checkpoint pathway, and p16 was induced in primary cultures of normal epithelial cells by ionizing irradiation (IR). However, induction by IR displayed delayed kinetics, implying that p16 is not an immediate target of the checkpoint pathway. These findings support a model in which p16 is induced as an “emergency brake” in cells experiencing sustained replicative stress. PMID:16820088

Esophageal squamous cell carcinomas with DNA replication errors (RER+) are associated with p16/pRb loss and wild-type p53.

PubMed

Mathew, R; Arora, S; Mathur, M; Chattopadhyay, T K; Ralhan, R

2001-10-01

Microsatellite instability (MSI) as a determinant of propensity to esophageal squamous cell carcinoma (ESCC) at seven microsatellite markers at 2p (2p15-16), 3p (3p13, 3p14.1-3, 3p25, and 3p26) and 16q (16q12.1-3) was investigated to analyze their putative role as indicators of predisposition to esophageal malignancies. Seven microsatellite loci were amplified by polymerase chain reaction, from surgically resected tumor tissues from 30 ESCC patients from Indian population, to assess the loss of heterozygosity (LOH) and replication error repeats (RER) and to correlate these alterations with aberrations in major cell cycle regulatory proteins and histopathological parameters. LOH and RER analyses at these loci demonstrated moderate microsatellite alterations, suggesting the involvement of MSI in esophageal tumorigenesis in a subset of the Indian population. MSI, defined as RER in at least two or more of the loci studied, was observed in ten of 30 (33%) patients. Twenty-two of 30 patients (73%) showed LOH at one or more loci, while 17 of the 30 patients (60%) showed RER in at least one of the loci studied. RER-positive patients showed a trend towards better prognosis when compared to RER-negative patients. MSI demonstrated a significant association with concomitant loss of p16 and pRb (p16-/pRb- phenotype) (P=0.046). Interestingly, we observed an inverse correlation between MSI and p53 mutations (P=0.03) suggesting that MSI may provide a p53-independent pathway for esophageal tumorigenesis in RER+ patients. MSI showed a trend towards longer survival and absence of distant organ metastasis (P=0.06). The present study demonstrates the probable role of MSI in esophageal squamous cell carcinoma in the Indian population. Instability associated with the repetitive sequences--the revealing marks of loss of DNA replication fidelity may serve as an indicator of predisposition to esophageal cancer.

In Vitro Synthesized RNA Generated from cDNA Clones of Both Genomic Components of Cucurbit yellow stunting disorder virus Replicates in Cucumber Protoplasts

PubMed Central

Owen, Carolyn A.; Moukarzel, Romy; Huang, Xiao; Kassem, Mona A.; Eliasco, Eleonora; Aranda, Miguel A.; Coutts, Robert H. A.; Livieratos, Ioannis C.

2016-01-01

Cucurbit yellow stunting disorder virus (CYSDV), a bipartite whitefly-transmitted virus, constitutes a major threat to commercial cucurbit production worldwide. Here, construction of full-length CYSDV RNA1 and RNA2 cDNA clones allowed the in vitro synthesis of RNA transcripts able to replicate in cucumber protoplasts. CYSDV RNA1 proved competent for replication; transcription of both polarities of the genomic RNA was detectable 24 h post inoculation. Hybridization of total RNA extracted from transfected protoplasts or from naturally CYSDV-infected cucurbits revealed high-level transcription of the p22 subgenomic RNA species. Replication of CYSDV RNA2 following co-transfection with RNA1 was also observed, with similar transcription kinetics. A CYSDV RNA2 cDNA clone (T3CM8Δ) comprising the 5′- and 3′-UTRs plus the 3′-terminal gene, generated a 2.8 kb RNA able to replicate to high levels in protoplasts in the presence of CYSDV RNA1. The clone T3CM8Δ will facilitate reverse genetics studies of CYSDV gene function and RNA replication determinants. PMID:27314380

GRECOS Project (Genotyping Recurrence Risk of Stroke): The Use of Genetics to Predict the Vascular Recurrence After Stroke.

PubMed

Fernández-Cadenas, Israel; Mendióroz, Maite; Giralt, Dolors; Nafria, Cristina; Garcia, Elena; Carrera, Caty; Gallego-Fabrega, Cristina; Domingues-Montanari, Sophie; Delgado, Pilar; Ribó, Marc; Castellanos, Mar; Martínez, Sergi; Freijo, Marimar; Jiménez-Conde, Jordi; Rubiera, Marta; Alvarez-Sabín, José; Molina, Carlos A; Font, Maria Angels; Grau Olivares, Marta; Palomeras, Ernest; Perez de la Ossa, Natalia; Martinez-Zabaleta, Maite; Masjuan, Jaime; Moniche, Francisco; Canovas, David; Piñana, Carlos; Purroy, Francisco; Cocho, Dolores; Navas, Inma; Tejero, Carlos; Aymerich, Nuria; Cullell, Natalia; Muiño, Elena; Serena, Joaquín; Rubio, Francisco; Davalos, Antoni; Roquer, Jaume; Arenillas, Juan Francisco; Martí-Fábregas, Joan; Keene, Keith; Chen, Wei-Min; Worrall, Bradford; Sale, Michele; Arboix, Adrià; Krupinski, Jerzy; Montaner, Joan

2017-05-01

Vascular recurrence occurs in 11% of patients during the first year after ischemic stroke (IS) or transient ischemic attack. Clinical scores do not predict the whole vascular recurrence risk; therefore, we aimed to find genetic variants associated with recurrence that might improve the clinical predictive models in IS. We analyzed 256 polymorphisms from 115 candidate genes in 3 patient cohorts comprising 4482 IS or transient ischemic attack patients. The discovery cohort was prospectively recruited and included 1494 patients, 6.2% of them developed a new IS during the first year of follow-up. Replication analysis was performed in 2988 patients using SNPlex or HumanOmni1-Quad technology. We generated a predictive model using Cox regression (GRECOS score [Genotyping Reurrence Risk of Stroke]) and generated risk groups using a classification tree method. The analyses revealed that rs1800801 in the MGP gene (hazard ratio, 1.33; P =9×10 - 03 ), a gene related to artery calcification, was associated with new IS during the first year of follow-up. This polymorphism was replicated in a Spanish cohort (n=1.305); however, it was not significantly associated in a North American cohort (n=1.683). The GRECOS score predicted new IS ( P =3.2×10 - 09 ) and could classify patients, from low risk of stroke recurrence (1.9%) to high risk (12.6%). Moreover, the addition of genetic risk factors to the GRECOS score improves the prediction compared with previous Stroke Prognosis Instrument-II score ( P =0.03). The use of genetics could be useful to estimate vascular recurrence risk after IS. Genetic variability in the MGP gene was associated with vascular recurrence in the Spanish population. © 2017 American Heart Association, Inc.

GRECOS project. The use of genetics to predict the vascular recurrence after stroke

PubMed Central

Fernández-Cadenas, Israel; Mendióroz, Maite; Giralt, Dolors; Nafria, Cristina; Garcia, Elena; Carrera, Caty; Gallego-Fabrega, Cristina; Domingues-Montanari, Sophie; Delgado, Pilar; Ribó, Marc; Castellanos, Mar; Martínez, Sergi; Freijo, Mari Mar; Jiménez-Conde, Jordi; Rubiera, Marta; Alvarez-Sabín, José; Molina, Carlos A.; Font, Maria Angels; Olivares, Marta Grau; Palomeras, Ernest; de la Ossa, Natalia Perez; Martinez-Zabaleta, Maite; Masjuan, Jaime; Moniche, Francisco; Canovas, David; Piñana, Carlos; Purroy, Francisco; Cocho, Dolores; Navas, Inma; Tejero, Carlos; Aymerich, Nuria; Cullell, Natalia; Muiño, Elena; Serena, Joaquín; Rubio, Francisco; Davalos, Antoni; Roquer, Jaume; Arenillas, Juan Francisco; Martí-Fábregas, Joan; Keene, Keith; Chen, Wei-Min; Worrall, Bradford; Sale, Michele; Arboix, Adrià; Krupinski, Jerzy; Montaner, Joan

2017-01-01

Background and Purpose Vascular recurrence occurs in 11% of patients during the first year after ischemic stroke (IS) or transient ischemic attack (TIA). Clinical scores do not predict the whole vascular recurrence risk, therefore we aimed to find genetic variants associated with recurrence that might improve the clinical predictive models in IS. Methods We analyzed 256 polymorphisms from 115 candidate genes in three patient cohorts comprising 4,482 IS or TIA patients. The discovery cohort was prospectively recruited and included 1,494 patients, 6.2% of them developed a new IS during the first year of follow-up. Replication analysis was performed in 2,988 patients using SNPlex or HumanOmni1-Quad technology. We generated a predictive model using Cox regression (GRECOS score), and generated risk groups using a classification tree method. Results The analyses revealed that rs1800801 in the MGP gene (HR: 1.33, p= 9×10−03), a gene related to artery calcification, was associated with new IS during the first year of follow-up. This polymorphism was replicated in a Spanish cohort (n=1.305), however it was not significantly associated in a North American cohort (n=1.683). The GRECOS score predicted new IS (p= 3.2×10−09) and could classify patients, from low risk of stroke recurrence (1.9%) to high risk (12.6%). Moreover, the addition of genetic risk factors to the GRECOS score improves the prediction compared to previous SPI-II score (p=0.03). Conclusions The use of genetics could be useful to estimate vascular recurrence risk after IS. Genetic variability in the MGP gene was associated with vascular recurrence in the Spanish population. PMID:28411264

Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.

PubMed

Schneider, T D

2001-12-01

The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation ( approximately 2 bits) at a minor groove that faces RepA. However, B-form DNA can support only 1 bit of sequence conservation via contacts into the minor groove. The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 alpha, EBNA1, ORC) and promoter binding proteins (sigma(70), sigma(D) factors). This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rudneva, Irina A.; Timofeeva, Tatiana A.; Ignatieva, Anna V.

In the present study we assessed pleiotropic characteristics of the antibody-selected mutations. We examined pH optimum of fusion, temperatures of HA heat inactivation, and in vitro and in vivo replication kinetics of the previously obtained influenza H5 escape mutants. Our results showed that HA1 N142K mutation significantly lowered the pH of fusion optimum. Mutations of the escape mutants located in the HA lateral loop significantly affected H5 HA thermostability (P<0.05). HA changes at positions 131, 144, 145, and 156 and substitutions at positions 131, 142, 145, and 156 affected the replicative ability of H5 escape mutants in vitro and inmore » vivo, respectively. Overall, a co-variation between antigenic specificity and different HA phenotypic properties has been demonstrated. We believe that the monitoring of pleiotropic effects of the HA mutations found in H5 escape mutants is essential for accurate prediction of mutants with pandemic potential. - Highlights: • HA1 N142K mutation significantly lowered the pH of fusion optimum. • Mutations located in the HA lateral loop significantly affected H5 HA thermostability. • HA changes at positions 131, 142, 144, 145, and 156 affected the replicative ability of H5 mutants. • Acquisition of glycosylation site could lead to the emergence of multiple pleiotropic effects.« less

Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells.

PubMed

Foxman, Ellen F; Storer, James A; Fitzgerald, Megan E; Wasik, Bethany R; Hou, Lin; Zhao, Hongyu; Turner, Paul E; Pyle, Anna Marie; Iwasaki, Akiko

2015-01-20

Most isolates of human rhinovirus, the common cold virus, replicate more robustly at the cool temperatures found in the nasal cavity (33-35 °C) than at core body temperature (37 °C). To gain insight into the mechanism of temperature-dependent growth, we compared the transcriptional response of primary mouse airway epithelial cells infected with rhinovirus at 33 °C vs. 37 °C. Mouse airway cells infected with mouse-adapted rhinovirus 1B exhibited a striking enrichment in expression of antiviral defense response genes at 37 °C relative to 33 °C, which correlated with significantly higher expression levels of type I and type III IFN genes and IFN-stimulated genes (ISGs) at 37 °C. Temperature-dependent IFN induction in response to rhinovirus was dependent on the MAVS protein, a key signaling adaptor of the RIG-I-like receptors (RLRs). Stimulation of primary airway cells with the synthetic RLR ligand poly I:C led to greater IFN induction at 37 °C relative to 33 °C at early time points poststimulation and to a sustained increase in the induction of ISGs at 37 °C relative to 33 °C. Recombinant type I IFN also stimulated more robust induction of ISGs at 37 °C than at 33 °C. Genetic deficiency of MAVS or the type I IFN receptor in infected airway cells permitted higher levels of viral replication, particularly at 37 °C, and partially rescued the temperature-dependent growth phenotype. These findings demonstrate that in mouse airway cells, rhinovirus replicates preferentially at nasal cavity temperature due, in part, to a less efficient antiviral defense response of infected cells at cool temperature.

A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3.

PubMed

Tomlinson, Ian P M; Webb, Emily; Carvajal-Carmona, Luis; Broderick, Peter; Howarth, Kimberley; Pittman, Alan M; Spain, Sarah; Lubbe, Steven; Walther, Axel; Sullivan, Kate; Jaeger, Emma; Fielding, Sarah; Rowan, Andrew; Vijayakrishnan, Jayaram; Domingo, Enric; Chandler, Ian; Kemp, Zoe; Qureshi, Mobshra; Farrington, Susan M; Tenesa, Albert; Prendergast, James G D; Barnetson, Rebecca A; Penegar, Steven; Barclay, Ella; Wood, Wendy; Martin, Lynn; Gorman, Maggie; Thomas, Huw; Peto, Julian; Bishop, D Timothy; Gray, Richard; Maher, Eamonn R; Lucassen, Anneke; Kerr, David; Evans, D Gareth R; Schafmayer, Clemens; Buch, Stephan; Völzke, Henry; Hampe, Jochen; Schreiber, Stefan; John, Ulrich; Koessler, Thibaud; Pharoah, Paul; van Wezel, Tom; Morreau, Hans; Wijnen, Juul T; Hopper, John L; Southey, Melissa C; Giles, Graham G; Severi, Gianluca; Castellví-Bel, Sergi; Ruiz-Ponte, Clara; Carracedo, Angel; Castells, Antoni; Försti, Asta; Hemminki, Kari; Vodicka, Pavel; Naccarati, Alessio; Lipton, Lara; Ho, Judy W C; Cheng, K K; Sham, Pak C; Luk, J; Agúndez, Jose A G; Ladero, Jose M; de la Hoya, Miguel; Caldés, Trinidad; Niittymäki, Iina; Tuupanen, Sari; Karhu, Auli; Aaltonen, Lauri; Cazier, Jean-Baptiste; Campbell, Harry; Dunlop, Malcolm G; Houlston, Richard S

2008-05-01

To identify colorectal cancer (CRC) susceptibility alleles, we conducted a genome-wide association study. In phase 1, we genotyped 550,163 tagSNPs in 940 familial colorectal tumor cases (627 CRC, 313 high-risk adenoma) and 965 controls. In phase 2, we genotyped 42,708 selected SNPs in 2,873 CRC cases and 2,871 controls. In phase 3, we evaluated 11 SNPs showing association at P < 10(-4) in a joint analysis of phases 1 and 2 in 4,287 CRC cases and 3,743 controls. Two SNPs were taken forward to phase 4 genotyping (10,731 CRC cases and 10,961 controls from eight centers). In addition to the previously reported 8q24, 15q13 and 18q21 CRC risk loci, we identified two previously unreported associations: rs10795668, located at 10p14 (P = 2.5 x 10(-13) overall; P = 6.9 x 10(-12) replication), and rs16892766, at 8q23.3 (P = 3.3 x 10(-18) overall; P = 9.6 x 10(-17) replication), which tags a plausible causative gene, EIF3H. These data provide further evidence for the 'common-disease common-variant' model of CRC predisposition.

Cyclin-dependent Kinases Phosphorylate the Cytomegalovirus RNA Export Protein pUL69 and Modulate Its Nuclear Localization and Activity*S⃞

PubMed Central

Rechter, Sabine; Scott, Gillian M.; Eickhoff, Jan; Zielke, Katrin; Auerochs, Sabrina; Müller, Regina; Stamminger, Thomas; Rawlinson, William D.; Marschall, Manfred

2009-01-01

Replication of human cytomegalovirus (HCMV) is subject to regulation by cellular protein kinases. Recently, we and others reported that inhibition of cyclin-dependent protein kinases (CDKs) or the viral CDK ortholog pUL97 can induce intranuclear speckled aggregation of the viral mRNA export factor, pUL69. Here we provide the first evidence for a direct regulatory role of CDKs on pUL69 functionality. Although replication of all HCMV strains was dependent on CDK activity, we found strain-specific differences in the amount of CDK inhibitor-induced pUL69 aggregate formation. In all cases analyzed, the inhibitor-induced pUL69 aggregates were clearly localized within viral replication centers but not subnuclear splicing, pore complex, or aggresome structures. The CDK9 and cyclin T1 proteins colocalized with these pUL69 aggregates, whereas other CDKs behaved differently. Phosphorylation analyses in vivo and in vitro demonstrated pUL69 was strongly phosphorylated in HCMV-infected fibroblasts and that CDKs represent a novel class of pUL69-phosphorylating kinases. Moreover, the analysis of CDK inhibitors in a pUL69-dependent nuclear mRNA export assay provided evidence for functional impairment of pUL69 under suppression of CDK activity. Thus, our data underline the crucial importance of CDKs for HCMV replication, and indicate a direct impact of CDK9-cyclin T1 on the nuclear localization and activity of the viral regulator pUL69. PMID:19179338

Deficient BIM Expression as a Mechanism of Intrinsic and Acquired Resistance to Targeted Therapies in EGFR-Mutant and ALK-Positive Lung Cancers

DTIC Science & Technology

2016-10-01

CT-BCT-A Replicate number CT-C 0 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 Unique barcodes shared by: other replicates 01234 P er ce nt ag e of un iq ue b ar co...of response to first-line EGFR inhibi- tor therapy before the development of drug resistance (Fig. 4f), raising the possibility that the EGFRT790M...frequency EGFRT790M-positive clones in clinical specimens from patients who had not started treatment yet9,35, although doubts have been raised as to

Self-affirming trait kindness regulates disgust toward one's physical appearance.

PubMed

Powell, Philip A; Simpson, Jane; Overton, Paul G

2015-01-01

In two studies, self-affirming the behavioral trait of kindness was examined as a method of regulating state disgust toward one's physical appearance. In Study 1, 56 participants (37 women, 19 men, Mage=33.16 years) completed either a questionnaire designed to self-affirm kindness or a control equivalent and rated their disgust, anger, sadness, and happiness toward their appearance and behavior. In Study 2, 116 individuals (83 women, 33 men, Mage=24.90 years) participated in the same experiment over the internet in an ecologically valid context. When controlling for trait self-disgust, the self-affirmed in Study 1 reported significantly less disgust toward their appearance (ηp(2)=.12, p=.011). This effect was replicated in Study 2, but driven by lower state disgust levels in those higher in trait self-disgust (f(2)=.10, p=.001). Affirming valued traits, like kindness, may be a useful tool for regulating disgust toward body image. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative Characterization of the Sindbis Virus Proteome from Mammalian and Invertebrate Hosts Identifies nsP2 as a Component of the Virus Nucleocapsid and Sorting Nexin 5 as a Significant Host Factor for Alphavirus Replication.

PubMed

Schuchman, Ryan; Kilianski, Andy; Piper, Amanda; Vancini, Ricardo; Ribeiro, José M C; Sprague, Thomas R; Nasar, Farooq; Boyd, Gabrielle; Hernandez, Raquel; Glaros, Trevor

2018-05-09

Recent advances in mass spectrometry methods and instrumentation now allow for more accurate identification of proteins in low abundance. This technology was applied to Sindbis virus, the prototypical alphavirus to investigate the viral proteome. To determine if host proteins are specifically packaged into alphavirus virions, Sindbis virus (SINV) was grown in multiple host cells representing vertebrate and mosquito hosts and total protein content of purified virions was determined. This analysis identified host factors not previously associated with alphavirus entry, replication, or egress. One host protein, sorting nexin 5 (SNX5), was shown to be critical for the replication of three different alphaviruses, Sindbis, Mayaro and Chikungunya virus. The most significant finding was that in addition to the host proteins, SINV non-structural protein 2 (nsP2) was detected within virions grown in all host cells examined. The protein and RNA-interacting capabilities of nsP2 coupled with its presence in the virion support a role for nsP2 during packaging and/or entry of progeny virus. This function has not been identified for this protein. Taken together, this strategy identified at least one host factor integrally involved in alphavirus replication. Identification of other host proteins provides insight into alphavirus-host interactions during viral replication in both vertebrate and invertebrate hosts. This method of virus proteome analysis may also be useful for the identification of protein candidates for host-based therapeutics. IMPORTANCE Pathogenic Alphaviruses, such as Chikungunya and Mayaro virus, continue to plague public health in developing and developed countries alike. Alphaviruses belong to a group of viruses vectored in nature by hematophagous (blood-feeding) insects and are termed Arboviruses (arthropod-borne viruses). This group of viruses contains many human pathogens such as dengue fever, West Nile and Yellow fever viruses. With few exceptions there are no vaccines or prophylactics for these agents leaving one third of the world population at risk of infection. Identifying effective antivirals has been a long term goal for combating these diseases not only because of the lack of vaccines but also because they are effective during an ongoing epidemic. Mass spectrometry-based analysis of the Sindbis virus proteome can be effective in identifying host genes involved in virus replication and novel functions for virus proteins. Identification of these factors is invaluable for the prophylaxis of this group of viruses. Copyright © 2018 Schuchman et al.

Increased Long Chain acyl-Coa Synthetase Activity and Fatty Acid Import Is Linked to Membrane Synthesis for Development of Picornavirus Replication Organelles

PubMed Central

Scott, Alison J.; Ford, Lauren A.; Pei, Zhengtong; Watkins, Paul A.; Ernst, Robert K.; Belov, George A.

2013-01-01

All positive strand (+RNA) viruses of eukaryotes replicate their genomes in association with membranes. The mechanisms of membrane remodeling in infected cells represent attractive targets for designing future therapeutics, but our understanding of this process is very limited. Elements of autophagy and/or the secretory pathway were proposed to be hijacked for building of picornavirus replication organelles. However, even closely related viruses differ significantly in their requirements for components of these pathways. We demonstrate here that infection with diverse picornaviruses rapidly activates import of long chain fatty acids. While in non-infected cells the imported fatty acids are channeled to lipid droplets, in infected cells the synthesis of neutral lipids is shut down and the fatty acids are utilized in highly up-regulated phosphatidylcholine synthesis. Thus the replication organelles are likely built from de novo synthesized membrane material, rather than from the remodeled pre-existing membranes. We show that activation of fatty acid import is linked to the up-regulation of cellular long chain acyl-CoA synthetase activity and identify the long chain acyl-CoA syntheatse3 (Acsl3) as a novel host factor required for polio replication. Poliovirus protein 2A is required to trigger the activation of import of fatty acids independent of its protease activity. Shift in fatty acid import preferences by infected cells results in synthesis of phosphatidylcholines different from those in uninfected cells, arguing that the viral replication organelles possess unique properties compared to the pre-existing membranes. Our data show how poliovirus can change the overall cellular membrane homeostasis by targeting one critical process. They explain earlier observations of increased phospholipid synthesis in infected cells and suggest a simple model of the structural development of the membranous scaffold of replication complexes of picorna-like viruses, that may be relevant for other (+)RNA viruses as well. PMID:23762027

Developmental expression patterns of candidate co-factors for vertebrate Six family transcription factors

PubMed Central

Neilson, Karen M.; Pignoni, Francesca; Yan, Bo; Moody, Sally A.

2010-01-01

Six family transcription factors play important roles in craniofacial development. Their transcriptional activity can be modified by co-factor proteins. Two Six genes and one co-factor gene (Eya1) are involved in the human Branchio-otic (BO) and Branchio-otic-renal (BOR) syndromes. However, mutations in Six and Eya genes only account for about half of these patients. To discover potential new causative genes, we searched the Xenopus genome for orthologues of Drosophila co-factor proteins that interact with the fly Six-related factor, SO. We identified 33 Xenopus genes with high sequence identity to 20 of the 25 fly SO-interacting proteins. We provide the developmental expression patterns of the Xenopus orthologues for 11 of the fly genes, and demonstrate that all are expressed in developing craniofacial tissues with at least partial overlap with Six1/Six2. We speculate that these genes may function as Six-interacting partners with important roles in vertebrate craniofacial development and perhaps congenital syndromes. PMID:21089078

Agents for replacement of NAD+/NADH system in enzymatic reactions

DOEpatents

Fish, Richard H.; Kerr, John B.; Lo, Christine H.

2004-04-06

Novel agents acting as co-factors for replacement of NAD(P).sup.+ /NAD(P)H co-enzyme systems in enzymatic oxido-reductive reactions. Agents mimicking the action of NAD(P).sup.+ /NAD(P)H system in enzymatic oxidation/reduction of substrates into reduced or oxidized products. A method for selection and preparation of the mimicking agents for replacement of NAD(P).sup.+ /NAD(P)H system and a device comprising co-factors for replacement of NAD(P).sup.+ /NAD(P)H system.

[Ni III(OMe)]-mediated reductive activation of CO 2 affording a Ni(κ 1-OCO) complex

DOE PAGES

Chiou, Tzung -Wen; Tseng, Yen -Ming; Lu, Tsai -Te; ...

2016-02-24

Here, carbon dioxide is expected to be employed as an inexpensive and potential feedstock of C 1 sources for the mass production of valuable chemicals and fuel. Versatile chemical transformations of CO 2, i.e. insertion of CO 2 producing bicarbonate/acetate/formate, cleavage of CO 2 yielding μ-CO/μ-oxo transition-metal complexes, and electrocatalytic reduction of CO 2 affording CO/HCOOH/CH 3OH/CH 4/C 2H 4/oxalate were well documented. Herein, we report a novel pathway for the reductive activation of CO 2 by the [Ni III(OMe)(P(C 6H 3-3-SiMe 3-2-S) 3)] – complex, yielding the [Ni III(κ 1-OCO˙ –)(P(C 6H 3-3-SiMe 3-2-S) 3)] – complex. The formationmore » of this unusual Ni III(κ 1-OCO ˙–) complex was characterized by single-crystal X-ray diffraction, EPR, IR, SQUID, Ni/S K-edge X-ray absorption spectroscopy, and Ni valence-to-core X-ray emission spectroscopy. The inertness of the analogous complexes [Ni III(SPh)], [Ni II(CO)], and [Ni II(N 2H 4)] toward CO 2, in contrast, demonstrates that the ionic [Ni III(OMe)] core attracts the binding of weak σ-donor CO 2 and triggers the subsequent reduction of CO 2 by the nucleophilic [OMe] – in the immediate vicinity. This metal–ligand cooperative activation of CO 2 may open a novel pathway promoting the subsequent incorporation of CO 2 in the buildup of functionalized products.« less

Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links

PubMed Central

Nicholls, Andrew W.; Salek, Reza M.; Marques-Vidal, Pedro; Morya, Edgard; Sameshima, Koichi; Montoliu, Ivan; Da Silva, Laeticia; Collino, Sebastiano; Martin, François-Pierre; Rezzi, Serge; Steinbeck, Christoph; Waterworth, Dawn M.; Waeber, Gérard; Vollenweider, Peter; Beckmann, Jacques S.; Le Coutre, Johannes; Mooser, Vincent; Bergmann, Sven; Genick, Ulrich K.; Kutalik, Zoltán

2014-01-01

Metabolic traits are molecular phenotypes that can drive clinical phenotypes and may predict disease progression. Here, we report results from a metabolome- and genome-wide association study on 1H-NMR urine metabolic profiles. The study was conducted within an untargeted approach, employing a novel method for compound identification. From our discovery cohort of 835 Caucasian individuals who participated in the CoLaus study, we identified 139 suggestively significant (P<5×10−8) and independent associations between single nucleotide polymorphisms (SNP) and metabolome features. Fifty-six of these associations replicated in the TasteSensomics cohort, comprising 601 individuals from São Paulo of vastly diverse ethnic background. They correspond to eleven gene-metabolite associations, six of which had been previously identified in the urine metabolome and three in the serum metabolome. Our key novel findings are the associations of two SNPs with NMR spectral signatures pointing to fucose (rs492602, P = 6.9×10−44) and lysine (rs8101881, P = 1.2×10−33), respectively. Fine-mapping of the first locus pinpointed the FUT2 gene, which encodes a fucosyltransferase enzyme and has previously been associated with Crohn's disease. This implicates fucose as a potential prognostic disease marker, for which there is already published evidence from a mouse model. The second SNP lies within the SLC7A9 gene, rare mutations of which have been linked to severe kidney damage. The replication of previous associations and our new discoveries demonstrate the potential of untargeted metabolomics GWAS to robustly identify molecular disease markers. PMID:24586186

Inhibition of human T cell leukemia virus type 2 replication by the suppressive action of class II transactivator and nuclear factor Y.

PubMed

Tosi, Giovanna; Pilotti, Elisabetta; Mortara, Lorenzo; De Lerma Barbaro, Andrea; Casoli, Claudio; Accolla, Roberto S

2006-08-22

The master regulator of MHC-II gene transcription, class II transactivator (CIITA), acts as a potent inhibitor of human T cell leukemia virus type 2 (HTLV-2) replication by blocking the activity of the viral Tax-2 transactivator. Here, we show that this inhibitory effect takes place at the nuclear level and maps to the N-terminal 1-321 region of CIITA, where we identified a minimal domain, from positions 64-144, that is strictly required to suppress Tax-2 function. Furthermore, we show that Tax-2 specifically cooperates with cAMP response element binding protein-binding protein (CBP) and p300, but not with p300/CBP-associated factor, to enhance transcription from the viral promoter. This finding represents a unique difference with respect to Tax-1, which uses all three coactivators to transactivate the human T cell leukemia virus type 1 LTR. Direct sequestering of CBP or p300 is not the primary mechanism by which CIITA causes suppression of Tax-2. Interestingly, we found that the transcription factor nuclear factor Y, which interacts with CIITA to increase transcription of MHC-II genes, exerts a negative regulatory action on the Tax-2-mediated HTLV-2 LTR transactivation. Thus, CIITA may inhibit Tax-2 function, at least in part, through nuclear factor Y. These findings demonstrate the dual defensive role of CIITA against pathogens: it increases the antigen-presenting function for viral determinants and suppresses HTLV-2 replication in infected cells.

[Association of IL-10-1082 and IL-10-592 polymorphisms with chronic hepatitis B and/or hepatitis C virus infection among plasma donors in a rural area of Hebei Province, China].

PubMed

Gao, Qiuju; Zhang, Shiyong; Wu, Lihong; Jia, Min; Mi, Yu; Liu, Dianwu

2011-11-01

To study the relationship between the polymorphisms of interleukin-10 gene at position--1082,-592 (IL-10-1082, IL-10-592) and chronic HBV and/or HCV infection. 277 subjects (79 chronic HCV/HBV co-infection,69 chronic HBV infection, 55 chronic HCV infection and 74 control subjects) were recruited from plasma donors in a rural area of Hebei Province, China. The single nucleotide polymorphism of IL-10-1082 and IL-10-592 was investigated by sequence specific primer-PCR (SSP-PCR) and restricted fragment long polymorphism-PCR (RFLP-PCR). Hepatocellular injury was detected by alanine aminotransferase (ALT) with Beckman LX-20 analyzer. The presence of hepatitis C viral particles in serum was determined by RT-nPCR. (1) Chronic HCV or HBV infection or HCV/HBV co-infection was associated with higher frequency of IL-10-1082 AA genotype [chi2 = 13.05, P = 0.04; OR = 2.29 (1.10-4.78), 2.34 (1.07-5.10), 2.56 (1.25 -5.21)]. There was no significant association of IL-10-1082 allele frequency with HCV or HBV infection or HCV/HBV co-infections (chi2 = 4.65, P = 0.20). There was no significant association of IL-10-592 genotype and allele frequency with chronic HBV and/or HCV infection (chi2 = 2.83, P = 0.83; chi2 = 1.10, P = 0.78) (2) There were obvious associations of higher IL-10-1082 AA genotype and A allele frequency with HCV replication [(chi2 = 12.27, P = 0.00; chi2 = 5.36, P = 0.02), OR = 3.36 (1.67-6.76) and 1.67 (1.08-2.57)]. The polymorphism of IL-10592 was not associated with HCV RNA replication (chi2 = 2.10, P = 0.35; chi2 = 1.88, P = 0.17). (3) The polymorphism of IL-10-1082 was not significantly associated with abnormal ALT (chi2 = 3.25, P = 0.20; chi2 = 1.79, P = 0.18). Abnormal serum ALT level was associated with IL-10-592 AC genotype [(chi2 = 6.32, P = 0.04), OR = 2.83 (1.26- 6.37)), but the IL-10-592 A/C allele frequency was not associated with abnormal serum ALT level (chi2 = 2.30, P = 0.09). These results suggested that the polymorphism of IL-10-1082 appears to have some influences on the chronic infection of HCV and/or HBV and HCV replication. IL-10-592 AC genotype frequency has influence on inflammatory liver injury.

Inside the lifestyle of the virophage.

PubMed

Desnues, C; Raoult, D

2010-01-01

We sought to better characterize Sputnik, the first isolated virophage, and to analyze its parasitic lifestyle during co-infection with Marseillevirus (a new giant virus) in Acanthamoeba castellanii. A combination of electron microscopy, immunofluorescence microscopy, and real-time PCR was used to characterize the kinetics of the viral replication cycle. RT-PCR was performed to detect RNAs inside the Sputnik virions. Sputnik is a new viral entity carrying an almost complete ready-to-use set of viral RNAs (20 out of 21). Sputnik does not replicate with Marseillevirus but delays its replication cycle. While Marseillevirus is successfully internalized by A. castellanii following co-infections with Mamavirus and Sputnik, it does not initiate a replication cycle. In contrast, both Marseillevirus and Mamavirus can replicate in the amoeba in case of co-infection, but the development of one is exclusive from the other inside a single amoeba cell. This work provides new insight into the Sputnik replication cycle with another giant virus and confirms that Sputnik is a virophage. It shows new dimensions of the interactions existing among giant viruses. Copyright 2010 S. Karger AG, Basel.

Enhanced HIV-1 replication in ex vivo ectocervical tissues from post-menopausal women correlates with increased inflammatory responses.

PubMed

Rollenhagen, C; Asin, S N

2011-11-01

Knowledge about early innate immune responses at the mucosal surfaces of the female genital tract is important in understanding the pathogenesis of heterosexual transmission of human immunodeficiency virus type-1 (HIV-1). As estradiol decreases inflammatory responses, we postulated that an estradiol-deficient state such as post-menopause could enhance expression of inflammatory factors that stimulate HIV-1 replication. We compare HIV-1 integration, transcription, and viral p24 release levels among ectocervical tissues obtained from pre- and post-menopausal donors. We detected enhanced HIV-1 p24 release levels in post- compared with pre-menopausal tissues (P<0.0001), but saw no difference in HIV-1 integration. Overall, 100% of post-menopausal tissues exhibited levels of HIV-1 transcription above background compared with only 60% of pre-menopausal tissues. Increased HIV-1 transcription was associated with enhanced interleukin (IL)-1β, IL-6, monocyte chemotactic protein-1, growth-regulated oncogene-α, and interferon-γ-inducible protein-10 expression. Neutralization and nuclear factor-κB-targeting small-interfering RNA experiments both decreased HIV-1 transcription, suggesting that the early inflammatory response may facilitate HIV-1 replication in ex vivo ectocervical tissues from post-menopausal women.

Computer-delivered screening and brief intervention (e-SBI) for postpartum drug use: a randomized trial.

PubMed

Ondersma, Steven J; Svikis, Dace S; Thacker, Leroy R; Beatty, Jessica R; Lockhart, Nancy

2014-01-01

Electronic screening and brief intervention (e-SBI) approaches for substance use have shown early promise. This trial was designed to replicate previous findings from a single 20-minute e-SBI for drug use among postpartum women. A total of 143 postpartum, primarily low-income African-American women meeting criteria for drug use, were randomly assigned to either a tailored e-SBI or a time-matched control condition. Blinded follow-up evaluation 3- and 6-months following childbirth revealed strong effects for confirmed illicit drug use abstinence at the 3-month observation (OR=3.3, p=.01), as did hair analysis at 6months (OR=4.8, p=.018). Additional primary outcomes suggested small to moderate effect sizes in favor of the e-SBI, but did not reach significance. This result replicates previous findings but fails to show durable effects. Assessment reactivity, e-SBI design, and possible extension of e-SBI via tailored messaging all merit careful consideration. © 2013 Elsevier Inc. All rights reserved.

Risk Factors for Death from Visceral Leishmaniasis in an Urban Area of Brazil

PubMed Central

Druzian, Angelita F.; de Souza, Albert S.; de Campos, Diogo N.; Croda, Julio; Higa, Minoru G.; Dorval, Maria Elizabeth C.; Pompilio, Mauricio A.; de Oliveira, Polliana A.; Paniago, Anamaria M. M.

2015-01-01

Background Over the last three decades, the epidemiological profile of visceral leishmaniasis (VL) has changed with epidemics occurring in large urban centers of Brazil, an increase in HIV/AIDS co-infection, and a significant increase in mortality. The objective of this study was to identify the risk factors associated with death among adult patients with VL from an urban endemic area of Brazil. Methodology A prospective cohort study included 134 adult patients with VL admitted to the University Hospital of the Federal University of Mato Grosso do Sul between August 2011 and August 2013. Principal Findings Patients ranged from 18 to 93 years old, with a mean age of 43.6 (±15.7%). Of these patients, 36.6% were co-infected with HIV/AIDS, and the mortality rate was 21.6%. In a multivariate analysis, the risk factors associated with death were secondary bacterial infection (42.86, 5.05–363.85), relapse (12.17, 2.06–71.99), edema (7.74, 1.33–45.05) and HIV/AIDS co-infection (7.33, 1.22–43.98). Conclusions/Significance VL has a high mortality rate in adults from endemic urban areas, especially when coinciding with high rates of HIV/AIDS co-infection. PMID:26274916

Exercise-induced oxyhaemoglobin desaturation, ventilatory limitation and lung diffusing capacity in women during and after exercise.

PubMed

Walls, Justin; Maskrey, Michael; Wood-Baker, Richard; Stedman, Wade

2002-06-01

Arterial haemoglobin saturation during exercise in healthy young women [eight subjects mean (SEM) age 20.8 (1.8) years] was measured to confirm the theory that young women experience exercise-induced arterial hypoxaemia (EIAH) at a lower relative percentage of maximal oxygen uptake (VO(2max)) than has been documented in their male counterparts. To determine if flow limitation [the percentage of the tidal volume ( V(T)) that met or exceeded the boundary established by multiple maximal expiratory manoeuvres] and/or post-exercise lung diffusing capacity are linked to EIAH in women, and to investigate the influence of exercise intensity and duration on post-exercise carbon monoxide lung diffusing capacity ( D(L, CO)), these parameters were measured during and after three exercise tests (incremental test until exhaustion, 5 km run and 5 km run with sprint). All subjects experienced physiologically significant EIAH (a fall of more than 3% in oxygen saturation of arterial blood from levels at rest) and seven subjects experienced flow limitation during the VO(2max) protocol [mean (SD) 12.2 (8.8)% of V(T)]. Even though there was no significant relationship between aerobic capacity and the degree of flow limitation ( r=0.33, P>0.05), the flow limitation was related to absolute ventilation in the subjects studied ( r=0.82, P<0.05). There was no significant relationship between decrements in post exercise D(L, CO) and EIAH ( r=0.05, P>0.05), however there was a strong correlation between the extent of flow limitation (% of V(T)) and EIAH ( r=0.71). Significant decreases in D(L, CO) lasted for up to 16 h after each of the exercise tests ( P<0.05) and lasted for a further 8 h after the maximal test ( P<0.05). Exercise intensity was the main contributing factor to the observed decreases in post-exercise D(L, CO) with the percentage of VO(2max) attained during the various tests being significantly related to the fall in D(L, CO) for 1, 2, 3, 16 and 24 h after exercise ( P<0.05). As the appearance of flow limitation closely coincided with the appearance of EIAH, the results from the present study suggest that flow limitation is a contributing factor to EIAH in women although the exact mechanism remains unclear.

Utilizing Co 2+/Co 3+ Redox Couple in P2-Layered Na 0.66Co 0.22Mn 0.44Ti 0.34O 2 Cathode for Sodium-Ion Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Qin-Chao; Hu, Enyuan; Pan, Yang

Developing sodium-ion batteries for large-scale energy storage applications is facing big challenges of the lack of high-performance cathode materials. Here, a series of new cathode materials Na 0.66Co xMn 0.66–xTi 0.34O 2 for sodium-ion batteries are designed and synthesized aiming to reduce transition metal-ion ordering, charge ordering, as well as Na+ and vacancy ordering. An interesting structure change of Na 0.66Co xMn 0.66–xTi 0.34O 2 from orthorhombic to hexagonal is revealed when Co content increases from x = 0 to 0.33. In particular, Na 0.66Co 0.22Mn 0.44Ti 0.34O 2 with a P2-type layered structure delivers a reversible capacity of 120more » mAh g -1 at 0.1 C. When the current density increases to 10 C, a reversible capacity of 63.2 mAh g -1 can still be obtained, indicating a promising rate capability. The low valence Co 2+ substitution results in the formation of average Mn 3.7+ valence state in Na 0.66Co 0.22Mn 0.44Ti 0.34O 2, effectively suppressing the Mn3+-induced Jahn–Teller distortion, and in turn stabilizing the layered structure. X-ray absorption spectroscopy results suggest that the charge compensation of Na 0.66Co 0.22Mn 0.44Ti 0.34O 2 during charge/discharge is contributed by Co 2.2+/Co 3+ and Mn 3.3+/Mn 4+ redox couples. This is the first time that the highly reversible Co 2+/Co 3+ redox couple is observed in P2-layered cathodes for sodium-ion batteries. This finding may open new approaches to design advanced intercalation-type cathode materials.« less

Utilizing Co 2+/Co 3+ Redox Couple in P2-Layered Na 0.66Co 0.22Mn 0.44Ti 0.34O 2 Cathode for Sodium-Ion Batteries

DOE PAGES

Wang, Qin-Chao; Hu, Enyuan; Pan, Yang; ...

2017-07-06

Developing sodium-ion batteries for large-scale energy storage applications is facing big challenges of the lack of high-performance cathode materials. Here, a series of new cathode materials Na 0.66Co xMn 0.66–xTi 0.34O 2 for sodium-ion batteries are designed and synthesized aiming to reduce transition metal-ion ordering, charge ordering, as well as Na+ and vacancy ordering. An interesting structure change of Na 0.66Co xMn 0.66–xTi 0.34O 2 from orthorhombic to hexagonal is revealed when Co content increases from x = 0 to 0.33. In particular, Na 0.66Co 0.22Mn 0.44Ti 0.34O 2 with a P2-type layered structure delivers a reversible capacity of 120more » mAh g -1 at 0.1 C. When the current density increases to 10 C, a reversible capacity of 63.2 mAh g -1 can still be obtained, indicating a promising rate capability. The low valence Co 2+ substitution results in the formation of average Mn 3.7+ valence state in Na 0.66Co 0.22Mn 0.44Ti 0.34O 2, effectively suppressing the Mn3+-induced Jahn–Teller distortion, and in turn stabilizing the layered structure. X-ray absorption spectroscopy results suggest that the charge compensation of Na 0.66Co 0.22Mn 0.44Ti 0.34O 2 during charge/discharge is contributed by Co 2.2+/Co 3+ and Mn 3.3+/Mn 4+ redox couples. This is the first time that the highly reversible Co 2+/Co 3+ redox couple is observed in P2-layered cathodes for sodium-ion batteries. This finding may open new approaches to design advanced intercalation-type cathode materials.« less

Utilizing Co2+/Co3+ Redox Couple in P2-Layered Na0.66Co0.22Mn0.44Ti0.34O2 Cathode for Sodium-Ion Batteries.

PubMed

Wang, Qin-Chao; Hu, Enyuan; Pan, Yang; Xiao, Na; Hong, Fan; Fu, Zheng-Wen; Wu, Xiao-Jing; Bak, Seong-Min; Yang, Xiao-Qing; Zhou, Yong-Ning

2017-11-01

Developing sodium-ion batteries for large-scale energy storage applications is facing big challenges of the lack of high-performance cathode materials. Here, a series of new cathode materials Na 0.66 Co x Mn 0.66- x Ti 0.34 O 2 for sodium-ion batteries are designed and synthesized aiming to reduce transition metal-ion ordering, charge ordering, as well as Na + and vacancy ordering. An interesting structure change of Na 0.66 Co x Mn 0.66- x Ti 0.34 O 2 from orthorhombic to hexagonal is revealed when Co content increases from x = 0 to 0.33. In particular, Na 0.66 Co 0.22 Mn 0.44 Ti 0.34 O 2 with a P2-type layered structure delivers a reversible capacity of 120 mAh g -1 at 0.1 C. When the current density increases to 10 C, a reversible capacity of 63.2 mAh g -1 can still be obtained, indicating a promising rate capability. The low valence Co 2+ substitution results in the formation of average Mn 3.7+ valence state in Na 0.66 Co 0.22 Mn 0.44 Ti 0.34 O 2 , effectively suppressing the Mn 3+ -induced Jahn-Teller distortion, and in turn stabilizing the layered structure. X-ray absorption spectroscopy results suggest that the charge compensation of Na 0.66 Co 0.22 Mn 0.44 Ti 0.34 O 2 during charge/discharge is contributed by Co 2.2+ /Co 3+ and Mn 3.3+ /Mn 4+ redox couples. This is the first time that the highly reversible Co 2+ /Co 3+ redox couple is observed in P2-layered cathodes for sodium-ion batteries. This finding may open new approaches to design advanced intercalation-type cathode materials.

CO32- concentration and pCO2 thresholds for calcification and dissolution on the Molokai reef flat, Hawaii

USGS Publications Warehouse

Yates, K.K.; Halley, R.B.

2006-01-01

The severity of the impact of elevated atmospheric pCO2 to coral reef ecosystems depends, in part, on how sea-water pCO2 affects the balance between calcification and dissolution of carbonate sediments. Presently, there are insufficient published data that relate concentrations of pCO 2 and CO32- to in situ rates of reef calcification in natural settings to accurately predict the impact of elevated atmospheric pCO2 on calcification and dissolution processes. Rates of net calcification and dissolution, CO32- concentrations, and pCO2 were measured, in situ, on patch reefs, bare sand, and coral rubble on the Molokai reef flat in Hawaii. Rates of calcification ranged from 0.03 to 2.30 mmol CaCO3 m-2 h-1 and dissolution ranged from -0.05 to -3.3 mmol CaCO3 m-2 h-1. Calcification and dissolution varied diurnally with net calcification primarily occurring during the day and net dissolution occurring at night. These data were used to calculate threshold values for pCO2 and CO32- at which rates of calcification and dissolution are equivalent. Results indicate that calcification and dissolution are linearly correlated with both CO32- and pCO2. Threshold pCO2 and CO32- values for individual substrate types showed considerable variation. The average pCO2 threshold value for all substrate types was 654??195 ??atm and ranged from 467 to 1003 ??atm. The average CO32- threshold value was 152??24 ??mol kg-1, ranging from 113 to 184 ??mol kg-1. Ambient seawater measurements of pCO2 and CO32- indicate that CO32- and pCO2 threshold values for all substrate types were both exceeded, simultaneously, 13% of the time at present day atmospheric pCO2 concentrations. It is predicted that atmospheric pCO2 will exceed the average pCO2 threshold value for calcification and dissolution on the Molokai reef flat by the year 2100.

Co-Infection of Mosquitoes with Chikungunya and Dengue Viruses Reveals Modulation of the Replication of Both Viruses in Midguts and Salivary Glands of Aedes aegypti Mosquitoes

PubMed Central

Le Coupanec, Alain; Tchankouo-Nguetcheu, Stéphane; Roux, Pascal; Khun, Huot; Huerre, Michel; Morales-Vargas, Ronald; Enguehard, Margot; Lavillette, Dimitri; Missé, Dorothée

2017-01-01

Arthropod-borne virus (arbovirus) infections cause several emerging and resurgent infectious diseases in humans and animals. Chikungunya-affected areas often overlap with dengue-endemic areas. Concurrent dengue virus (DENV) and chikungunya virus (CHIKV) infections have been detected in travelers returning from regions of endemicity. CHIKV and DENV co-infected Aedes albopictus have also been collected in the vicinity of co-infected human cases, emphasizing the need to study co-infections in mosquitoes. We thus aimed to study the pathogen-pathogen interaction involved in these co-infections in DENV/CHIKV co-infected Aedes aegypti mosquitoes. In mono-infections, we detected CHIKV antigens as early as 4 days post-virus exposure in both the midgut (MG) and salivary gland (SG), whereas we detected DENV serotype 2 (DENV-2) antigens from day 5 post-virus exposure in MG and day 10 post-virus exposure in SG. Identical infection rates were observed for singly and co-infected mosquitoes, and facilitation of the replication of both viruses at various times post-viral exposure. We observed a higher replication for DENV-2 in SG of co-infected mosquitoes. We showed that mixed CHIKV and DENV infection facilitated viral replication in Ae. aegypti. The outcome of these mixed infections must be further studied to increase our understanding of pathogen-pathogen interactions in host cells. PMID:28777313

Co-Infection of Mosquitoes with Chikungunya and Dengue Viruses Reveals Modulation of the Replication of Both Viruses in Midguts and Salivary Glands of Aedes aegypti Mosquitoes.

PubMed

Le Coupanec, Alain; Tchankouo-Nguetcheu, Stéphane; Roux, Pascal; Khun, Huot; Huerre, Michel; Morales-Vargas, Ronald; Enguehard, Margot; Lavillette, Dimitri; Missé, Dorothée; Choumet, Valérie

2017-08-04

Arthropod-borne virus (arbovirus) infections cause several emerging and resurgent infectious diseases in humans and animals. Chikungunya-affected areas often overlap with dengue-endemic areas. Concurrent dengue virus (DENV) and chikungunya virus (CHIKV) infections have been detected in travelers returning from regions of endemicity. CHIKV and DENV co-infected Aedes albopictus have also been collected in the vicinity of co-infected human cases, emphasizing the need to study co-infections in mosquitoes. We thus aimed to study the pathogen-pathogen interaction involved in these co-infections in DENV/CHIKV co-infected Aedes aegypti mosquitoes. In mono-infections, we detected CHIKV antigens as early as 4 days post-virus exposure in both the midgut (MG) and salivary gland (SG), whereas we detected DENV serotype 2 (DENV-2) antigens from day 5 post-virus exposure in MG and day 10 post-virus exposure in SG. Identical infection rates were observed for singly and co-infected mosquitoes, and facilitation of the replication of both viruses at various times post-viral exposure. We observed a higher replication for DENV-2 in SG of co-infected mosquitoes. We showed that mixed CHIKV and DENV infection facilitated viral replication in Ae. aegypti . The outcome of these mixed infections must be further studied to increase our understanding of pathogen-pathogen interactions in host cells.

Identification of cellular and viral factors related to anti-hepatitis C virus activity of cyclophilin inhibitor.

PubMed

Goto, Kaku; Watashi, Koichi; Inoue, Daisuke; Hijikata, Makoto; Shimotohno, Kunitada

2009-10-01

We have so far reported that an immunosuppressant cyclosporin A (CsA), a well-known cyclophilin (CyP) inhibitor (CPI), strongly suppressed hepatitis C virus (HCV) replication in cell culture, and that CyPB was a cellular cofactor for viral replication. To further investigate antiviral mechanisms of CPI, we here developed cells carrying CsA-resistant HCV replicons, by culturing the HCV subgenomic replicon cells for 4 weeks in the presence of CsA with G418. Transfection of total RNA from the isolated CsA-resistant cells to naïve Huh7 cells conferred CsA resistance, suggesting that the replicon RNA itself was responsible for the resistant phenotype. Of the identified amino acid mutations, D320E in NS5A conferred the CsA resistance. The replicon carrying the D320E mutation was sensitive to interferon-alpha, but was resistant to CsA and other CPIs including NIM811 and sanglifehrin A. Knockdown of individual CyP subtypes revealed CyP40, in addition to CyPA and CyPB, contributed to viral replication, and CsA-resistant replicons acquired independence from CyPA for efficient replication. These data provide important evidence on the mechanisms underlying the regulation of HCV replication by CyP and for designing novel and specific anti-HCV strategies with CPIs.

Genetic dissection of the pre-eclampsia susceptibility locus on chromosome 2q22 reveals shared novel risk factors for cardiovascular disease

PubMed Central

Johnson, Matthew P.; Brennecke, Shaun P.; East, Christine E.; Dyer, Thomas D.; Roten, Linda T.; Proffitt, J. Michael; Melton, Phillip E.; Fenstad, Mona H.; Aalto-Viljakainen, Tia; Mäkikallio, Kaarin; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Laivuori, Hannele; Austgulen, Rigmor; Blangero, John; Moses, Eric K.; Pouta, Anneli; Kivinen, Katja; Ekholm, Eeva; Hietala, Reija; Sainio, Susanna; Saisto, Terhi; Uotila, Jukka; Klemetti, Miira; Inkeri Lokki, Anna; Georgiadis, Leena; Huovari, Elina; Kortelainen, Eija; Leminen, Satu; Lähdesmäki, Aija; Mehtälä, Susanna; Salmen, Christina

2013-01-01

Pre-eclampsia is an idiopathic pregnancy disorder promoting morbidity and mortality to both mother and child. Delivery of the fetus is the only means to resolve severe symptoms. Women with pre-eclamptic pregnancies demonstrate increased risk for later life cardiovascular disease (CVD) and good evidence suggests these two syndromes share several risk factors and pathophysiological mechanisms. To elucidate the genetic architecture of pre-eclampsia we have dissected our chromosome 2q22 susceptibility locus in an extended Australian and New Zealand familial cohort. Positional candidate genes were prioritized for exon-centric sequencing using bioinformatics, SNPing, transcriptional profiling and QTL-walking. In total, we interrogated 1598 variants from 52 genes. Four independent SNP associations satisfied our gene-centric multiple testing correction criteria: a missense LCT SNP (rs2322659, P = 0.0027), a synonymous LRP1B SNP (rs35821928, P = 0.0001), an UTR-3 RND3 SNP (rs115015150, P = 0.0024) and a missense GCA SNP (rs17783344, P = 0.0020). We replicated the LCT SNP association (P = 0.02) and observed a borderline association for the GCA SNP (P = 0.07) in an independent Australian case–control population. The LRP1B and RND3 SNP associations were not replicated in this same Australian singleton cohort. Moreover, these four SNP associations could not be replicated in two additional case–control populations from Norway and Finland. These four SNPs, however, exhibit pleiotropic effects with several quantitative CVD-related traits. Our results underscore the genetic complexity of pre-eclampsia and present novel empirical evidence of possible shared genetic mechanisms underlying both pre-eclampsia and other CVD-related risk factors. PMID:23420841

Development of an Advanced Respirometer for Experimental Studies of Benthic Rate Processes

NASA Astrophysics Data System (ADS)

Barry, J. P.; Buck, K. R.; Okuda, C.; Risi, M.; Parker, M.; Levesque, C.

2005-05-01

Rates of carbon remineralization and nutrient cycling by seafloor biotic assemblages are influenced by the availability of organic material, temperature, and oxygen availability, among other factors. The relative importance of various factors in controlling carbon cycling by the sediment community is poorly constrained, in part by technological limits on experiments that evaluate independently the effects of these factors. We have developed an advanced respiration chamber system capable of repeated rate measurements during a single deployment, with added capabilities for manipulating conditions within replicate chambers to test hypotheses concerning biogeochemical cycling by the benthos. The ROV-deployed respiration system has 12 syringes for tracer injection or sample withdrawal from 3 respiration chambers, pH, oxygen, and temperature sensors, stirring paddles, and a recirculation pump. The pump system is used to flush each chamber at preprogrammed intervals or oxygen tensions. Areas of investigation that are enabled by the system include the effects various factors on benthic oxygen consumptions (e.g. hypercapnia (elevated CO2), acidosis, ambient oxygen availability, temperature, organic carbon availability), rates of nutrient regeneration by the benthos in response to organic enrichments (labile and refractory organic carbon), time lags in carbon uptake and trophic pathways in responses to organic enrichment.

Oysters and eelgrass: potential partners in a high pCO2 ocean.

PubMed

Groner, Maya L; Burge, Colleen A; Cox, Ruth; Rivlin, Natalie; Turner, Mo; Van Alstyne, Kathryn L; Wyllie-Echeverria, Sandy; Bucci, John; Staudigel, Philip; Friedman, Carolyn S

2018-05-25

Climate change is affecting the health and physiology of marine organisms and altering species interactions. Ocean acidification (OA) threatens calcifying organisms such as the Pacific oyster, Crassostrea gigas. In contrast, seagrasses, such as the eelgrass Zostera marina, can benefit from the increase in available carbon for photosynthesis found at a lower seawater pH. Seagrasses can remove dissolved inorganic carbon from OA environments, creating local daytime pH refugia. Pacific oysters may improve the health of eelgrass by filtering out pathogens such as Labyrinthula zosterae (LZ), which causes eelgrass wasting disease (EWD). We examined how co-culture of eelgrass ramets and juvenile oysters affected the health and growth of eelgrass and the mass of oysters under different pCO 2 exposures. In Phase I, each species was cultured alone or in co-culture at 12°C across ambient, medium, and high pCO 2 conditions, (656, 1158 and1606 μatm pCO 2 , respectively). Under high pCO 2 , eelgrass grew faster and had less severe EWD (contracted in the field prior to the experiment). Co-culture with oysters also reduced the severity of EWD. While the presence of eelgrass decreased daytime pCO 2 , this reduction was not substantial enough to ameliorate the negative impact of high pCO 2 on oyster mass. In Phase II, eelgrass alone or oysters and eelgrass in co-culture were held at 15°C under ambient and high pCO 2 conditions, (488 and 2013 μatm pCO 2 , respectively). Half of the replicates were challenged with cultured LZ. Concentrations of defensive compounds in eelgrass (total phenolics and tannins), were altered by LZ exposure and pCO 2 treatments. Greater pathogen loads and increased EWD severity were detected in LZ exposed eelgrass ramets; EWD severity was reduced at high relative to low pCO 2 . Oyster presence did not influence pathogen load or EWD severity; high LZ concentrations in experimental treatments may have masked the effect of this treatment. Collectively, these results indicate that, when exposed to natural concentrations of LZ under high pCO 2 conditions, eelgrass can benefit from co-culture with oysters. Further experimentation is necessary to quantify how oysters may benefit from co-culture with eelgrass, examine these interactions in the field and quantify context-dependency. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

VizieR Online Data Catalog: Effective collision strengths of Si VII (Sossah+, 2014)

NASA Astrophysics Data System (ADS)

Sossah, A. M.; Tayal, S. S.

2017-08-01

The purpose of present work is to calculate more accurate data for Si VII by using highly accurate target descriptions and by including a sufficient number of target states in the close-coupling expansion. We also included fine-structure effects in the close-coupling expansions to account for the relativistic effects. We used the B-spline Breit-Pauli R-matrix (BSR) codes (Zatsarinny 2006CoPhC.174..273Z) in our scattering calculations. The present method utilizes the term-dependent non-orthogonal orbital sets for the description of the target wave functions and scattering functions. The collisional and radiative parameters have been calculated for all forbidden and allowed transitions between the lowest 92 LSJ levels of 2s22p4, 2s2p5, 2p6, 2s22p33s, 2s22p33p, 2s22p33d, and 2s2p43s configurations of Si VII. (3 data files).

Baicalin benefits the anti-HBV therapy via inhibiting HBV viral RNAs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Hai, E-mail: HHai3552@sina.cn

Background: Although current antiviral treatments (nucleoside analogs, NAs) for chronic hepatitis B virus (HBV) infection are effective in suppressing HBV-DNA replication, their clinical outcomes can be compromised by the increasing drug resistance and the inefficiency in promoting HBsAg/HBeAg seroconversion. Objectives: In this study, we will explore possible effects and mechanism of a natural product baicalin (BA) with the anti-HBV efficacy of entecavir (ETV), a first-line anti-HBV drug, in HBV-DNA, HBsAg/HBeAg seroconversion and drug-resistance. Methods: The co-effects of BA and ETV were conducted in wild-type/NA-resistance mutant HBV cell lines and DHBV-infected duckling models. HBV-DNA/RNAs, HBsAg/HBeAg, host factors (hepatocyte nuclear factors) weremore » explored for possible anti-HBV mechanism. Results and discussion: BA could significantly enhance and reduced HBsAg and HBeAg in hepG2.2.15, a wild-type HBV cell line. Co-treatment of BA and ETV had a more dramatic effect in NA-resistant HBV{sup rtM204V/rtLl80M} transfected hepG2 cells. Our study further revealed that BA mainly inhibited the production of HBV RNAs (3.5, 2.4, 2.1 kb), the templates for viral proteins and HBV-DNA synthesis. BA blocked HBV RNAs transcription possibly by down-regulating transcription and expression of HBV replication dependent hepatocyte nuclear factors (HNF1α and HNF4α). Thus, BA may benefit the anti-HBV therapy via inhibiting HBV viral RNAs. - Highlights: • Baicalin benefits the anti-HBV therapy. • Baicalin enhances ETV antiviral efficacy and overcomes NA-resistant HBV mutation. • The anti-HBV effect of baicalin is achieved by inhibiting HBV RNAs. • Baicalin down-regulates HBV replication-dependent host factors HNF 1α and HNF 4α.« less

The phosphoprotein genes of measles viruses from subacute sclerosing panencephalitis cases encode functional as well as non-functional proteins and display reduced editing.

PubMed

Millar, E L; Rennick, L J; Weissbrich, B; Schneider-Schaulies, J; Duprex, W P; Rima, B K

2016-01-04

Products expressed from the second (P/V/C) gene are important in replication and abrogating innate immune responses during acute measles virus (MV) infection. Thirteen clone sets were derived from the P/V/C genes of measles virus (MV) RNA extracted from brains of a unique collection of seven cases of subacute sclerosing panencephalitis (SSPE) caused by persistent MV in the central nervous system (CNS). Whether these functions are fully maintained when MV replicates in the CNS has not been previously determined. Co-transcriptional editing of the P mRNAs by non-template insertion of guanine (G) nucleotides, which generates mRNAs encoding the viral V protein, occurs much less frequently (9%) in the SSPE derived samples than during the acute infection (30-50%). Thus it is likely that less V protein, which is involved in combatting the innate immune response, is produced. The P genes in MV from SSPE cases were not altered by biased hypermutation but exhibited a high degree of variation within each case. Most but not all SSPE derived phospho-(P) proteins were functional in mini genome replication/transcription assays. An eight amino acid truncation of the carboxyl-terminus made the P protein non-functional while the insertion of an additional glycine residue by insertion of G nucleotides at the editing site had no effect on protein function. Copyright © 2015 Elsevier B.V. All rights reserved.

Non-structural protein P6 encoded by rice black-streaked dwarf virus is recruited to viral inclusion bodies by binding to the viroplasm matrix protein P9-1.

PubMed

Sun, Liying; Xie, Li; Andika, Ida Bagus; Tan, Zilong; Chen, Jianping

2013-08-01

Like other members of the family Reoviridae, rice black-streaked dwarf virus (RBSDV, genus Fijivirus) is thought to replicate and assemble within cytoplasmic viral inclusion bodies, commonly called viroplasms. RBSDV P9-1 is the key protein for the formation of viroplasms, but little is known about the other proteins of the viroplasm or the molecular interactions amongst its components. RBSDV non-structural proteins were screened for their association with P9-1 using a co-immunoprecipitation assay. Only P6 was found to directly interact with P9-1, an interaction that was confirmed by bimolecular fluorescence complementation assay in Spodoptera frugiperda (Sf9) cells. Immunoelectron microscopy showed that P6 and P9-1 co-localized in electron-dense inclusion bodies, indicating that P6 is a constituent of the viroplasm. In addition, non-structural protein P5 also localized to viroplasms and interacted with P6. In Sf9 cells, P6 was diffusely distributed throughout the cytoplasm when expressed alone, but localized to inclusions when co-expressed with P9-1, suggesting that P6 is recruited to viral inclusion bodies by binding to P9-1. P5 localized to the inclusions formed by P9-1 when co-expressed with P6 but did not when P6 was absent, suggesting that P5 is recruited to viroplasms by binding to P6. This study provides a model by which viral non-structural proteins are recruited to RBSDV viroplasms.

Inhibition of Hepatitis B Virus and Induction of Hepatoma Cell Apoptosis by ASGPR-Directed Delivery of shRNAs

PubMed Central

Yao, Xinxin; Shi, Chuan; Sun, Lifang; Yuan, Lu; Lei, Ping; Zhu, Huifen; Liu, Hongbo; Wu, Xiongwen; Ning, Qin; Zhou, Chun; Shen, Guanxin

2012-01-01

Hepatitis B virus (HBV) infection is a worldwide liver disease and nearly 25% of chronic HBV infections terminate in hepatocellular carcinoma (HCC). Currently, there is no effective therapy to inhibit HBV replication and to eliminate hepatoma cells, making it highly desired to develop novel therapies for these two stages of the HBV-caused detrimental disease. Recently, short hairpin RNA (shRNA) has emerged as a potential therapy for virus-infected disease and cancer. Here, we have generated a shRNA, pGenesil-siHBV4, which effectively inhibits HBV replication in the human hepatoma cell line HepG2.2.15. The inhibitory effects of pGenesil-siHBV4 are manifested by the decrease of both the HBV mRNA level and the protein levels of the secreted HBV surface antigen (HBsAg) and HBV e antigen (HBeAg), and by the reduction of secreted HBV DNA. Using mouse hydrodynamic tail vein injection, we demonstrate that pGenesil-siHBV4 is effective in inhibiting HBV replication in vivo. Because survivin plays a key role in cancer cell escape from apoptosis, we further generated pGenesil-siSurvivin, a survivin-silencing shRNA, and showed its effect of triggering apoptosis of HBV-containing hepatoma cells. To develop targeted shRNA therapy, we have identified that as a specific binder of the asialoglycoprotein receptor (ASGPR), jetPEI-Hepatocyte delivers pGenesil-siHBV4 and pGenesil-siSurvivin specifically to hepatocytes, not other types of cells. Finally, co-transfection of pGenesil-siHBV4 and pGenesil-siSurvivin exerts synergistic effects in inducing hepatoma cell apoptosis, a novel approach to eliminate hepatoma by downregulating survivin via multiple mechanisms. The application of these novel shRNAs with the jetPEI-Hepatocyte targeting strategy demonstrates the proof-of-principle for a promising approach to inhibit HBV replication and eliminate hepatoma cells with high specificity. PMID:23094023

Large-scale gene-centric analysis identifies novel variants for coronary artery disease.

PubMed

2011-09-01

Coronary artery disease (CAD) has a significant genetic contribution that is incompletely characterized. To complement genome-wide association (GWA) studies, we conducted a large and systematic candidate gene study of CAD susceptibility, including analysis of many uncommon and functional variants. We examined 49,094 genetic variants in ∼2,100 genes of cardiovascular relevance, using a customised gene array in 15,596 CAD cases and 34,992 controls (11,202 cases and 30,733 controls of European descent; 4,394 cases and 4,259 controls of South Asian origin). We attempted to replicate putative novel associations in an additional 17,121 CAD cases and 40,473 controls. Potential mechanisms through which the novel variants could affect CAD risk were explored through association tests with vascular risk factors and gene expression. We confirmed associations of several previously known CAD susceptibility loci (eg, 9p21.3:p<10(-33); LPA:p<10(-19); 1p13.3:p<10(-17)) as well as three recently discovered loci (COL4A1/COL4A2, ZC3HC1, CYP17A1:p<5×10(-7)). However, we found essentially null results for most previously suggested CAD candidate genes. In our replication study of 24 promising common variants, we identified novel associations of variants in or near LIPA, IL5, TRIB1, and ABCG5/ABCG8, with per-allele odds ratios for CAD risk with each of the novel variants ranging from 1.06-1.09. Associations with variants at LIPA, TRIB1, and ABCG5/ABCG8 were supported by gene expression data or effects on lipid levels. Apart from the previously reported variants in LPA, none of the other ∼4,500 low frequency and functional variants showed a strong effect. Associations in South Asians did not differ appreciably from those in Europeans, except for 9p21.3 (per-allele odds ratio: 1.14 versus 1.27 respectively; P for heterogeneity = 0.003). This large-scale gene-centric analysis has identified several novel genes for CAD that relate to diverse biochemical and cellular functions and clarified the literature with regard to many previously suggested genes.

Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.

PubMed

Walsh, Kyle M; Anderson, Erik; Hansen, Helen M; Decker, Paul A; Kosel, Matt L; Kollmeyer, Thomas; Rice, Terri; Zheng, Shichun; Xiao, Yuanyuan; Chang, Jeffrey S; McCoy, Lucie S; Bracci, Paige M; Wiemels, Joe L; Pico, Alexander R; Smirnov, Ivan; Lachance, Daniel H; Sicotte, Hugues; Eckel-Passow, Jeanette E; Wiencke, John K; Jenkins, Robert B; Wrensch, Margaret R

2013-02-01

Genomewide association studies (GWAS) and candidate-gene studies have implicated single-nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case-control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate-gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P < 0.05), with all associations in the same direction as in previous reports. Several SNP associations showed considerable differences across histologic subtype. All eight successfully replicated associations were first identified by GWAS, although none of the putative risk SNPs from candidate-gene studies was associated in the full case-control sample (all P values > 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes. © 2012 WILEY PERIODICALS, INC.

Legionella and Coxiella effectors: strength in diversity and activity.

PubMed

Qiu, Jiazhang; Luo, Zhao-Qing

2017-10-01

Legionella pneumophila and Coxiella burnetii are two evolutionarily related intracellular pathogens that use the Dot/Icm type IV secretion system to translocate effectors into host cells. These effectors are essential for the establishment of membrane-bound compartments known as replication vacuoles, which enable the survival and replication of bacteria inside host cells. The effectors interfere with diverse signalling pathways to co-opt host processes, such as vesicle trafficking, ubiquitylation, gene expression and lipid metabolism, to promote pathogen survival. In this Review, we explore Dot/Icm effectors from L. pneumophila and C. burnetii as key virulence factors, and we examine the biochemical and cell biological functions of these effectors and their roles in our understanding of bacterial virulence.

Liming induces carbon dioxide (CO2) emission in PSB inoculated alkaline soil supplemented with different phosphorus sources.

PubMed

Adnan, Muhammad; Shah, Zahir; Sharif, Muhammad; Rahman, Hidayatur

2018-04-01

Agricultural land is a major sink of global organic carbon (C). Its suitable management is crucial for improving C sequestration and reducing soil CO 2 emission. Incubation experiments were performed to assess the impact of phosphate solubilizing bacterial (PSB) inoculation (inoculated and uninoculated) and soil calcification (4.78, 10, 15, and 20% crushed CaCO 3 ) with phosphorus (P) sources [single superphosphate (SSP), rock phosphate (RP), farm yard manure (FYM), and poultry manure (PM)] in experiment 1 and with various rates of PM (4, 8, and 12 kg ha -1 ) in experiment 2 on cumulative soil respiration. These experiments were arranged in three factorial, complete randomize design (CRD) with three replications. Interactively, lime with P sources (at day 1 and 3) and lime with PSB (at day 1) significantly expedited soil respiration. Mainly, PSB inoculation, liming, PM fertilization, and its various rates significantly enhanced soil respiration with time over control/minimum in alkaline soil at all incubation periods. Higher CO 2 emission was detected in soil supplemented with organic P sources (PM and FYM) than mineral sources (SSP and RP). CO 2 emission was noted to increase with increasing PM content. Since liming intensified CO 2 discharge from soil, therefore addition of lime to an alkaline soil should be avoided; instead, integrated approaches must be adopted for P management in alkaline calcareous soils for climate-smart agriculture.

Genome-wide association analysis and replication of coronary artery disease in South Korea suggests a causal variant common to diverse populations

PubMed Central

Cho, Eun Young; Jang, Yangsoo; Shin, Eun Soon; Jang, Hye Yoon; Yoo, Yeon-Kyeong; Kim, Sook; Jang, Ji Hyun; Lee, Ji Yeon; Yun, Min Hye; Park, Min Young; Chae, Jey Sook; Lim, Jin Woo; Shin, Dong Jik; Park, Sungha; Lee, Jong Ho; Han, Bok Ghee; Rae, Kim Hyung; Cardon, Lon R; Morris, Andrew P; Lee, Jong Eun; Clarke, Geraldine M

2010-01-01

Background Recent genome-wide association (GWA) studies have identified and replicated several genetic loci associated with the risk of development of coronary artery disease (CAD) in samples from populations of Caucasian and Asian descent. However, only chromosome 9p21 has been confirmed as a major susceptibility locus conferring risk for development of CAD across multiple ethnic groups. The authors aimed to find evidence of further similarities and differences in genetic risk of CAD between Korean and other populations. Methods The authors performed a GWA study comprising 230 cases and 290 controls from a Korean population typed on 490 032 single nucleotide polymorphisms (SNPs). A total of 3148 SNPs were taken forward for genotyping in a subsequent replication study using an independent sample of 1172 cases and 1087 controls from the same population. Results The association previously observed on chromosome 9p21 was independently replicated (p=3.08e–07). Within this region, the same risk haplotype was observed in samples from both Korea and of Western European descent, suggesting that the causal mutation carried on this background occurred on a single ancestral allele. Other than 9p21, the authors were unable to replicate any of the previously reported signals for association with CAD. Furthermore, no evidence of association was found at chromosome 1q41 for risk of myocardial infarction, previously identified as conferring risk in a Japanese population. Conclusion A common causal variant is likely to be responsible for risk of CAD in Korean and Western European populations at chromosome 9p21.3. Further investigations are required to confirm non-replication of any other cross-race genetic risk factors. PMID:27325954

The Potyviral P3 Protein Targets Eukaryotic Elongation Factor 1A to Promote the Unfolded Protein Response and Viral Pathogenesis1[OPEN

PubMed Central

Shine, M.B.; Cui, Xiaoyan; Chen, Xin; Ma, Na; Kachroo, Pradeep; Zhi, Haijan; Kachroo, Aardra

2016-01-01

The biochemical function of the potyviral P3 protein is not known, although it is known to regulate virus replication, movement, and pathogenesis. We show that P3, the putative virulence determinant of soybean mosaic virus (SMV), targets a component of the translation elongation complex in soybean. Eukaryotic elongation factor 1A (eEF1A), a well-known host factor in viral pathogenesis, is essential for SMV virulence and the associated unfolded protein response (UPR). Silencing GmEF1A inhibits accumulation of SMV and another ER-associated virus in soybean. Conversely, endoplasmic reticulum (ER) stress-inducing chemicals promote SMV accumulation in wild-type, but not GmEF1A-knockdown, plants. Knockdown of genes encoding the eEF1B isoform, which is important for eEF1A function in translation elongation, has similar effects on UPR and SMV resistance, suggesting a link to translation elongation. P3 and GmEF1A promote each other’s nuclear localization, similar to the nuclear-cytoplasmic transport of eEF1A by the Human immunodeficiency virus 1 Nef protein. Our results suggest that P3 targets host elongation factors resulting in UPR, which in turn facilitates SMV replication and place eEF1A upstream of BiP in the ER stress response during pathogen infection. PMID:27356973

Trehalose Biosynthesis Promotes Pseudomonas aeruginosa Pathogenicity in Plants

PubMed Central

Djonović, Slavica; Urbach, Jonathan M.; Drenkard, Eliana; Bush, Jenifer; Feinbaum, Rhonda; Ausubel, Jonathan L.; Traficante, David; Risech, Martina; Kocks, Christine; Fischbach, Michael A.; Priebe, Gregory P.; Ausubel, Frederick M.

2013-01-01

Pseudomonas aeruginosa strain PA14 is a multi-host pathogen that infects plants, nematodes, insects, and vertebrates. Many PA14 factors are required for virulence in more than one of these hosts. Noting that plants have a fundamentally different cellular architecture from animals, we sought to identify PA14 factors that are specifically required for plant pathogenesis. We show that synthesis by PA14 of the disaccharide trehalose is required for pathogenesis in Arabidopsis, but not in nematodes, insects, or mice. In-frame deletion of two closely-linked predicted trehalose biosynthetic operons, treYZ and treS, decreased growth in Arabidopsis leaves about 50 fold. Exogenously co-inoculated trehalose, ammonium, or nitrate, but not glucose, sulfate, or phosphate suppressed the phenotype of the double ΔtreYZΔtreS mutant. Exogenous trehalose or ammonium nitrate does not suppress the growth defect of the double ΔtreYZΔtreS mutant by suppressing the plant defense response. Trehalose also does not function intracellularly in P. aeruginosa to ameliorate a variety of stresses, but most likely functions extracellularly, because wild-type PA14 rescued the in vivo growth defect of the ΔtreYZΔtreS in trans. Surprisingly, the growth defect of the double ΔtreYZΔtreS double mutant was suppressed by various Arabidopsis cell wall mutants that affect xyloglucan synthesis, including an xxt1xxt2 double mutant that completely lacks xyloglucan, even though xyloglucan mutants are not more susceptible to pathogens and respond like wild-type plants to immune elicitors. An explanation of our data is that trehalose functions to promote the acquisition of nitrogen-containing nutrients in a process that involves the xyloglucan component of the plant cell wall, thereby allowing P. aeruginosa to replicate in the intercellular spaces in a leaf. This work shows how P. aeruginosa, a multi-host opportunistic pathogen, has repurposed a highly conserved “house-keeping” anabolic pathway (trehalose biosynthesis) as a potent virulence factor that allows it to replicate in the intercellular environment of a leaf. PMID:23505373

Selection on oxidative phosphorylation and ribosomal structure as a multigenerational response to ocean acidification in the common copepod Pseudocalanus acuspes.

PubMed

De Wit, Pierre; Dupont, Sam; Thor, Peter

2016-10-01

Ocean acidification is expected to have dramatic impacts on oceanic ecosystems, yet surprisingly few studies currently examine long-term adaptive and plastic responses of marine invertebrates to p CO 2 stress. Here, we exposed populations of the common copepod Pseudocalanus acuspes to three p CO 2 regimes (400, 900, and 1550 μatm) for two generations, after which we conducted a reciprocal transplant experiment. A de novo transcriptome was assembled, annotated, and gene expression data revealed that genes involved in RNA transcription were strongly down-regulated in populations with long-term exposure to a high p CO 2 environment, even after transplantation back to control levels. In addition, 747 000 SNPs were identified, out of which 1513 showed consistent changes in nucleotide frequency between replicates of control and high p CO 2 populations. Functions involving RNA transcription and ribosomal function, as well as ion transport and oxidative phosphorylation, were highly overrepresented. We thus conclude that p CO 2 stress appears to impose selection in copepods on RNA synthesis and translation, possibly modulated by helicase expression. Using a physiological hypothesis-testing strategy to mine gene expression data, we herein increase the power to detect cellular targets of ocean acidification. This novel approach seems promising for future studies of effects of environmental changes in ecologically important nonmodel organisms.

Coronavirus virulence genes with main focus on SARS-CoV envelope gene.

PubMed

DeDiego, Marta L; Nieto-Torres, Jose L; Jimenez-Guardeño, Jose M; Regla-Nava, Jose A; Castaño-Rodriguez, Carlos; Fernandez-Delgado, Raul; Usera, Fernando; Enjuanes, Luis

2014-12-19

Coronavirus (CoV) infection is usually detected by cellular sensors, which trigger the activation of the innate immune system. Nevertheless, CoVs have evolved viral proteins that target different signaling pathways to counteract innate immune responses. Some CoV proteins act as antagonists of interferon (IFN) by inhibiting IFN production or signaling, aspects that are briefly addressed in this review. After CoV infection, potent cytokines relevant in controlling virus infections and priming adaptive immune responses are also generated. However, an uncontrolled induction of these proinflammatory cytokines can lead to pathogenesis and disease severity as described for SARS-CoV and MERS-CoV. The cellular pathways mediated by interferon regulatory factor (IRF)-3 and -7, activating transcription factor (ATF)-2/jun, activator protein (AP)-1, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), and nuclear factor of activated T cells (NF-AT), are the main drivers of the inflammatory response triggered after viral infections, with NF-κB pathway the most frequently activated. Key CoV proteins involved in the regulation of these pathways and the proinflammatory immune response are revisited in this manuscript. It has been shown that the envelope (E) protein plays a variable role in CoV morphogenesis, depending on the CoV genus, being absolutely essential in some cases (genus α CoVs such as TGEV, and genus β CoVs such as MERS-CoV), but not in others (genus β CoVs such as MHV or SARS-CoV). A comprehensive accumulation of data has shown that the relatively small E protein elicits a strong influence on the interaction of SARS-CoV with the host. In fact, after infection with viruses in which this protein has been deleted, increased cellular stress and unfolded protein responses, apoptosis, and augmented host immune responses were observed. In contrast, the presence of E protein activated a pathogenic inflammatory response that may cause death in animal models and in humans. The modification or deletion of different motifs within E protein, including the transmembrane domain that harbors an ion channel activity, small sequences within the middle region of the carboxy-terminus of E protein, and its most carboxy-terminal end, which contains a PDZ domain-binding motif (PBM), is sufficient to attenuate the virus. Interestingly, a comprehensive collection of SARS-CoVs in which these motifs have been modified elicited full and long-term protection even in old mice, making those deletion mutants promising vaccine candidates. These data indicate that despite its small size, E protein drastically influences the replication of CoVs and their pathogenicity. Although E protein is not essential for CoV genome replication or subgenomic mRNA synthesis, it affects virus morphogenesis, budding, assembly, intracellular trafficking, and virulence. In fact, E protein is responsible in a significant proportion of the inflammasome activation and the associated inflammation elicited by SARS-CoV in the lung parenchyma. This exacerbated inflammation causes edema accumulation leading to acute respiratory distress syndrome (ARDS) and, frequently, to the death of infected animal models or human patients. Copyright © 2014 Elsevier B.V. All rights reserved.

CORONAVIRUS VIRULENCE GENES WITH MAIN FOCUS ON SARS-CoV ENVELOPE GENE

PubMed Central

DeDiego, Marta L.; Nieto-Torres, Jose L.; Jimenez-Guardeño, Jose M.; Regla-Nava, Jose A.; Castaño-Rodriguez, Carlos; Fernandez-Delgado, Raul; Usera, Fernando; Enjuanes, Luis

2014-01-01

Coronavirus (CoV) infection is usually detected by cellular sensors, which trigger the activation of the innate immune system. Nevertheless, CoVs have evolved viral proteins that target different signaling pathways to counteract innate immune responses. Some CoV proteins act as antagonists of interferon (IFN) by inhibiting IFN production or signaling, aspects that are briefly addressed in this review. After CoV infection, potent cytokines relevant in controlling virus infections and priming adaptive immune responses are also generated. However, an uncontrolled induction of these proinflammatory cytokines can lead to pathogenesis and disease severity as described for SARS-CoV and MERS-CoV. The cellular pathways mediated by interferon regulatory factor (IRF)-3 and 7, activating transcription factor (ATF)-2/jun, activator protein (AP)-1, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), and nuclear factor of activated T cells (NF-AT), are the main drivers of the inflammatory response triggered after viral infections, with NF-κB pathway the most frequently activated. Key CoV proteins involved in the regulation of these pathways and the proinflammatory immune response are revisited in this manuscript. It has been shown that the envelope (E) protein plays a variable role in CoV morphogenesis, depending on the CoV genus, being absolutely essential in some cases (genus α CoVs such as TGEV, and genus β CoVs such as MERS-CoV), but not in others (genus β CoVs such as MHV or SARS-CoV). A comprehensive accumulation of data has shown that the relatively small E protein elicits a strong influence on the interaction of SARS-CoV with the host. In fact, after infection with viruses in which this protein has been deleted, increased cellular stress and unfolded protein responses, apoptosis, and augmented host immune responses were observed. In contrast, the presence of E protein activated a pathogenic inflammatory response that may cause death in animal models and in humans. The modification or deletion of different motifs within E protein, including the transmembrane domain that harbors an ion channel activity, small sequences within the middle region of the carboxy-terminus of E protein, and its most carboxy-terminal end, which contains a PDZ domain-binding motif (PBM) is sufficient to attenuate the virus. Interestingly, a comprehensive collection of SARS-CoVs in which these motifs have been modified elicited full and long-term protection even in old mice, making those deletion mutants promising vaccine candidates. These data indicate that despite its small size, E protein drastically influences the replication of CoVs and their pathogenicity. Although E protein is not essential for CoV genome replication or subgenomic mRNA synthesis, it affects virus morphogenesis, budding, assembly, intracellular trafficking, and virulence. In fact, E protein is responsible in a significant proportion of the inflammasome activation and the associated inflammation elicited by SARS-CoV in the lung parenchyma. This exacerbated inflammation causes edema accumulation leading to acute respiratory distress syndrome (ARDS) and, frequently, to the death of infected animal models or human patients. PMID:25093995

Y-box-binding protein 1 interacts with hepatitis C virus NS3/4A and influences the equilibrium between viral RNA replication and infectious particle production.

PubMed

Chatel-Chaix, Laurent; Melançon, Pierre; Racine, Marie-Ève; Baril, Martin; Lamarre, Daniel

2011-11-01

The hepatitis C virus (HCV) NS3/4A protein has several essential roles in the virus life cycle, most probably through dynamic interactions with host factors. To discover cellular cofactors that are co-opted by HCV for its replication, we elucidated the NS3/4A interactome using mass spectrometry and identified Y-box-binding protein 1 (YB-1) as an interacting partner of NS3/4A protein and HCV genomic RNA. Importantly, silencing YB-1 expression decreased viral RNA replication and severely impaired the propagation of the infectious HCV molecular clone JFH-1. Immunofluorescence studies further revealed a drastic HCV-dependent redistribution of YB-1 to the surface of the lipid droplets, an important organelle for HCV assembly. Core and NS3 protein-dependent polyprotein maturation were shown to be required for YB-1 relocalization. Unexpectedly, YB-1 knockdown cells showed the increased production of viral infectious particles while HCV RNA replication was impaired. Our data support that HCV hijacks YB-1-containing ribonucleoparticles and that YB-1-NS3/4A-HCV RNA complexes regulate the equilibrium between HCV RNA replication and viral particle production.

Proline substitution independently enhances H-2D(b) complex stabilization and TCR recognition of melanoma-associated peptides.

PubMed

Uchtenhagen, Hannes; Abualrous, Esam T; Stahl, Evi; Allerbring, Eva B; Sluijter, Marjolein; Zacharias, Martin; Sandalova, Tatyana; van Hall, Thorbald; Springer, Sebastian; Nygren, Per-Åke; Achour, Adnane

2013-11-01

The immunogenicity of H-2D(b) (D(b)) restricted epitopes can be significantly increased by substituting peptide position 3 to a proline (p3P). The p3P modification enhances MHC stability without altering the conformation of the modified epitope allowing for T-cell cross-reactivity with the native peptide. The present study reveals how specific interactions between p3P and the highly conserved MHC heavy chain residue Y159 increase the stability of D(b) in complex with an optimized version of the melanoma-associated epitope gp10025-33 . Furthermore, the p3P modification directly increased the affinity of the D(b)/gp10025-33 -specific T-cell receptor (TCR) pMel. Surprisingly, the enhanced TCR binding was independent from the observed increased stability of the optimized D(b)/gp10025-33 complex and from the interactions formed between p3P and Y159, indicating a direct effect of the p3P modification on TCR recognition. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Prevention strategies differentially modulate the impact of cytomegalovirus replication on CD8(+) T-cell differentiation in high-risk solid organ transplant patients.

PubMed

Cantisán, Sara; Páez-Vega, Aurora; Pérez-Romero, Pilar; Montejo, Miguel; Cordero, Elisa; Gracia-Ahufinger, Irene; Martín-Gandul, Cecilia; Maruri, Naroa; Aguado, Rocío; Solana, Rafael; Torre-Cisneros, Julián

2016-08-01

The present study aimed to determine whether antiviral prevention strategies against cytomegalovirus (CMV) infection used in high-risk D+R- solid organ transplanted patients can modulate the impact of CMV replication on CD8(+) T-cell differentiation. The different CD8(+) T-cell subpopulations were measured at a single point when at least one year had elapsed since transplantation. A total of 68 D+R- patients were included, of which 33 underwent pre-emptive therapy and 35 received prophylaxis. Multivariate analysis showed that CMV replication was associated with the expansion of CD28־ EMRA CD8(+) T cells in patients managed pre-emptively but not in patients under prophylaxis (21.4% vs. 3.6%). This finding is likely related to the higher frequency of CMV recurrence observed in patients under pre-emptive therapy compared to those under prophylaxis (75% vs. 14.3%; p < 0.001). In fact, multivariate analysis showed that having more than one replication episode was associated with a 17.2% increase (p = 0.001) in the percentage of CD28־ EMRA CD8(+) T cells compared to "no episode" and with a 10.9% increase with respect to "single episodes" (p = 0.025). Additionally, patients with IFNγ response to CMV (QuantiFERON-CMV Reactive) had a higher percentage of late-differentiated CD8(+) T cells than patients lacking this response. In summary, recurrent CMV replication in D+R- patients under pre-emptive therapy was associated with the expansion of CD28־ EMRA CD8(+) T cells, which might have a short-term beneficial effect related to the high functionality of this T-cell subpopulation. Nevertheless, we cannot rule out that this accumulation might have a long-term detrimental effect related to immunosenescence and inflammation. Copyright © 2016 Elsevier B.V. All rights reserved.

High-level replication of human immunodeficiency virus in thymocytes requires NF-kappaB activation through interaction with thymic epithelial cells.

PubMed

Chêne, L; Nugeyre, M T; Barré-Sinoussi, F; Israël, N

1999-03-01

We have previously demonstrated that interaction of infected thymocytes with autologous thymic epithelial cells (TEC) is a prerequisite for a high level of human immunodeficiency virus type 1 (HIV-1) replication in thymocytes (M. Rothe, L. Chêne, M. Nugeyre, F. Barré-Sinoussi, and N. Israël, J. Virol. 72:5852-5861, 1998). We report here that this activation of HIV replication takes place at the transcriptional level through activation of the Rel/NF-kappaB transcription factors. We first demonstrate that an HIV-1 provirus (SF-2 strain) very effectively replicates in thymocytes cocultured with TEC whereas this provirus, with kappaB sites deleted, fails to replicate. We provide evidence that several NF-kappaB complexes are constitutively found in the nuclei of thymocytes either freshly isolated from the thymus or maintained in coculture with autologous or heterologous TEC. The prevalent complex is the heterodimer p50-p65. NF-kappaB activity is tightly correlated with the transcriptional activity of a long terminal repeat (LTR) of HIV-1 transfected in thymocytes. The cotransfection of this LTR with a mutated IkappaBalpha molecule formally demonstrates that LTR transactivation is regulated by members of the Rel/NF-kappaB family in thymocytes. We also showed that tumor necrosis factor (TNF) and to a lesser extent interleukin-1 (IL-1), secreted within the coculture, induce NF-kappaB activity and a correlative LTR transactivation. However IL-7, a crucial factor for thymopoiesis that is secreted mainly by TEC, is a necessary cofactor for NF-kappaB activation elicited by TNF or IL-1. Together, these data indicate that NF-kappaB activation, required for a high level of HIV replication in thymocytes, is regulated in a specific manner in the thymic microenvironment which provides the necessary cytokines: TNF, IL-1, and IL-7.

Potential autotrophic metabolisms in ultra-basic reducing springs associated with present-day continental serpentinization

NASA Astrophysics Data System (ADS)

Morrill, P. L.; Miles, S.; Kohl, L.; Kavanagh, H.; Ziegler, S. E.; Brazelton, W. J.; Schrenk, M. O.

2013-12-01

Ultra-basic reducing springs at continental sites of serpentinization act as windows into the biogeochemistry of this subsurface exothermic environment rich in H2 and CH4 gases. Biogeochemical carbon transformations in these systems are of interest because serpentinization creates conditions that are amenable to abiotic and biotic reduction of carbon. However, little is known about the metabolic capabilities of the microorganisms that live in this environment. To determine the potential for autotrophic metabolisms, bicarbonate and CO substrate addition microcosm experiments were performed using water and sediment from an ultra-basic reducing spring in the Tablelands, Newfoundland, Canada, a site of present-day continental serpentinization. CO was consistently observed to be utilized in the Live but not the Killed controlled replicates amended with 10% 13C labelled CO and non-labelled (natural C isotope abundance) CO. In the Live CO microcosms with natural C isotope abundance, the residual CO became enriched in 13C (~10 ‰) consistent with a decrease in the fraction of CO remaining. In the Killed CO controlled replicates with natural C isotope abundance the CO showed little 13C enrichment (~1.3 ‰). The data from the Live CO microcosms were well described by a Rayleigh isotopic distillation model, yielding an isotopic enrichment factor for microbial CO uptake of 15.7 ×0.5 ‰ n=2. These data suggest that there was microbial CO utilization in these experiments. The sediment and water from the 13C-labelled and non-labelled, Live and Killed microcosms were extracted for phospholipid fatty acids (PLFAs) to determine changes in community composition between treatments as well as to determine the microbial uptake of CO. The difference in community composition between the Live and Killed microcosms was not readily resolvable based on PLFA distributions. Additionally, the microbial uptake of 13CO had minimal to no affect on the δ13C of the cellular biomarkers, with the exception of C16 saturated and a C16 monounsaturated PLFAs in one live microcosm which showed >2 ‰ and >10 ‰ enrichment, respectively, compared to the average δ13C values of the same PLFA in the 13C Killed controlled replicates. Therefore the uptake of CO had minimal effect on the overall biomass and community composition in the system. The 13C labelled bicarbonate anaerobic microcosm experiments showed little to no methane production. The methane detected in the 13C labelled Live experiments were not isotopically enriched in 13C compared to the CH4 in the labelled Killed controlled replicates. Therefore bicarbonate was not used as a substrate for microbial methanogenesis via the CO2 reduction pathway. These results are generally consistent with genomic and metagenomic data, which discovered the potential for a carbon fixation pathway involving carbon monoxide, but little evidence for archaea or methanogenesis in the ultra-basic springs in the Tablelands (Brazelton et al., 2012). Reference: Brazelton WJ, Nelson B, & Schrenk MO (2012) Frontiers in Microbiology 2:1-16.

Effects of experimental long-term CO2 exposure on Daphnia magna (Straus 1820): From physiological effects to ecological consequences.

PubMed

Parra, Gema; Galotti, Andréa; Jiménez-Melero, Raquel; Guerrero, Francisco; Sánchez-Moyano, Emilio; Jiménez-Gómez, Francisco; Conradi, Mercedes

2016-08-01

The carbon capture and storage (CCS) technologies that were proposed to mitigate environmental problems arising from anthropogenic CO2 emissions, also have potential environmental risks. An eventual CCS leak might induce very low pH values in the aquatic system. Due to the lack of knowledge of long-term CO2 exposures with very low pH values, this study aims to know the effects and consequences of such a situation for zooplankton, using the Daphnia magna experimental model. A CO2 injection system was used to provide the experimental condition. A twenty-one days experiment with control and low pH treatment (pH = 7) replicates was carried out under light and temperature-controlled conditions. Survival, individual growth, RNA:DNA ratio, and neonates production were analysed during the aforementioned period. No differences on survival (except last day), individual growth and RNA:DNA ratio were observed between both control and low pH treatments. However, clear differences were detected in neonates production and, consequently, in population growth rates and secondary production. The observed differences could be related with an energy allocation strategy to ensure individual survival but would have ecological consequences affecting higher trophic levels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genomewide linkage scan of resting blood pressure: HERITAGE Family Study. Health, Risk Factors, Exercise Training, and Genetics.

PubMed

Rice, Treva; Rankinen, Tuomo; Chagnon, Yvon C; Province, Michael A; Pérusse, Louis; Leon, Arthur S; Skinner, James S; Wilmore, Jack H; Bouchard, Claude; Rao, Dabeeru C

2002-06-01

The purpose of this study was to search for genomic regions influencing resting systolic (SBP) and diastolic (DBP) blood pressure (BP) in sedentary families (baseline), and for resting BP responses (changes) resulting from a 20-week exercise training intervention (post-training-baseline) in the Health, Risk Factors, Exercise Training, and Genetics (HERITAGE) Family Study. A genome-wide scan was conducted on 317 black individuals from 114 families and 519 white individuals from 99 families using a multipoint variance-components linkage model and a panel of 509 markers. Promising results were primarily, but not exclusively, found in the black families. Linkage evidence (P<0.0023) with baseline BP replicated other studies within a 1-logarithm of odds (LOD) interval on 2p14, 3p26.3, and 12q21.33, and provided new evidence on 3q28, 11q21, and 19p12. Results for several known hypertension genes were less compelling. For response BP, results were not very strong, although markers on 13q11 were mildly suggestive (P<0.01). In conclusion, these HERITAGE data, in conjunction with results from previous genomewide scans, provide a basis for planning future investigations. The major areas warranting further study involve fine mapping to narrow down 3 regions on 2q, 3p, and 12q that may contain "novel" hypertension genes, additional typing of some biological candidate genes to determine whether they are the sources of these and other signals, multilocus investigations to understand how and to what extent some of these candidates may interact, and multivariate studies to characterize any pleiotropy.

Respiratory CO2 response depends on plasma bicarbonate concentration in mechanically ventilated patients.

PubMed

Rialp, G; Raurich, J M; Llompart-Pou, J A; Ayestarán, I; Ibáñez, J

2014-05-01

There is controversy about the effects of high plasma bicarbonate concentration ([HCO3(-)]) and the CO2 response test. We analyzed the relationship between [HCO3(-)] and the variation in hydrogen ion concentration (pH) for a given change in PaCO2, and its effects upon CO2 response. A retrospective study was carried out. Two intensive care units. Subjects with and without chronic obstructive pulmonary disease (COPD), at the beginning of weaning from mechanical ventilation. The CO2 response was evaluated by the re-inhalation of expired air method, measuring the hypercapnic ventilatory response (ΔVE/ΔPaCO2) and hypercapnic drive response (ΔP01/ΔPaCO2), where VE is minute volume and P0.1 is airway occlusion pressure 0.1s after the initiation of inspiration. [HCO3(-)] and CO2 response. A total of 120 patients in the non-COPD group and 48 in the COPD group were studied. COPD patients had higher mean [HCO3(-)] than non-COPD patients (33.2 ± 5.4 vs. 25.7 ± 3.7 mmol/l, p<0.001). In both non-COPD and COPD patients we observed a significant inverse linear relationship between [HCO3(-)] and pH change per mmHg of PaCO2 (p<0.001), ΔVE/ΔPaCO2 (p<0.001) and ΔP0.1/ΔPaCO2 (p<0.001). There is an inverse linear relationship between [HCO3(-)] and the variation of pH for a given change in PaCO2 and the CO2 response. Copyright © 2013 Elsevier España, S.L. and SEMICYUC. All rights reserved.

Characterization of a Drosophila ortholog of the Cdc7 kinase: a role for Cdc7 in endoreplication independent of Chiffon.

PubMed

Stephenson, Robert; Hosler, Marcus R; Gavande, Navnath S; Ghosh, Arun K; Weake, Vikki M

2015-01-16

Cdc7 is a serine-threonine kinase that phosphorylates components of the pre-replication complex during DNA replication initiation. Cdc7 is highly conserved, and Cdc7 orthologs have been characterized in organisms ranging from yeast to humans. Cdc7 is activated specifically during late G1/S phase by binding to its regulatory subunit, Dbf4. Drosophila melanogaster contains a Dbf4 ortholog, Chiffon, which is essential for chorion amplification in Drosophila egg chambers. However, no Drosophila ortholog of Cdc7 has yet been characterized. Here, we report the functional and biochemical characterization of a Drosophila ortholog of Cdc7. Co-expression of Drosophila Cdc7 and Chiffon is able to complement a growth defect in yeast containing a temperature-sensitive Cdc7 mutant. Cdc7 and Chiffon physically interact and can be co-purified from insect cells. Cdc7 phosphorylates the known Cdc7 substrates Mcm2 and histone H3 in vitro, and Cdc7 kinase activity is stimulated by Chiffon and inhibited by the Cdc7-specific inhibitor XL413. Drosophila egg chamber follicle cells deficient for Cdc7 have a defect in two types of DNA replication, endoreplication and chorion gene amplification. However, follicle cells deficient for Chiffon have a defect in chorion gene amplification but still undergo endocycling. Our results show that Cdc7 interacts with Chiffon to form a functional Dbf4-dependent kinase complex and that Cdc7 is necessary for DNA replication in Drosophila egg chamber follicle cells. Additionally, we show that Chiffon is a member of an expanding subset of DNA replication initiation factors that are not strictly required for endoreplication in Drosophila. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

The Development of the General Factor of Psychopathology 'p Factor' Through Childhood and Adolescence.

PubMed

Murray, Aja Louise; Eisner, Manuel; Ribeaud, Denis

2016-11-01

Recent studies have suggested that the structure of psychopathology may be usefully represented in terms of a general factor of psychopathology (p-factor) capturing variance common to a broad range of symptoms transcending diagnostic domains in addition to specific factors capturing variance common to smaller subsets of more closely related symptoms. Little is known about how the general co-morbidity captured by this p-factor develops and whether general co-morbidity increases or decreases over childhood and adolescence. We evaluated two competing hypotheses: 1) dynamic mutualism which predicts growth in general co-morbidity and associated p-factor strength over time and 2) p-differentiation which predicts that manifestations of liabilities towards psychopathology become increasingly specific over time. Data came from the Zurich Project on the Social Development of Children and Youths (z-proso), a longitudinal study of a normative sample (approx. 50 % male) measured at 8 time points from ages 7 to 15. We operationalised general co-morbidity as p-factor strength in a bi-factor model and used omega hierarchical to track how this changed over development. In contrast to the predictions of both dynamic mutualism and p-differentiation, p-factor strength remained relatively constant over the studied period suggesting that such processes do not govern the interplay between psychopathological symptoms during this phase of development. Future research should focus on earlier phases of development and on factors that maintain the consistency of symptom-general covariation across this period.

Hemodynamic exercise testing. A valuable tool in the selection of cardiac transplantation candidates.

PubMed

Chomsky, D B; Lang, C C; Rayos, G H; Shyr, Y; Yeoh, T K; Pierson, R N; Davis, S F; Wilson, J R

1996-12-15

Peak exercise oxygen consumption (Vo2), a noninvasive index of peak exercise cardiac output (CO), is widely used to select candidates for heart transplantation. However, peak exercise Vo2 can be influenced by noncardiac factors such as deconditioning, motivation, or body composition and may yield misleading prognostic information. Direct measurement of the CO response to exercise may avoid this problem and more accurately predict prognosis. Hemodynamic and ventilatory responses to maximal treadmill exercise were measured in 185 ambulatory patients with chronic heart failure who had been referred for cardiac transplantation (mean left ventricular ejection fraction, 22 +/- 7%; mean peak Vo2, 12.9 +/- 3.0 mL. min-1.kg-1). CO response to exercise was normal in 83 patients and reduced in 102. By univariate analysis, patients with normal CO responses had a better 1-year survival rate (95%) than did those with reduced CO responses (72%) (P < .0001). Survival in patients with peak Vo2 of > 14 mL.min-1.kg-1 (88%) was not different from that of patients with peak Vo2 of < or = 14 mL.min-1.kg-1 (79%) (P = NS). However, survival was worse in patients with peak Vo2 of < or = 10 mL.min-1.kg-1 (52%) versus those with peak Vo2 of > 10 mL.min-1.kg-1 (89%) (P < .0001). By Cox regression analysis, exercise CO response was the strongest independent predictor of survival (risk ratio, 4.3), with peak Vo2 dichotomized at 10 mL. min-1.kg-1 (risk ratio, 3.3) as the only other independent predictor. Patients with reduced CO responses and peak Vo2 of < or = 10 mL.min-1.kg-1 had an extremely poor 1-year survival rate (38%). Both CO response to exercise and peak exercise Vo2 provide valuable independent prognostic information in ambulatory patients with heart failure. These variables should be used in combination to select potential heart transplantation candidates.

Evidence for a link between TNFRSF11A and risk of breast cancer.

PubMed

Bonifaci, Núria; Palafox, Marta; Pellegrini, Pasquale; Osorio, Ana; Benítez, Javier; Peterlongo, Paolo; Manoukian, Siranoush; Peissel, Bernard; Zaffaroni, Daniela; Roversi, Gaia; Barile, Monica; Viel, Alessandra; Mariette, Frederique; Bernard, Loris; Radice, Paolo; Kaufman, Bella; Laitman, Yael; Milgrom, Roni; Friedman, Eitan; Sáez, María E; Climent, Fina; Soler, María Teresa; Diez, Orland; Balmaña, Judith; Lasa, Adriana; Ramón y Cajal, Teresa; Miramar, María-Dolores; de la Hoya, Miguel; Pérez-Segura, Pedro; Caldés, Trinidad; Moreno, Víctor; Urruticoechea, Ander; Brunet, Joan; Lázaro, Conxi; Blanco, Ignacio; Pujana, Miguel Angel; González-Suárez, Eva

2011-10-01

Intracellular signaling mediated by the receptor activator of nuclear factor-κB [Rank, encoded by the tumor necrosis factor receptor superfamily, member 11a (Tnfrsf11a) gene] is fundamental for mammary gland development in mice, regulating the expansion of stem and progenitor cell compartments. Conversely, Rank overexpression in mice promotes abnormal proliferation and impairs differentiation, leading to an increased incidence of tumorigenesis. Here, we show that a common genetic variant near the 5'-end of TNFRSF11A, rs7226991, is associated with breast cancer risk in the general population and among carriers of mutations in the breast cancer 2, early onset (BRCA2) gene. Akin to the results of the Cancer and Genetics Markers of Susceptibility initiative, combined analysis of rs7226991 in two Spanish case-control studies (1,365 controls and 1,323 cases in total) revealed a significant association with risk: odds ratio (OR) = 0.88, 95% confidence interval (CI) 0.78-0.98, P (trend) = 0.025. Subsequent examination of BRCA1 (n = 1,017) and BRCA2 (n = 885) mutation carriers revealed a consistent association in the latter group: weighted hazard ratio ((w)HR) = 0.70; 95% CI 0.55-0.88; and P (trend) = 0.003; compared to BRCA1 mutation carriers, (w)HR = 0.91; 95% CI 0.76-1.10; and P (trend) = 0.33. The results of this study need to be replicated in other populations and with larger numbers of BRCA1/2 mutation carriers.

Polygamy and the use of contraceptives.

PubMed

Audu, Bala; Yahya, Shaibu; Geidam, Ado; Abdussalam, Hadiza; Takai, Idrisa; Kyari, Othman

2008-04-01

To compare contraceptive use among women in monogamous and polygamous marriages in Nigeria. Structured questionnaires administered to married women enquired about their marriage type, sociodemographic characteristics, and contraceptive use. Of the 532 respondents, 33.6% were in polygamous marriages. There was a statistically significant association between monogamy and nonutilization of contraception (P=0.03); however, women in polygamous marriages were more likely not to use contraception when they were older than 35 years, had 4 or more living children, had no male child, had 3 or more female children, or lived in rural areas. There was also a statistically significant association between nonutilization of contraception and number of male children of co-wives (P=0.003), number of female children of co-wives (P=0.05), and use of contraception by co-wives (P=0.002). Polygamy influences contraceptive use and the role of co-wives in this regard merits further study.

Characterization of a baculovirus lacking the DBP (DNA-binding protein) gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vanarsdall, Adam L.; Mikhailov, Victor S.; N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 117808

2007-08-01

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) encodes two proteins that possess properties typical of single-stranded DNA-binding proteins (SSBs), late expression factor-3 (LEF-3), and a protein referred to as DNA-binding protein (DBP). Whereas LEF-3 is a multi-functional protein essential for viral DNA replication, transporting helicase into the nucleus, and forms a stable complex with the baculovirus alkaline nuclease, the role for DBP in baculovirus replication remains unclear. Therefore, to better understand the functional role of DBP in viral replication, a DBP knockout virus was generated from an AcMNPV bacmid and analyzed. The results of a growth curve analysis indicated that the dbpmore » knockout construct was unable to produce budded virus indicating that dbp is essential. The lack of DBP does not cause a general shutdown of the expression of viral genes, as was revealed by accumulation of early (LEF-3), late (VP39), and very late (P10) proteins in cells transfected with the dbp knockout construct. To investigate the role of DBP in DNA replication, a real-time PCR-based assay was employed and showed that, although viral DNA synthesis occurred in cells transfected with the dbp knockout, the levels were less than that of the control virus suggesting that DBP is required for normal levels of DNA synthesis or for stability of nascent viral DNA. In addition, analysis of the viral DNA replicated by the dbp knockout by using field inversion gel electrophoresis failed to detect the presence of genome-length DNA. Furthermore, analysis of DBP from infected cells indicated that similar to LEF-3, DBP was tightly bound to viral chromatin. Assessment of the cellular localization of DBP relative to replicated viral DNA by immunoelectron microscopy indicated that, at 24 h post-infection, DBP co-localized with nascent DNA at distinct electron-dense regions within the nucleus. Finally, immunoelectron microscopic analysis of cells transfected with the dbp knockout revealed that DBP is required for the production of normal-appearing nucleocapsids and for the generation of the virogenic stroma.« less

Identification of a novel malonyl-CoA IC(50) for CPT-I: implications for predicting in vivo fatty acid oxidation rates.

PubMed

Smith, Brennan K; Perry, Christopher G R; Koves, Timothy R; Wright, David C; Smith, Jeffrey C; Neufer, P Darrell; Muoio, Deborah M; Holloway, Graham P

2012-11-15

Published values regarding the sensitivity (IC(50)) of CPT-I (carnitine palmitoyltransferase I) to M-CoA (malonyl-CoA) inhibition in isolated mitochondria are inconsistent with predicted in vivo rates of fatty acid oxidation. Therefore we have re-examined M-CoA inhibition kinetics under various P-CoA (palmitoyl-CoA) concentrations in both isolated mitochondria and PMFs (permeabilized muscle fibres). PMFs have an 18-fold higher IC(50) (0.61 compared with 0.034 μM) in the presence of 25 μM P-CoA and a 13-fold higher IC(50) (6.3 compared with 0.49 μM) in the presence of 150 μM P-CoA compared with isolated mitochondria. M-CoA inhibition kinetics determined in PMFs predicts that CPT-I activity is inhibited by 33% in resting muscle compared with >95% in isolated mitochondria. Additionally, the ability of M-CoA to inhibit CPT-I appears to be dependent on P-CoA concentration, as the relative inhibitory capacity of M-CoA is decreased with increasing P-CoA concentrations. Altogether, the use of PMFs appears to provide an M-CoA IC(50) that better reflects the predicted in vivo rates of fatty acid oxidation. These findings also demonstrate that the ratio of [P-CoA]/[M-CoA] is critical for regulating CPT-I activity and may partially rectify the in vivo disconnect between M-CoA content and CPT-I flux within the context of exercise and Type 2 diabetes.

YAP controls retinal stem cell DNA replication timing and genomic stability

PubMed Central

Cabochette, Pauline; Vega-Lopez, Guillermo; Bitard, Juliette; Parain, Karine; Chemouny, Romain; Masson, Christel; Borday, Caroline; Hedderich, Marie; Henningfeld, Kristine A; Locker, Morgane; Bronchain, Odile; Perron, Muriel

2015-01-01

The adult frog retina retains a reservoir of active neural stem cells that contribute to continuous eye growth throughout life. We found that Yap, a downstream effector of the Hippo pathway, is specifically expressed in these stem cells. Yap knock-down leads to an accelerated S-phase and an abnormal progression of DNA replication, a phenotype likely mediated by upregulation of c-Myc. This is associated with an increased occurrence of DNA damage and eventually p53-p21 pathway-mediated cell death. Finally, we identified PKNOX1, a transcription factor involved in the maintenance of genomic stability, as a functional and physical interactant of YAP. Altogether, we propose that YAP is required in adult retinal stem cells to regulate the temporal firing of replication origins and quality control of replicated DNA. Our data reinforce the view that specific mechanisms dedicated to S-phase control are at work in stem cells to protect them from genomic instability. DOI: http://dx.doi.org/10.7554/eLife.08488.001 PMID:26393999

Transferability of genome-wide associated loci for asthma in African Americans

PubMed Central

Faruque, Mezbah U.; Chen, Guanjie; Doumatey, Ayo P.; Zhou, Jie; Huang, Hanxia; Shriner, Daniel; Adeyemo, Adebowale A.; Rotimi, Charles N.; Dunston, Georgia M.

2017-01-01

Objective Transferability of significantly associated loci or GWAS “hits” adds credibility to genotype-disease associations and provides evidence for generalizability across different ancestral populations. We sought evidence of association of known asthma-associated single nucleotide polymorphisms (SNPs) in an African American population. Methods Subjects comprised 661 participants (261 asthma cases and 400 controls) from the Howard University Family Study. Forty-eight SNPs previously reported to be associated with asthma by GWAS were selected for testing. We adopted a combined strategy by first adopting an “exact” approach where we looked-up only the reported index SNP. For those index SNPs missing form our dataset, we used a “local” approach that examined all the regional SNPs in LD with the index SNP. Results Out of the 48 SNPs, our cohort had genotype data available for 27, which were examined for exact replication. Of these, two SNPs were found positively associated with asthma. These included: rs10508372 (OR = 1.567 [95%CI, 1.133–2.167], P = 0.0066) and rs2378383 (OR = 2.147 [95%CI, 1.149–4.013], P = 0.0166), located on chromosomal bands 10p14 and 9q21.31, respectively. Local replication of the remaining 21 loci showed association at two chromosomal loci (9p24.1-rs2381413 and 6p21.32-rs3132947; Bonferroni-corrected P values: 0.0033 and 0.0197, respectively). Of note, multiple SNPs in LD with rs2381413 located upstream of IL33 were significantly associated with asthma. Conclusions This study has successfully transferred four reported asthma-associated loci in an independent African American population. Identification of several asthma-associated SNPs in the upstream of the IL33, a gene previously implicated in allergic inflammation of asthmatic airway, supports the generalizability of this finding. PMID:27177148

Resistance of Adenoviral DNA Replication to Aphidicolin Is Dependent on the 72-Kilodalton DNA-Binding Protein

PubMed Central

Foster, David A.; Hantzopoulos, Petros; Zubay, Geoffrey

1982-01-01

Aphidicolin is a highly specific inhibitor of DNA polymerase α and has been most useful for assessing the role of this enzyme in various replication processes (J. A. Huberman, Cell 23:647-648, 1981). Both nuclear DNA replication and simian virus 40 DNA replication are highly sensitive to this drug (Krokan et al., Biochemistry 18:4431-4443, 1979), whereas mitochondrial DNA synthesis is completely insensitive (Zimmerman et al., J. Biol. Chem. 255:11847-11852, 1980). Adenovirus DNA replication is sensitive to aphidicolin, but only at much higher concentrations. These patterns of sensitivity are seen both in vivo and in vitro (Krokan et al., Biochemistry 18:4431-4443, 1979). A temperature-sensitive mutant of adenovirus type 5 known as H5ts125 is able to complete but not initiate new rounds of replication at nonpermissive temperatures (P. C. van der Vliet and J. S. Sussenbach, Virology 67:415-426, 1975). When cells infected with H5ts125 were shifted from permissive (33°C) to nonpermissive (41°C) conditions, the residual DNA synthesis (elongation) showed a striking increase in sensitivity to aphidicolin. The temperature-sensitive mutation of H5ts125 is in the gene for the 72-kilodalton single-stranded DNA-binding protein. This demonstrated that the increased resistance to aphidicolin shown by adenovirus DNA replication was dependent on that protein. It also supports an elongation role for both DNA polymerase α and the 72-kilodalton single-stranded DNA-binding protein in adenovirus DNA replication. Further support for an elongation role of DNA polymerase α came from experiments with permissive temperature conditions and inhibiting levels of aphidicolin in which it was shown that newly initiated strands failed to elongate to completion. Images PMID:6809958

Strategic Use of Random Subsample Replication and a Coefficient of Factor Replicability

ERIC Educational Resources Information Center

Katzenmeyer, William G.; Stenner, A. Jackson

1975-01-01

The problem of demonstrating replicability of factor structure across random variables is addressed. Procedures are outlined which combine the use of random subsample replication strategies with the correlations between factor score estimates across replicate pairs to generate a coefficient of replicability and confidence intervals associated with…

Implications of prion adaptation and evolution paradigm for human neurodegenerative diseases.

PubMed

Kabir, M Enamul; Safar, Jiri G

2014-01-01

There is a growing body of evidence indicating that number of human neurodegenerative diseases, including Alzheimer disease, Parkinson disease, fronto-temporal dementias, and amyotrophic lateral sclerosis, propagate in the brain via prion-like intercellular induction of protein misfolding. Prions cause lethal neurodegenerative diseases in humans, the most prevalent being sporadic Creutzfeldt-Jakob disease (sCJD); they self-replicate and spread by converting the cellular form of prion protein (PrP(C)) to a misfolded pathogenic conformer (PrP(Sc)). The extensive phenotypic heterogeneity of human prion diseases is determined by polymorphisms in the prion protein gene, and by prion strain-specific conformation of PrP(Sc). Remarkably, even though informative nucleic acid is absent, prions may undergo rapid adaptation and evolution in cloned cells and upon crossing the species barrier. In the course of our investigation of this process, we isolated distinct populations of PrP(Sc) particles that frequently co-exist in sCJD. The human prion particles replicate independently and undergo competitive selection of those with lower initial conformational stability. Exposed to mutant substrate, the winning PrP(Sc) conformers are subject to further evolution by natural selection of the subpopulation with the highest replication rate due to the lowest stability. Thus, the evolution and adaptation of human prions is enabled by a dynamic collection of distinct populations of particles, whose evolution is governed by the selection of progressively less stable, faster replicating PrP(Sc) conformers. This fundamental biological mechanism may explain the drug resistance that some prions gained after exposure to compounds targeting PrP(Sc). Whether the phenotypic heterogeneity of other neurodegenerative diseases caused by protein misfolding is determined by the spectrum of misfolded conformers (strains) remains to be established. However, the prospect that these conformers may evolve and adapt by a prion-like mechanism calls for the reevaluation of therapeutic strategies that target aggregates of misfolded proteins, and argues for new therapeutic approaches that will focus on prior pathogenetic steps.

Inhibition of host protein synthesis by Sindbis virus: correlation with viral RNA replication and release of nuclear proteins to the cytoplasm.

PubMed

Sanz, Miguel A; García-Moreno, Manuel; Carrasco, Luis

2015-04-01

Infection of mammalian cells by Sindbis virus (SINV) profoundly blocks cellular mRNA translation. Experimental evidence points to viral non-structural proteins (nsPs), in particular nsP2, as the mediator of this inhibition. However, individual expression of nsP1, nsP2, nsP3 or nsP1-4 does not block cellular protein synthesis in BHK cells. Trans-complementation of a defective SINV replicon lacking most of the coding region for nsPs by the co-expression of nsP1-4 propitiates viral RNA replication at low levels, and inhibition of cellular translation is not observed. Exit of nuclear proteins including T-cell intracellular antigen and polypyrimidine tract-binding protein is clearly detected in SINV-infected cells, but not upon the expression of nsPs, even when the defective replicon was complemented. Analysis of a SINV variant with a point mutation in nsP2, exhibiting defects in the shut-off of host protein synthesis, indicates that both viral RNA replication and the release of nuclear proteins to the cytoplasm are greatly inhibited. Furthermore, nucleoside analogues that inhibit cellular and viral RNA synthesis impede the blockade of host mRNA translation, in addition to the release of nuclear proteins. Prevention of the shut-off of host mRNA translation by nucleoside analogues is not due to the inhibition of eIF2α phosphorylation, as this prevention is also observed in PKR(-/-) mouse embryonic fibroblasts that do not phosphorylate eIF2α after SINV infection. Collectively, our observations are consistent with the concept that for the inhibition of cellular protein synthesis to occur, viral RNA replication must take place at control levels, leading to the release of nuclear proteins to the cytoplasm. © 2014 John Wiley & Sons Ltd.

TXNIP regulates myocardial fatty acid oxidation via miR-33a signaling.

PubMed

Chen, Junqin; Young, Martin E; Chatham, John C; Crossman, David K; Dell'Italia, Louis J; Shalev, Anath

2016-07-01

Myocardial fatty acid β-oxidation is critical for the maintenance of energy homeostasis and contractile function in the heart, but its regulation is still not fully understood. While thioredoxin-interacting protein (TXNIP) has recently been implicated in cardiac metabolism and mitochondrial function, its effects on β-oxidation have remained unexplored. Using a new cardiomyocyte-specific TXNIP knockout mouse and working heart perfusion studies, as well as loss- and gain-of-function experiments in rat H9C2 and human AC16 cardiomyocytes, we discovered that TXNIP deficiency promotes myocardial β-oxidation via signaling through a specific microRNA, miR-33a. TXNIP deficiency leads to increased binding of nuclear factor Y (NFYA) to the sterol regulatory element binding protein 2 (SREBP2) promoter, resulting in transcriptional inhibition of SREBP2 and its intronic miR-33a. This allows for increased translation of the miR-33a target genes and β-oxidation-promoting enzymes, carnitine octanoyl transferase (CROT), carnitine palmitoyl transferase 1 (CPT1), hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase-β (HADHB), and AMPKα and is associated with an increase in phospho-AMPKα and phosphorylation/inactivation of acetyl-CoA-carboxylase. Thus, we have identified a novel TXNIP-NFYA-SREBP2/miR-33a-AMPKα/CROT/CPT1/HADHB pathway that is conserved in mouse, rat, and human cardiomyocytes and regulates myocardial β-oxidation. Copyright © 2016 the American Physiological Society.

Explaining CO2 fluctuations observed in snowpacks

NASA Astrophysics Data System (ADS)

Graham, Laura; Risk, David

2018-02-01

Winter soil carbon dioxide (CO2) respiration is a significant and understudied component of the global carbon (C) cycle. Winter soil CO2 fluxes can be surprisingly variable, owing to physical factors such as snowpack properties and wind. This study aimed to quantify the effects of advective transport of CO2 in soil-snow systems on the subdiurnal to diurnal (hours to days) timescale, use an enhanced diffusion model to replicate the effects of CO2 concentration depletions from persistent winds, and use a model-measure pairing to effectively explore what is happening in the field. We took continuous measurements of CO2 concentration gradients and meteorological data at a site in the Cape Breton Highlands of Nova Scotia, Canada, to determine the relationship between wind speeds and CO2 levels in snowpacks. We adapted a soil CO2 diffusion model for the soil-snow system and simulated stepwise changes in transport rate over a broad range of plausible synthetic cases. The goal was to mimic the changes we observed in CO2 snowpack concentration to help elucidate the mechanisms (diffusion, advection) responsible for observed variations. On subdiurnal to diurnal timescales with varying winds and constant snow levels, a strong negative relationship between wind speed and CO2 concentration within the snowpack was often identified. Modelling clearly demonstrated that diffusion alone was unable to replicate the high-frequency CO2 fluctuations, but simulations using above-atmospheric snowpack diffusivities (simulating advective transport within the snowpack) reproduced snow CO2 changes of the observed magnitude and speed. This confirmed that wind-induced ventilation contributed to episodic pulsed emissions from the snow surface and to suppressed snowpack concentrations. This study improves our understanding of winter CO2 dynamics to aid in continued quantification of the annual global C cycle and demonstrates a preference for continuous wintertime CO2 flux measurement systems.

IDH mutant and 1p/19q co-deleted oligodendrogliomas: tumor grade stratification using diffusion-, susceptibility-, and perfusion-weighted MRI.

PubMed

Lin, Yu; Xing, Zhen; She, Dejun; Yang, Xiefeng; Zheng, Yingyan; Xiao, Zebin; Wang, Xingfu; Cao, Dairong

2017-06-01

Currently, isocitrate dehydrogenase (IDH) mutation and 1p/19q co-deletion are proven diagnostic biomarkers for both grade II and III oligodendrogliomas (ODs). Non-invasive diffusion-weighted imaging (DWI), susceptibility-weighted imaging (SWI), and dynamic susceptibility contrast perfusion-weighted imaging (DSC-PWI) are widely used to provide physiological information (cellularity, hemorrhage, calcifications, and angiogenesis) of neoplastic histology and tumor grade. However, it is unclear whether DWI, SWI, and DSC-PWI are able to stratify grades of IDH-mutant and 1p/19q co-deleted ODs. We retrospectively reviewed the conventional MRI (cMRI), DWI, SWI, and DSC-PWI obtained on 33 patients with IDH-mutated and 1p/19q co-deleted ODs. Features of cMRI, normalized ADC (nADC), intratumoral susceptibility signals (ITSSs), normalized maxim CBV (nCBV), and normalized maximum CBF (nCBF) were compared between low-grade ODs (LGOs) and high-grade ODs (HGOs). Receiver operating characteristic curve and logistic regression were applied to determine diagnostic performances. HGOs tended to present with prominent edema and enhancement. nADC, ITSSs, nCBV, and nCBF were significantly different between groups (all P < 0.05). The combination of SWI and DSC-PWI for grading resulted in sensitivity and specificity of 100.00 and 93.33%, respectively. IDH-mutant and 1p/19q co-deleted ODs can be stratified by grades using cMRI and advanced magnetic resonance imaging techniques including DWI, SWI, and DSC-PWI. Combined ITSSs with nCBV appear to be a promising option for grading molecularly defined ODs in clinical practice.

Co-infection with human polyomavirus BK enhances gene expression and replication of human adenovirus.

PubMed

Bil-Lula, Iwona; Woźniak, Mieczysław

2018-03-26

Immunocompromised patients are susceptible to multiple viral infections. Relevant interactions between co-infecting viruses might result from viral regulatory genes which trans-activate or repress the expression of host cell genes as well as the genes of any co-infecting virus. The aim of the current study was to show that the replication of human adenovirus 5 is enhanced by co-infection with BK polyomavirus and is associated with increased expression of proteins including early region 4 open reading frame 1 and both the large tumor antigen and small tumor antigen. Clinical samples of whole blood and urine from 156 hematopoietic stem cell transplant recipients were tested. We also inoculated adenocarcinomic human alveolar basal epithelial cells with both human adenovirus 5 and BK polyomavirus to evaluate if co-infection of viruses affected their replication. Data showed that adenovirus load was significantly higher in the plasma (mean 7.5 x 10 3  ± 8.5 x 10 2 copies/ml) and urine (mean 1.9 x 10 3  ± 8.0 x 10 2 copies/ml) of samples from patients with co-infections, in comparison to samples from patients with isolated adenovirus infection. In vitro co-infection led to an increased (8.6 times) expression of the adenovirus early region 4 open reading frame gene 48 hours post-inoculation. The expression of the early region 4 open reading frame gene positively correlated with the expression of BK polyomavirus large tumor antigen (r = 0.90, p < 0.0001) and small tumor antigen (r = 0.83, p < 0.001) genes. The enhanced expression of the early region 4 open reading frame gene due to co-infection with BK polyomavirus was associated with enhanced adenovirus, but not BK polyomavirus, replication. The current study provides evidence that co-infection of adenovirus and BK polyomavirus contributes to enhanced adenovirus replication. Data obtained from this study may have significant importance in the clinical setting.

Cyclin A recruits p33cdk2 to the cellular transcription factor DRTF1.

PubMed

Bandara, L R; Adamczewski, J P; Zamanian, M; Poon, R Y; Hunt, T; Thangue, N B

1992-01-01

Cyclins are regulatory molecules that undergo periodic accumulation and destruction during each cell cycle. By activating p34cdc2 and related kinase subunits they control important events required for normal cell cycle progression. Cyclin A, for example, regulates at least two distinct kinase subunits, the mitotic kinase subunit p34cdc2 and related subunit p33cdk2, and is widely believed to be necessary for progression through S phase. However, cyclin A also forms a stable complex with the cellular transcription factor DRTF1 and thus may perform other functions during S phase. DRTF1, in addition, associates with the tumour suppressor retinoblastoma (Rb) gene product and the Rb-related protein p107. We now show, using biologically active fusion proteins, that cyclin A can direct the binding of the cdc2-like kinase subunit, p33cdk2, to complexed DRTF1, containing either Rb or p107, as well as activate its histone H1 kinase activity. Cyclin A cannot, however, direct p34cdc2 to the DRTF1 complex and we present evidence suggesting that the stability of the cyclin A-p33cdk2 complex is influenced by DRTF1 or an associated protein. Cyclin A, therefore, serves as an activating and targeting subunit of p33cdk2. The ability of cyclin A to activate and recruit p33cdk2 to DRTF1 may play an important role in regulating cell cycle progression and moreover defines a mechanism for coupling cell-cycle events to transcriptional initiation.

Isolation of midgut escape mutants of two American genotype dengue 2 viruses from Aedes aegypti

PubMed Central

2013-01-01

Background Several studies have shown that American genotype dengue 2 viruses (DENV2) have reduced viral fitness in the mosquito vector, Aedes aegypti, compared to other DENV2 genotypes. Diminished replication efficiency or inability to efficiently traverse membrane barriers encompassing organs such as the midgut or salivary glands are considered major factors negatively impacting viral fitness in the mosquito. Results We analyzed the vector competence of Ae. aegypti for two American DENV2 strains, QR94 and PR159 originating from Mexico and Puerto-Rico, respectively. Both strains infected mosquito midguts following acquisition of infectious bloodmeals. However, DENV2-QR94 and DENV2-PR159 poorly disseminated from the midgut at 7 or 14 days post-bloodmeal (pbm). We detected one virus isolate, EM33, among 31 DENV2-QR94 infected mosquitoes, and one isolate, EM41, among 121 DENV2-PR159 infected mosquitoes, generating high virus titers in mosquito carcasses at 7 days pbm. In oral challenge experiments, EM33 and EM41 showed midgut dissemination rates of 40-50%. Replication efficiency of EM41 in secondary mosquito tissue was similar to that of a dissemination-competent control strain, whereas the replication efficiency of EM33 was significantly lower than that of the control virus. The genome sequence of DENV2-QR94 encoded seven unique amino acids (aa), which were not found in 100 of the most closely related DENV2 strains. EM33 had one additional aa change, E202K, in the E protein. DENV2-PR159 encoded four unique aa residues, one of them E202K, whereas EM41 had two additional aa substitutions, Q77E in the E protein and E93D in NS3. Conclusions Our results indicate that the midgut of Ae. aegypti acts as a selective sieve for DENV2 in which genetically distinct, dissemination-competent virus variants are rapidly selected from the viral quasispecies to be transmitted to vertebrates. PMID:23937713

Genome-Wide Association Study of Personality Traits in the Long Life Family Study

PubMed Central

Bae, Harold T.; Sebastiani, Paola; Sun, Jenny X.; Andersen, Stacy L.; Daw, E. Warwick; Terracciano, Antonio; Ferrucci, Luigi; Perls, Thomas T.

2013-01-01

Personality traits have been shown to be associated with longevity and healthy aging. In order to discover novel genetic modifiers associated with personality traits as related with longevity, we performed a genome-wide association study (GWAS) on personality factors assessed by NEO-five-factor inventory in individuals enrolled in the Long Life Family Study (LLFS), a study of 583 families (N up to 4595) with clustering for longevity in the United States and Denmark. Three SNPs, in almost perfect LD, associated with agreeableness reached genome-wide significance (p < 10−8) and replicated in an additional sample of 1279 LLFS subjects, although one (rs9650241) failed to replicate and the other two were not available in two independent replication cohorts, the Baltimore Longitudinal Study of Aging and the New England Centenarian Study. Based on 10,000,000 permutations, the empirical p-value of 2 × 10−7 was observed for the genome-wide significant SNPs. Seventeen SNPs that reached marginal statistical significance in the two previous GWASs (p-value <10−4 and 10−5), were also marginally significantly associated in this study (p-value <0.05), although none of the associations passed the Bonferroni correction. In addition, we tested age-by-SNP interactions and found some significant associations. Since scores of personality traits in LLFS subjects change in the oldest ages, and genetic factors outweigh environmental factors to achieve extreme ages, these age-by-SNP interactions could be a proxy for complex gene–gene interactions affecting personality traits and longevity. PMID:23658558

Insulin-like growth factor-I extends in vitro replicative life span of skeletal muscle satellite cells by enhancing G1/S cell cycle progression via the activation of phosphatidylinositol 3'-kinase/Akt signaling pathway

NASA Technical Reports Server (NTRS)

Chakravarthy, M. V.; Abraha, T. W.; Schwartz, R. J.; Fiorotto, M. L.; Booth, F. W.

2000-01-01

Interest is growing in methods to extend replicative life span of non-immortalized stem cells. Using the insulin-like growth factor I (IGF-I) transgenic mouse in which the IGF-I transgene is expressed during skeletal muscle development and maturation prior to isolation and during culture of satellite cells (the myogenic stem cells of mature skeletal muscle fibers) as a model system, we elucidated the underlying molecular mechanisms of IGF-I-mediated enhancement of proliferative potential of these cells. Satellite cells from IGF-I transgenic muscles achieved at least five additional population doublings above the maximum that was attained by wild type satellite cells. This IGF-I-induced increase in proliferative potential was mediated via activation of the phosphatidylinositol 3'-kinase/Akt pathway, independent of mitogen-activated protein kinase activity, facilitating G(1)/S cell cycle progression via a down-regulation of p27(Kip1). Adenovirally mediated ectopic overexpression of p27(Kip1) in exponentially growing IGF-I transgenic satellite cells reversed the increase in cyclin E-cdk2 kinase activity, pRb phosphorylation, and cyclin A protein abundance, thereby implicating an important role for p27(Kip1) in promoting satellite cell senescence. These observations provide a more complete dissection of molecular events by which increased local expression of a growth factor in mature skeletal muscle fibers extends replicative life span of primary stem cells than previously known.

Changes in anthropogenic carbon storage in the Northeast Pacific in the last decade

NASA Astrophysics Data System (ADS)

Chu, Sophie N.; Wang, Zhaohui Aleck; Doney, Scott C.; Lawson, Gareth L.; Hoering, Katherine A.

2016-07-01

In order to understand the ocean's role as a sink for anthropogenic carbon dioxide (CO2), it is important to quantify changes in the amount of anthropogenic CO2 stored in the ocean interior over time. From August to September 2012, an ocean acidification cruise was conducted along a portion of the P17N transect (50°N 150°W to 33.5°N 135°W) in the Northeast Pacific. These measurements are compared with data from the previous occupation of this transect in 2001 to estimate the change in the anthropogenic CO2 inventory in the Northeast Pacific using an extended multiple linear regression (eMLR) approach. Maximum increases in the surface waters were 11 µmol kg-1 over 11 years near 50°N. Here, the penetration depth of anthropogenic CO2 only reached ˜300 m depth, whereas at 33.5°N, penetration depth reached ˜600 m. The average increase of the depth-integrated anthropogenic carbon inventory was 0.41 ± 0.12 mol m-2 yr-1 across the transect. Lower values down to 0.20 mol m-2 yr-1 were observed in the northern part of the transect near 50°N and increased up to 0.55 mol m-2 yr-1 toward 33.5°N. This increase in anthropogenic carbon in the upper ocean resulted in an average pH decrease of 0.002 ± 0.0003 pH units yr-1 and a 1.8 ± 0.4 m yr-1 shoaling rate of the aragonite saturation horizon. An average increase in apparent oxygen utilization of 13.4 ± 15.5 µmol kg-1 centered on isopycnal surface 26.6 kg m-3 from 2001 to 2012 was also observed.

Different Pathogenesis of CCR5-Using Primary HIV-1 Isolates from Non-Switch and Switch Virus Patients in Human Lymphoid Tissue Ex Vivo

NASA Technical Reports Server (NTRS)

Iarlsson, Ingrid; Grivel, Jean-Charles; Chen. Silvia; Karlsson, Anders; Albert, Jan; Fenyol, Eva Maria; Margolis, Leonid B.

2005-01-01

CCR5-utilizing HIV-1 variants (R5) typically transmit infection and dominate its early stages, whereas emergence of CXCR4-using (X4 or R5X4) HIV-1 is often associated with disease progression. However, such a switch in co-receptor usage can only be detected in approximately onehalf of HIV-infected patients (switch virus patients), and progression to immunodeficiency may also occur in patients without detectable switch in co-receptor usage (non-switch virus patients). Here, we used a system of ex vivo-infected tonsillar tissue to compare the pathogenesis of sequential primary R5 HIV-1 isolates from the switch and non-switch patients. Inoculation of ex vivo tissue with these R5 isolates resulted in viral replication and CCR5(+)CD4(+) T cell depletion. The levels of such depletion by HIV-1 isolated from non-switch virus patients were significantly higher than those by R5 HIV-1 isolates from switch virus patients. T cell depletion seemed to be controlled by viral factors and did not significantly vary between tissues from different donors. In contrast, viral replication did not correlate with the switch status of the patients; in tissues fiom different donors it varied 30-fold and seemed to be controlled by a combination of viral and tissue factors. Nevertheless, replication-level hierarchy among sequential isolates remained constant in tissues from various donors. Viral load in vivo was higher in switch virus patients compared to non-switch virus patients. The high cytopathogenicity of CCR5(+)CD4(+) T cells by R5 HIV-1 isolates from non-switch virus patients may explain the steady decline of CD4(+) T cells in the absence of CXCR4 using virus; elimination of target cells by these isolates may limit their own replication in vivo.

Mechanisms responsible for two possible electrochemical reactions in Li1.2Ni0.13Mn0.54Co0.13O2 used for lithium ion batteries

NASA Astrophysics Data System (ADS)

Konishi, Hiroaki; Hirano, Tatsumi; Takamatsu, Daiko; Gunji, Akira; Feng, Xiaoliang; Furutsuki, Sho; Okumura, Takefumi; Terada, Shohei; Tamura, Kazuhisa

2018-02-01

Two electrochemical reactions are possible in regard to Li1.2Ni0.13Mn0.54Co0.13O2 (0.5Li2MnO3-0.5LiNi0.33Mn0.33Co0.33O2), viz, Li2MnO3-like and LiNi0.33Mn0.33Co0.33O2-like reactions. The open circuit potential (OCP) and changes in crystal structure during the charge-discharge process of Li1.2Ni0.13Mn0.54Co0.13O2 were investigated to clarify the mechanism responsible for the two reactions. Li2MnO3 and LiNi0.33Mn0.33Co0.33O2 were separately prepared for the investigation, and the OCPs and crystal structures in these cathodes were measured and then compared with those for Li1.2Ni0.13Mn0.54Co0.13O2. The results obtained using X-ray diffraction (XRD) indicated that two phases existed in Li1.2Ni0.13Mn0.54Co0.13O2. The changes in crystal structure of the two phases during the charge-discharge process were similar to those in Li2MnO3 and LiNi0.33Mn0.33Co0.33O2. This indicated that two phases, viz, Li2MnO3-like and LiNi0.33Mn0.33Co0.33O2-like, existed in Li1.2Ni0.13Mn0.54Co0.13O2. Li2MnO3-like, LiNi0.33Mn0.33Co0.33O2-like, and Li2MnO3-like phases were found to contribute mainly to electrochemical reactions in the low, middle, and high state of charge (SOC) ranges during the charge process from the results obtained using XRD and electrochemical measurements carried out on Li1.2Ni0.13Mn0.54Co0.13O2. In contrast, the Li2MnO3-like and LiNi0.33Mn0.33Co0.33O2-like phases mainly contributed to electrochemical reactions in the low and high SOC ranges during the discharge process. Furthermore, the high polarization and potential decay during the charge-discharge cycling of Li1.2Ni0.13Mn0.54Co0.13O2 were mainly attributed to the Li2MnO3-like phase.

Effects of coenzyme Q10 on statin-induced myopathy: a meta-analysis of randomized controlled trials.

PubMed

Banach, Maciej; Serban, Corina; Sahebkar, Amirhossein; Ursoniu, Sorin; Rysz, Jacek; Muntner, Paul; Toth, Peter P; Jones, Steven R; Rizzo, Manfredi; Glasser, Stephen P; Lip, Gregory Y H; Dragan, Simona; Mikhailidis, Dimitri P

2015-01-01

To evaluate the efficacy of coenzyme Q10 (CoQ10) supplementation on statin-induced myopathy. We searched the MEDLINE, Cochrane Library, Scopus, and EMBASE databases (November 1, 1987, to May 1, 2014) to identify randomized controlled trials investigating the impact of CoQ10 on muscle pain and plasma creatine kinase (CK) activity as 2 measures of statin-induced myalgia. Two independent reviewers extracted data on study characteristics, methods, and outcomes. We included 6 studies with 302 patients receiving statin therapy: 5 studies with 226 participants evaluated the effect of CoQ10 supplementation on plasma CK activity, and 5 studies (4 used in the CK analysis and 1 other study) with 253 participants were included to assess the effect of CoQ10 supplementation on muscle pain. Compared with the control group, plasma CK activity was increased after CoQ10 supplementation, but this change was not significant (mean difference, 11.69 U/L [to convert to μkat/L, multiply by 0.0167]; 95% CI, -14.25 to 37.63 U/L; P=.38). Likewise, CoQ10 supplementation had no significant effect on muscle pain despite a trend toward a decrease (standardized mean difference, -0.53; 95% CI, -1.33 to 0.28; P=.20). No dose-effect association between changes in plasma CK activity (slope, -0.001; 95% CI, -0.004 to 0.001; P=.33) or in the indices of muscle pain (slope, 0.002; 95% CI, -0.005 to 0.010; P=.67) and administered doses of CoQ10 were observed. The results of this meta-analysis of available randomized controlled trials do not suggest any significant benefit of CoQ10 supplementation in improving statin-induced myopathy. Larger, well-designed trials are necessary to confirm the findings from this meta-analysis. Copyright © 2015 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

Erosive arthritis in systemic lupus erythematosus: analysis of a distinct clinical and serological subset.

PubMed

Richter Cohen, M; Steiner, G; Smolen, J S; Isenberg, D A

1998-04-01

Erosive arthritis (EA) in systemic lupus erythematosus (SLE) can be debilitating and deforming with uncertain factors for risk, although antibodies to the A2 hnRNP core protein, known as anti-RA33, have been associated with EA. Two hundred patients under long-term follow-up for SLE were evaluated for EA and associated clinical and serological abnormalities. In addition, sera were tested in a masked fashion for anti-RA33 antibodies in a total of 60 patients: 10 with EA and 50 age-, sex- and ethnically matched controls. Ten of 200 (5%) patients with SLE, mainly non-white women, had EA. There were trends for increased renal involvement (P = 0.06), Sjögren's syndrome (P = 0.07) and Raynaud's phenomenon (P = 0.03) in patients with EA compared to those without EA. Rheumatoid factor (RF) was increased in patients with EA (P < 0.02), as were antibodies to double-stranded DNA (P < 0.05), Sm (P < 0.01) and La/SS-B (P < 0.001). Anti-RA33 antibodies were present in 70% with EA compared to 28% without EA (P < 0.05). RF correlated with anti-RA33 antibodies in patients with EA, but not with the presence of anti-RA33 alone. Thus, anti-RA33 antibodies may identify those patients with SLE who are at risk for EA, and an association with RF suggests a common immune response or pathological mechanism in autoimmune erosive joint disease.

New features of mitochondrial DNA replication system in yeast and man.

PubMed

Lecrenier, N; Foury, F

2000-04-04

In this review, we sum up the research carried out over two decades on mitochondrial DNA (mtDNA) replication, primarily by comparing this system in Saccharomyces cerevisiae and Homo sapiens. Brief incursions into systems of other organisms have also been achieved when they provide new information.S. cerevisiae and H. sapiens mitochondrial DNA (mtDNA) have been thought for a long time to share closely related architecture and replication mechanisms. However, recent studies suggest that mitochondrial genome of S. cerevisiae may be formed, at least partially, from linear multimeric molecules, while human mtDNA is circular. Although several proteins involved in the replication of these two genomes are very similar, divergences are also now increasingly evident. As an example, the recently cloned human mitochondrial DNA polymerase beta-subunit has no counterpart in yeast. Yet, yeast Abf2p and human mtTFA are probably not as closely functionally related as thought previously. Some mtDNA metabolism factors, like DNA ligases, were until recently largely uncharacterized, and have been found to be derived from alternative nuclear products. Many factors involved in the metabolism of mitochondrial DNA are linked through genetic or biochemical interconnections. These links are presented on a map. Finally, we discuss recent studies suggesting that the yeast mtDNA replication system diverges from that observed in man, and may involve recombination, possibly coupled to alternative replication mechanisms like rolling circle replication.

Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses.

PubMed

Hamperl, Stephan; Bocek, Michael J; Saldivar, Joshua C; Swigut, Tomek; Cimprich, Karlene A

2017-08-10

Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states. Copyright © 2017 Elsevier Inc. All rights reserved.

Blocking phosphatidylcholine utilization in Pseudomonas aeruginosa, via mutagenesis of fatty acid, glycerol and choline degradation pathways, confirms the importance of this nutrient source in vivo.

PubMed

Sun, Zhenxin; Kang, Yun; Norris, Michael H; Troyer, Ryan M; Son, Mike S; Schweizer, Herbert P; Dow, Steven W; Hoang, Tung T

2014-01-01

Pseudomonas aeruginosa can grow to very high-cell-density (HCD) during infection of the cystic fibrosis (CF) lung. Phosphatidylcholine (PC), the major component of lung surfactant, has been hypothesized to support HCD growth of P. aeruginosa in vivo. The phosphorylcholine headgroup, a glycerol molecule, and two long-chain fatty acids (FAs) are released by enzymatic cleavage of PC by bacterial phospholipase C and lipases. Three different bacterial pathways, the choline, glycerol, and fatty acid degradation pathways, are then involved in the degradation of these PC components. Here, we identified five potential FA degradation (Fad) related fadBA-operons (fadBA1-5, each encoding 3-hydroxyacyl-CoA dehydrogenase and acyl-CoA thiolase). Through mutagenesis and growth analyses, we showed that three (fadBA145) of the five fadBA-operons are dominant in medium-chain and long-chain Fad. The triple fadBA145 mutant also showed reduced ability to degrade PC in vitro. We have previously shown that by partially blocking Fad, via mutagenesis of fadBA5 and fadDs, we could significantly reduce the ability of P. aeruginosa to replicate on FA and PC in vitro, as well as in the mouse lung. However, no studies have assessed the ability of mutants, defective in choline and/or glycerol degradation in conjunction with Fad, to grow on PC or in vivo. Hence, we constructed additional mutants (ΔfadBA145ΔglpD, ΔfadBA145ΔbetAB, and ΔfadBA145ΔbetABΔglpD) significantly defective in the ability to degrade FA, choline, and glycerol and, therefore, PC. The analysis of these mutants in the BALB/c mouse lung infection model showed significant inability to utilize PC in vitro, resulted in decreased replication fitness and competitiveness in vivo compared to the complement strain, although there was little to no variation in typical virulence factor production (e.g., hemolysin, lipase, and protease levels). This further supports the hypothesis that lung surfactant PC serves as an important nutrient for P. aeruginosa during CF lung infection.

Overexpression of pig selenoprotein S blocks OTA-induced promotion of PCV2 replication by inhibiting oxidative stress and p38 phosphorylation in PK15 cells.

PubMed

Gan, Fang; Hu, Zhihua; Huang, Yu; Xue, Hongxia; Huang, Da; Qian, Gang; Hu, Junfa; Chen, Xingxiang; Wang, Tian; Huang, Kehe

2016-04-12

Porcine circovirus type 2 (PCV2) is the primary cause of porcine circovirus disease, and ochratoxin A (OTA)-induced oxidative stress promotes PCV2 replication. In humans, selenoprotein S (SelS) has antioxidant ability, but it is unclear whether SelS affects viral infection. Here, we stably transfected PK15 cells with pig pCDNA3.1-SelS to overexpress SelS. Selenium (Se) at 2 or 4 μM and SelS overexpression blocked the OTA-induced increases of PCV2 DNA copy number and infected cell numbers. SelS overexpression also increased glutathione (GSH), NF-E2-related factor 2 (Nrf2) mRNA, and γ-glutamyl-cysteine synthetase mRNA levels; decreased reactive oxygen species (ROS) levels; and inhibited p38 phosphorylation in PCV2-infected PK15 cells, regardless of OTA treatment. Buthionine sulfoximine reversed all of the above SelS-induced changes. siRNA-mediated SelS knockdown decreased Nrf2 mRNA and GSH levels, increased ROS levels, and promoted PCV2 replication in OTA-treated PK15 cells. These data indicate that pig SelS blocks OTA-induced promotion of PCV2 replication by inhibiting the oxidative stress and p38 phosphorylation in PK15 cells.

Overexpression of pig selenoprotein S blocks OTA-induced promotion of PCV2 replication by inhibiting oxidative stress and p38 phosphorylation in PK15 cells

PubMed Central

Gan, Fang; Hu, Zhihua; Huang, Yu; Xue, Hongxia; Huang, Da; Qian, Gang; Hu, Junfa; Chen, Xingxiang; Wang, Tian; Huang, Kehe

2016-01-01

Porcine circovirus type 2 (PCV2) is the primary cause of porcine circovirus disease, and ochratoxin A (OTA)-induced oxidative stress promotes PCV2 replication. In humans, selenoprotein S (SelS) has antioxidant ability, but it is unclear whether SelS affects viral infection. Here, we stably transfected PK15 cells with pig pCDNA3.1-SelS to overexpress SelS. Selenium (Se) at 2 or 4 μM and SelS overexpression blocked the OTA-induced increases of PCV2 DNA copy number and infected cell numbers. SelS overexpression also increased glutathione (GSH), NF-E2-related factor 2 (Nrf2) mRNA, and γ-glutamyl-cysteine synthetase mRNA levels; decreased reactive oxygen species (ROS) levels; and inhibited p38 phosphorylation in PCV2-infected PK15 cells, regardless of OTA treatment. Buthionine sulfoximine reversed all of the above SelS-induced changes. siRNA-mediated SelS knockdown decreased Nrf2 mRNA and GSH levels, increased ROS levels, and promoted PCV2 replication in OTA-treated PK15 cells. These data indicate that pig SelS blocks OTA-induced promotion of PCV2 replication by inhibiting the oxidative stress and p38 phosphorylation in PK15 cells. PMID:26943035

Genetically distinct populations of northern shrimp, Pandalus borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor.

PubMed

Jorde, Per Erik; Søvik, Guldborg; Westgaard, Jon-Ivar; Albretsen, Jon; André, Carl; Hvingel, Carsten; Johansen, Torild; Sandvik, Anne Dagrun; Kingsley, Michael; Jørstad, Knut Eirik

2015-04-01

The large-scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species' range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: FST = -0.0002 to 0.0475) with a highly significant average (FST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (FST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best-fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5-4.7%) on large-scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment. © 2015 John Wiley & Sons Ltd.

Identification of p90 Ribosomal S6 Kinase 2 as a Novel Host Protein in HBx Augmenting HBV Replication by iTRAQ-Based Quantitative Comparative Proteomics.

PubMed

Yan, Li-Bo; Yu, You-Jia; Zhang, Qing-Bo; Tang, Xiao-Qiong; Bai, Lang; Huang, FeiJun; Tang, Hong

2018-05-01

The aim of this study was to screen for novel host proteins that play a role in HBx augmenting Hepatitis B virus (HBV) replication. Three HepG2 cell lines stably harboring different functional domains of HBx (HBx, HBx-Cm6, and HBx-Cm16) were cultured. ITRAQ technology integrated with LC-MS/MS analysis was applied to identify the proteome differences among these three cell lines. In brief, a total of 70 different proteins were identified among HepG2-HBx, HepG2-HBx-Cm6, and HepG2-HBx-Cm16 by double repetition. Several differentially expressed proteins, including p90 ribosomal S6 kinase 2 (RSK2), were further validated. RSK2 was expressed at higher levels in HepG2-HBx and HepG2-HBx-Cm6 compared with HepG2-HBx-Cm16. Furthermore, levels of HBV replication intermediates were decreased after silencing RSK2 in HepG2.2.15. An HBx-minus HBV mutant genome led to decreased levels of HBV replication intermediates and these decreases were restored to levels similar to wild-type HBV by transient ectopic expression of HBx. After silencing RSK2 expression, the levels of HBV replication intermediates synthesized from the HBx-minus HBV mutant genome were not restored to levels that were observed with wild-type HBV by transient HBx expression. Based on iTRAQ quantitative comparative proteomics, RSK2 was identified as a novel host protein that plays a role in HBx augmenting HBV replication. © 2018 The Authors. Proteomics - Clinical Application Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterizing differences in the phosphorus activation coefficient of three typical cropland soils and the influencing factors under long-term fertilization.

PubMed

Wu, Qihua; Zhang, Shuxiang; Zhu, Ping; Huang, Shaomin; Wang, Boren; Zhao, LinPing; Xu, Minggang

2017-01-01

The phosphorus activation coefficient (PAC, the ratio of available P to total P) is an important indicator of soil P availability and the transformation of P fractions. Understanding the details of the PAC is useful to estimate soil available P status and to provide P management guidance. In this research, soils from five long-term (23 years) fertilization treatments in three croplands were selected to examine the relationships between the PAC and P fractions and to analyse the influencing factors. PAC was affected by both soil types and fertilization treatments. Compared to the unfertilized control (CK) treatment, long-term P application significantly increased the PAC, all of the inorganic P (Pi) fractions and most of the organic P (Po) fractions in all the three soils, particularly in chemical fertilizer combined with manure treatment (NPKM). The PAC was significantly correlated to all of the Pi fractions proportions (P<0.05) except for Dil. HCl-Pi and Conc. HCl-Pi. Compared with CK, the chemical P and chemical P combined with manure treatments increased the ratio of total Pi fractions to total Po fractions (Pit/Pot); furthermore, NPKM significantly increased the organic C (Co) content and decreased the Co/Pot ratio. Stepwise multiple regressions showed that PAC = 0.93 Co+0.69 Pit/Pot-0.07 Co/Pot-0.27CaCO3-3.79 (R2 = 0.924, P<0.001). In addition, the variance partitioning analysis showed that more variance of PAC is explained by soil factors (29.53%) than by P input (0.19%) and climate (0.25%) factors. Our findings demonstrate that P application increased the PAC by changing the Co content and the proportion of P fractions. Moreover, soil factors were the most important drivers of P transformations, and NPKM was optimal for improving soil fertility in Chinese croplands.

Characterizing differences in the phosphorus activation coefficient of three typical cropland soils and the influencing factors under long-term fertilization

PubMed Central

Wu, Qihua; Zhang, Shuxiang; Zhu, Ping; Huang, Shaomin; Wang, Boren; Zhao, LinPing; Xu, Minggang

2017-01-01

The phosphorus activation coefficient (PAC, the ratio of available P to total P) is an important indicator of soil P availability and the transformation of P fractions. Understanding the details of the PAC is useful to estimate soil available P status and to provide P management guidance. In this research, soils from five long-term (23 years) fertilization treatments in three croplands were selected to examine the relationships between the PAC and P fractions and to analyse the influencing factors. PAC was affected by both soil types and fertilization treatments. Compared to the unfertilized control (CK) treatment, long-term P application significantly increased the PAC, all of the inorganic P (Pi) fractions and most of the organic P (Po) fractions in all the three soils, particularly in chemical fertilizer combined with manure treatment (NPKM). The PAC was significantly correlated to all of the Pi fractions proportions (P<0.05) except for Dil. HCl-Pi and Conc. HCl-Pi. Compared with CK, the chemical P and chemical P combined with manure treatments increased the ratio of total Pi fractions to total Po fractions (Pit/Pot); furthermore, NPKM significantly increased the organic C (Co) content and decreased the Co/Pot ratio. Stepwise multiple regressions showed that PAC = 0.93 Co+0.69 Pit/Pot-0.07 Co/Pot-0.27CaCO3-3.79 (R2 = 0.924, P<0.001). In addition, the variance partitioning analysis showed that more variance of PAC is explained by soil factors (29.53%) than by P input (0.19%) and climate (0.25%) factors. Our findings demonstrate that P application increased the PAC by changing the Co content and the proportion of P fractions. Moreover, soil factors were the most important drivers of P transformations, and NPKM was optimal for improving soil fertility in Chinese croplands. PMID:28467425

Evidence from simultaneous intracellular- and surface-pH transients that carbonic anhydrase II enhances CO2 fluxes across Xenopus oocyte plasma membranes

PubMed Central

Occhipinti, Rossana; Boron, Walter F.

2014-01-01

The α-carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the interconversion of CO2 and HCO3−. Here, we focus on human CA II (CA II), a ubiquitous cytoplasmic enzyme. In the second paper in this series, we examine CA IV at the extracellular surface. After microinjecting recombinant CA II in a Tris solution (or just Tris) into oocytes, we expose oocytes to 1.5% CO2/10 mM HCO3−/pH 7.50 while using microelectrodes to monitor intracellular pH (pHi) and surface pH (pHS). CO2 influx causes the familiar sustained pHi fall as well as a transient pHS rise; CO2 efflux does the opposite. Both during CO2 addition and removal, CA II increases the magnitudes of the maximal rate of pHi change, (dpHi/dt)max, and the maximal change in pHS, ΔpHS. Preincubating oocytes with the inhibitor ethoxzolamide eliminates the effects of CA II. Compared with pHS, pHi begins to change only after a delay of ∼9 s and its relaxation has a larger (i.e., slower) time constant (τpHi > τpHS). Simultaneous measurements with two pHi electrodes, one superficial and one deep, suggest that impalement depth contributes to pHi delay and higher τpHi. Using higher CO2/HCO3− levels, i.e., 5%/33 mM HCO3− or 10%/66 mM HCO3−, increases (dpHi/dt)max and ΔpHS, though not in proportion to the increase in [CO2]. A reaction-diffusion mathematical model (described in the third paper in this series) accounts for the above general features and supports the conclusion that cytosolic CA—consuming entering CO2 or replenishing exiting CO2—increases CO2 fluxes across the cell membrane. PMID:24965587

Insect Cell-Derived Cofactors Become Fully Functional after Proteinase K and Heat Treatment for High-Fidelity Amplification of Glycosylphosphatidylinositol-Anchored Recombinant Scrapie and BSE Prion Proteins

PubMed Central

Imamura, Morikazu; Kato, Nobuko; Okada, Hiroyuki; Yoshioka, Miyako; Iwamaru, Yoshifumi; Shimizu, Yoshihisa; Mohri, Shirou; Yokoyama, Takashi; Murayama, Yuichi

2013-01-01

The central event in prion infection is the conformational conversion of host-encoded cellular prion protein (PrPC) into the pathogenic isoform (PrPSc). Diverse mammalian species possess the cofactors required for in vitro replication of PrPSc by protein-misfolding cyclic amplification (PMCA), but lower organisms, such as bacteria, yeasts, and insects, reportedly lack the essential cofactors. Various cellular components, such as RNA, lipids, and other identified cofactor molecules, are commonly distributed in both eukaryotes and prokaryotes, but the reasons for the absence of cofactor activity in lower organisms remain to be elucidated. Previously, we reported that brain-derived factors were necessary for the in vitro replication of glycosylphosphatidylinositol-anchored baculovirus-derived recombinant PrP (Bac-PrP). Here, we demonstrate that following protease digestion and heat treatment, insect cell lysates had the functional cofactor activity required for Bac-PrP replication by PMCA. Mammalian PrPSc seeds and Bac-PrPSc generated by PMCA using Bac-PrP and insect cell-derived cofactors showed similar pathogenicity and produced very similar lesions in the brains of inoculated mice. These results suggested that the essential cofactors required for the high-fidelity replication of mammalian PrPSc were present in the insect cells but that the cofactor activity was masked or inhibited in the native state. We suggest that not only RNA, but also DNA, are the key components of PMCA, although other cellular factors were necessary for the expression of the cofactor activity of nucleic acids. PMCA using only insect cell-derived substances (iPMCA) was highly useful for the ultrasensitive detection of PrPSc of some prion strains. PMID:24367521

[The effects of TorR protein on initiation of DNA replication in Escherichia coli].

PubMed

Yuan, Yao; Jiaxin, Qiao; Jing, Li; Hui, Li; Morigen, Morigen

2015-03-01

The two-component systems, which could sense and respond to environmental changes, widely exist in bacteria as a signal transduction pathway. The bacterial CckA/CtrA, ArcA/ArcB and PhoP/PhoQ two-component systems are associated with initiation of DNA replication and cell division, however, the effects of the TorS/TorR system on cell cycle and DNA replication remains unknown. The TorS/TorR system in Escherichia coli can sense changes in trimethylamine oxide (TMAO) concentration around the cells. However, it is unknown if it also affects initiation of DNA replication. We detected DNA replication patterns in ΔtorS and ΔtorR mutant strains by flow cytometry. We found that the average number of replication origins (oriCs) per cell and doubling time in ΔtorS mutants were the same while the average number of oriCs in ΔtorR mutants was increased compared with that in wild-type cells. These results indicated that absence of TorR led to an earlier initiation of DNA replication than that in wild-type cells. Strangely, neither overexpression of TorR nor co-expression of TorR and TorS could restore ΔtorR mutant phenotype to the wild type. However, overexpression of SufD in both wild type and ΔtorR mutants promoted initiation of DNA replication, while mutation of SufD delayed it in ΔtorR mutants. Thus, TorR may affect initiation of DNA replication indirectly through regulating gene expression of sufD.

Dextransucrase Expression Is Concomitant with that of Replication and Maintenance Functions of the pMN1 Plasmid in Lactobacillus sakei MN1

PubMed Central

Nácher-Vázquez, Montserrat; Ruiz-Masó, José A.; Mohedano, María L.; del Solar, Gloria; Aznar, Rosa; López, Paloma

2017-01-01

The exopolysaccharide synthesized by Lactobacillus sakei MN1 is a dextran with antiviral and immunomodulatory properties of potential utility in aquaculture. In this work we have investigated the genetic basis of dextran production by this bacterium. Southern blot hybridization experiments demonstrated the plasmidic location of the dsrLS gene, which encodes the dextransucrase involved in dextran synthesis. DNA sequencing of the 11,126 kbp plasmid (pMN1) revealed that it belongs to a family which replicates by the theta mechanism, whose prototype is pUCL287. The plasmid comprises the origin of replication, repA, repB, and dsrLS genes, as well as seven open reading frames of uncharacterized function. Lb. sakei MN1 produces dextran when sucrose, but not glucose, is present in the growth medium. Therefore, plasmid copy number and stability, as well as dsrLS expression, were investigated in cultures grown in the presence of either sucrose or glucose. The results revealed that pMN1 is a stable low-copy-number plasmid in both conditions. Gene expression studies showed that dsrLS is constitutively expressed, irrespective of the carbon source present in the medium. Moreover, dsrLS is expressed from a monocistronic transcript as well as from a polycistronic repA-repB-orf1-dsrLS mRNA. To our knowledge, this is the first report of a plasmid-borne dextransucrase-encoding gene, as well as the first time that co-transcription of genes involved in plasmid maintenance and replication with a gene encoding an enzyme has been established. PMID:29209293

Model of OSBP-Mediated Cholesterol Supply to Aichi Virus RNA Replication Sites Involving Protein-Protein Interactions among Viral Proteins, ACBD3, OSBP, VAP-A/B, and SAC1.

PubMed

Ishikawa-Sasaki, Kumiko; Nagashima, Shigeo; Taniguchi, Koki; Sasaki, Jun

2018-04-15

Positive-strand RNA viruses, including picornaviruses, utilize cellular machinery for genome replication. Previously, we reported that each of the 2B, 2BC, 2C, 3A, and 3AB proteins of Aichi virus (AiV), a picornavirus, forms a complex with the Golgi apparatus protein ACBD3 and phosphatidylinositol 4-kinase IIIβ (PI4KB) at viral RNA replication sites (replication organelles [ROs]), enhancing PI4KB-dependent phosphatidylinositol 4-phosphate (PI4P) production. Here, we demonstrate AiV hijacking of the cellular cholesterol transport system involving oxysterol-binding protein (OSBP), a PI4P-binding cholesterol transfer protein. AiV RNA replication was inhibited by silencing cellular proteins known to be components of this pathway, OSBP, the ER membrane proteins VAPA and VAPB (VAP-A/B), the PI4P-phosphatase SAC1, and PI-transfer protein β. OSBP, VAP-A/B, and SAC1 were present at RNA replication sites. We also found various previously unknown interactions among the AiV proteins (2B, 2BC, 2C, 3A, and 3AB), ACBD3, OSBP, VAP-A/B, and SAC1, and the interactions were suggested to be involved in recruiting the component proteins to AiV ROs. Importantly, the OSBP-2B interaction enabled PI4P-independent recruitment of OSBP to AiV ROs, indicating preferential recruitment of OSBP among PI4P-binding proteins. Protein-protein interaction-based OSBP recruitment has not been reported for other picornaviruses. Cholesterol was accumulated at AiV ROs, and inhibition of OSBP-mediated cholesterol transfer impaired cholesterol accumulation and AiV RNA replication. Electron microscopy showed that AiV-induced vesicle-like structures were close to ER membranes. Altogether, we conclude that AiV directly recruits the cholesterol transport machinery through protein-protein interactions, resulting in formation of membrane contact sites between the ER and AiV ROs and cholesterol supply to the ROs. IMPORTANCE Positive-strand RNA viruses utilize host pathways to modulate the lipid composition of viral RNA replication sites for replication. Previously, we demonstrated that Aichi virus (AiV), a picornavirus, forms a complex comprising certain proteins of AiV, the Golgi apparatus protein ACBD3, and the lipid kinase PI4KB to synthesize PI4P lipid at the sites for AiV RNA replication. Here, we confirmed cholesterol accumulation at the AiV RNA replication sites, which are established by hijacking the host cholesterol transfer machinery mediated by a PI4P-binding cholesterol transfer protein, OSBP. We showed that the component proteins of the machinery, OSBP, VAP, SAC1, and PITPNB, are all essential host factors for AiV replication. Importantly, the machinery is directly recruited to the RNA replication sites through previously unknown interactions of VAP/OSBP/SAC1 with the AiV proteins and with ACBD3. Consequently, we propose a specific strategy employed by AiV to efficiently accumulate cholesterol at the RNA replication sites via protein-protein interactions. Copyright © 2018 American Society for Microbiology.

Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response.

PubMed

Kindler, E; Thiel, V; Weber, F

2016-01-01

Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are the most severe coronavirus (CoV)-associated diseases in humans. The causative agents, SARS-CoV and MERS-CoV, are of zoonotic origin but may be transmitted to humans, causing severe and often fatal respiratory disease in their new host. The two coronaviruses are thought to encode an unusually large number of factors that allow them to thrive and replicate in the presence of efficient host defense mechanisms, especially the antiviral interferon system. Here, we review the recent progress in our understanding of the strategies that highly pathogenic coronaviruses employ to escape, dampen, or block the antiviral interferon response in human cells. © 2016 Elsevier Inc. All rights reserved.

Interferon signaling in Peromyscus leucopus confers a potent and specific restriction to vector-borne flaviviruses.

PubMed

Izuogu, Adaeze O; McNally, Kristin L; Harris, Stephen E; Youseff, Brian H; Presloid, John B; Burlak, Christopher; Munshi-South, Jason; Best, Sonja M; Taylor, R Travis

2017-01-01

Tick-borne flaviviruses (TBFVs), including Powassan virus and tick-borne encephalitis virus cause encephalitis or hemorrhagic fevers in humans with case-fatality rates ranging from 1-30%. Despite severe disease in humans, TBFV infection of natural rodent hosts has little noticeable effect. Currently, the basis for resistance to disease is not known. We hypothesize that the coevolution of flaviviruses with their respective hosts has shaped the evolution of potent antiviral factors that suppress virus replication and protect the host from lethal infection. In the current study, we compared virus infection between reservoir host cells and related susceptible species. Infection of primary fibroblasts from the white-footed mouse (Peromyscus leucopus, a representative host) with a panel of vector-borne flaviviruses showed up to a 10,000-fold reduction in virus titer compared to control Mus musculus cells. Replication of vesicular stomatitis virus was equivalent in P. leucopus and M. musculus cells suggesting that restriction was flavivirus-specific. Step-wise comparison of the virus infection cycle revealed a significant block to viral RNA replication, but not virus entry, in P. leucopus cells. To understand the role of the type I interferon (IFN) response in virus restriction, we knocked down signal transducer and activator of transcription 1 (STAT1) or the type I IFN receptor (IFNAR1) by RNA interference. Loss of IFNAR1 or STAT1 significantly relieved the block in virus replication in P. leucopus cells. The major IFN antagonist encoded by TBFV, nonstructural protein 5, was functional in P. leucopus cells, thus ruling out ineffective viral antagonism of the host IFN response. Collectively, this work demonstrates that the IFN response of P. leucopus imparts a strong and virus-specific barrier to flavivirus replication. Future identification of the IFN-stimulated genes responsible for virus restriction specifically in P. leucopus will yield mechanistic insight into efficient control of virus replication and may inform the development of antiviral therapeutics.

Growth of the parvovirus minute virus of mice MVMp3 in EL4 lymphocytes is restricted after cell entry and before viral DNA amplification: cell-specific differences in virus uncoating in vitro.

PubMed

Previsani, N; Fontana, S; Hirt, B; Beard, P

1997-10-01

Two murine parvoviruses with genomic sequences differing only in 33 nucleotides (8 amino acids) in the region coding for the capsid proteins show different host cell specificities: MVMi grows in EL4 T lymphocytes and MVMp3 grows in A9 fibroblasts. In this study we compared the courses of infections with these two viruses in EL4 cells in order to investigate at which step(s) the infection process of MVMp3 is interrupted. The two viruses bound equally well to EL4 cells, and similar amounts of MVMi and MVMp3 input virion DNA appeared in the nuclear fractions of EL4 cells 1 h after infection. However, double-stranded replicative-form (RF) DNA of the two viruses appeared at different times, at 10 h postinfection with MVMi and at 24 h postinfection with MVMp3. The amount of MVMp3 RF DNA detected at 24 h was very small because it was produced only in a tiny subset of the population of EL4 cells that proved to be permissive for MVMp3. Replication of double-stranded viral DNA in EL4 cells was measured after transfection of purified RF DNA, cloned viral DNA, and cloned viral DNA with a mutation preventing synthesis of the capsid proteins. In each of these cases, DNA replication was comparable for MVMi and MVMp3. Production of virus particles also appeared to be similar after transfection of the two types of RF DNA into EL4 cells. Conversion of incoming 32P-labeled single-stranded MVM DNA to 32P-labeled double-stranded RF DNA was detected only after RF DNA amplification, indicating that few molecules serve as templates for viral DNA amplification. We showed that extracts of EL4 cells contain a factor which can destabilize MVMi virions but not MVMp3 by testing the sensitivity of viral DNA to DNase and by CsCl gradient analyses of viral particles. We therefore conclude that the MVMp3 life cycle is arrested after the transport of virions to the nucleus and prior to the replication of RF DNA, most likely at the stage of viral decapsidation.

Cerebral interstitial tissue oxygen tension, pH, HCO3, CO2.

PubMed

Charbel, F T; Hoffman, W E; Misra, M; Hannigan, K; Ausman, J I

1997-10-01

There are many techniques for monitoring the injured brain following trauma, subarachnoid hemorrhage, or surgery. It is thought that the major determinants for recovery of injured cerebral tissue are oxygen, glucose delivery, and the clearance of metabolites. These factors, at optimal levels, are probably responsible for the regaining of neuronal functions. These parameters are in turn dependent on the tissue's blood flow and metabolism. We have been using a single, compact, polyethylene sensor, the Paratrend 7 for the measurement of cerebral oxygen tension, CO2, pH, and temperature. This sensor is designed for continuous blood gas analysis to aid in monitoring neurosurgical patients, both during surgery and in the intensive care unit. Using the Paratrend 7 sensor, we found the normal range of values to be: PO2 33 +/- 11 mm Hg; PCO2 48 +/- 7 mm Hg; pH 7.19 +/- 0.11. Critical measurements are considered to be tissue PO2 < 10 mm Hg; PCO2 > 60 mm Hg, and pH < 6.8. We have had no complications with this device; the risks are similar to those of placing a parenchymal intracranial pressure monitor. We believe that assessment of interstitial cerebral oxygen saturation can be of great value both intraoperatively and postoperatively. In our experience, the Paratrend 7 system is an effective method of measuring tissue cerebral oxygen tension, along with carbon dioxide levels, pH, and temperature.

Formation and emission of nitrogen oxide in gas turbine engines: plume effluent characteristics of TF3O-P111+ and TF33-P9 engines. Final technical report, 1 November-17 December 1993

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dill, J.W.; Sowa, W.A.; Samuelsen, G.S.

1996-06-30

Phase I of this project focused on the creation of a spatial emissions map of the plume effluent in the exhaust stream directly behind the engine in a jet engine test cell (JETC). Both afterburning TF30-P111+ and non-after-burning TF33-P9 engines were tested. Measurements were taken in conjunction with actual engine tests for validity of the data. Temperature, oxides of nitrogen (NOx), carbon monoxide (CO) concentration, and velocity were among the characteristics measured radially and axially in the plume for each engine type. The main focus of this study was on NOx, consisting of nitric oxide (NO) and nitrogen dioxide (NO2).more » Measurements in the P111+ plume reveal levels of NOx above 300 ppm along the centerline of the effluent. A dip in the NOx emissions at afterburner shows signs of a reburning and/or dilution effect by the atmospheric combustion in the effluent. Significant amounts of NO2 are present in the effluent over the entire power range. Temperatures at military power reach 1100 deg F along the centerline, and CO values are below 80 ppm. Carbon monoxide concentrations decrease from idle to military power (full power, no afterburner), then rise sharply in afterburner. The CO peaks shift outward from centerline as do the temperatures due to the radial geometry of the afterburner combustion (over 10 percent CO at 2850 deg F).« less

Chymotrypsinogen C Genetic Variants, Including c.180TT, Are Strongly Associated With Chronic Pancreatitis in Pediatric Patients.

PubMed

Grabarczyk, Alicja Monika; Oracz, Grzegorz; Wertheim-Tysarowska, Katarzyna; Kujko, Aleksandra Anna; Wejnarska, Karolina; Kolodziejczyk, Elwira; Bal, Jerzy; Koziel, Dorota; Kowalik, Artur; Gluszek, Stanislaw; Rygiel, Agnieszka Magdalena

2017-12-01

Genetic studies in adults/adolescent patients with chronic pancreatitis (CP) identified chymotrypsinogen C (CTRC) genetic variants but their association with CP risk has been difficult to replicate. To evaluate the risk of CP associated with CTRC variants in CP pediatric patients-control study. The distribution of CTRC variants in CP pediatric cohort (n = 136, median age at CP onset 8 years) with no history of alcohol/smoking abuse was compared with controls (n = 401, median age 45). We showed that p.Arg254Trp (4.6%) and p.Lys247_Arg254del (5.3%) heterozygous mutations are frequent and significantly associated with CP risk in pediatric patients (odds ratio [OR] = 19.1; 95% CI 2.8-160; P = 0.001 and OR = 5.5; 95% CI 1.6-19.4; P = 0.001, respectively). For the first time, we demonstrated that the c.180TT genotype of common p.Gly60Gly variant is strong, an independent CP risk factor (OR = 23; 95% CI 7.7-70; P < 0.001) with effect size comparable to p.Arg254Trp mutation. The other novel observation is that common c.493+51C>A variant, both CA and AA genotype, is significantly underrepresented in CP compared with controls (15% vs 35%; OR = 0.33; 95% CI 0.19-0.59; P < 0.001 and 2.8% vs 11%; OR = 0.24; 95% CI 0.06-0.85; P = 0.027, respectively). Our study provides evidence that CTRC variants, including c.180TT (p.Gly60Gly) are strong CP risk factors. The c.493+51C>A variant may play a protective role against CP development.

Mapping of Functional Domains of the Lipid Kinase Phosphatidylinositol 4-Kinase Type III Alpha Involved in Enzymatic Activity and Hepatitis C Virus Replication

PubMed Central

Harak, Christian; Radujkovic, Danijela; Taveneau, Cyntia; Reiss, Simon; Klein, Rahel; Bressanelli, Stéphane

2014-01-01

ABSTRACT The lipid kinase phosphatidylinositol 4-kinase III alpha (PI4KIIIα) is an endoplasmic reticulum (ER)-resident enzyme that synthesizes phosphatidylinositol 4-phosphate (PI4P). PI4KIIIα is an essential host factor for hepatitis C virus (HCV) replication. Interaction with HCV nonstructural protein 5A (NS5A) leads to kinase activation and accumulation of PI4P at intracellular membranes. In this study, we investigated the structural requirements of PI4KIIIα in HCV replication and enzymatic activity. Therefore, we analyzed PI4KIIIα mutants for subcellular localization, reconstitution of HCV replication in PI4KIIIα knockdown cell lines, PI4P induction in HCV-positive cells, and lipid kinase activity in vitro. All mutants still interacted with NS5A and localized in a manner similar to that of the full-length enzyme, suggesting multiple regions of PI4KIIIα are involved in NS5A interaction and subcellular localization. Interestingly, the N-terminal 1,152 amino acids were dispensable for HCV replication, PI4P induction, and enzymatic function, whereas further N-terminal or C-terminal deletions were deleterious, thereby defining the minimal PI4KIIIα core enzyme at a size of ca. 108 kDa. Additional deletion of predicted functional motifs within the C-terminal half of PI4KIIIα also were detrimental for enzymatic activity and for the ability of PI4KIIIα to rescue HCV replication, with the exception of a proposed nuclear localization signal, suggesting that the entire C-terminal half of PI4KIIIα is involved in the formation of a minimal enzymatic core. This view was supported by structural modeling of the PI4KIIIα C terminus, suggesting a catalytic center formed by an N- and C-terminal lobe and an armadillo-fold motif, which is preceded by three distinct alpha-helical domains probably involved in regulation of enzymatic activity. IMPORTANCE The lipid kinase PI4KIIIα is of central importance for cellular phosphatidylinositol metabolism and is a key host cell factor of hepatitis C virus replication. However, little is known so far about the structure of this 240-kDa protein and the functional importance of specific subdomains regarding lipid kinase activity and viral replication. This work focuses on the phenotypic analysis of distinct PI4KIIIα mutants in different biochemical and cell-based assays and develops a structural model of the C-terminal enzymatic core. The results shed light on the structural and functional requirements of enzymatic activity and the determinants required for HCV replication. PMID:24920820

Cross-cultural generalizability of personality dimensions: relating indigenous and imported dimensions in two cultures.

PubMed

Katigbak, M S; Church, A T; Akamine, T X

1996-01-01

The cross-cultural generalizability of personality dimensions was investigated by (a) identifying indigenous Philippine dimensions, (b) testing the cross-cultural replicability of the NEO 5-factor model (P. T. Costa & R.R. McCrae, 1992), and (c) relating Philippine and Western dimensions in Philippine and U.S. samples of college students. Filipino self-ratings (N = 536) on indigenous items were factor analyzed, and 6 Philippine dimensions were obtained. Conclusions about the replicability of the 5-factor model in the Philippines (N = 432) depended on whether exploratory, Procrustes, or confirmatory factor methods were used. In regression and joint factor analyses, moderate to strong associations were found between the Philippine dimensions and (a) dimensions from the 5-factor model in both Philippine (N = 387) and U.S. (N = 610) samples, and (b) the Tellegen model (A. Tellegen, 1985; A. Tellegen & N.G. Waller, in press) in a U.S. sample (N = 603).

Detection of porcine circovirus type 2 and viral replication by in situ hybridization in primary lymphoid organs from naturally and experimentally infected pigs.

PubMed

Hansen, M S; Segalés, J; Fernandes, L T; Grau-Roma, L; Bille-Hansen, V; Larsen, L E; Nielsen, O L

2013-11-01

Porcine circovirus type 2 (PCV2) infection is the cause of postweaning multisystemic wasting syndrome (PMWS). It has been speculated whether cell types permissive of replication are found in the primary lymphoid organs and whether infection of these tissues has an important role in the pathogenesis of PMWS. The aim of this study was to determine if primary lymphoid organ cells support viral replication during PCV2 infection. This was done by histopathological examination of thymus and bone marrow from pigs experimentally inoculated with PCV2 (n = 24), mock-infected pigs (n = 12), pigs naturally affected by PMWS (n = 33), and age-matched healthy control animals (n = 29). In situ hybridization (ISH) techniques were used to detect PCV2 nucleic acid irrespective of replicative status (complementary probe, CP) or to detect only the replicative form of the virus (replicative form probe, RFP). PCV2 was not detected in the experimentally PCV2-inoculated pigs or the control animals. Among the PMWS-affected pigs, 19 of 20 (95%) thymuses were positive for PCV2 by CP ISH, and 7 of 19 (37%) of these also supported viral replication. By CP ISH, PCV2 was detected in 16 of 33 (48%) bone marrow samples, and 5 of 16 (31%) of these also supported replication. The 2 ISH probes labeled the same cell types, which were histiocytes in both organs and lymphocytes in thymus. The RFP labeled fewer cells than the CP. Thus, PCV2 nucleic acids and replication were found in bone marrow and thymus of PMWS-affected pigs, but there was no evidence that primary lymphoid organ cells are major supporters of PCV2 replication.

Availability of phosphate for phytoplankton and bacteria and of labile organic carbon for bacteria at different pCO2 levels in a mesocosm study

NASA Astrophysics Data System (ADS)

Tanaka, T.; Thingstad, T. F.; Løvdal, T.; Grossart, H.-P.; Larsen, A.; Schulz, K. G.; Riebesell, U.

2007-11-01

Availability of phosphate for phytoplankton and bacteria and of labile organic carbon for bacteria at different pCO2 levels were studied in a mesocosm experiment (PeECE III). Using nutrient-depleted SW Norwegian fjord waters, three different levels of pCO2 (350 μatm: 1×CO2; 750 μatm: 2×CO2; 1050 μatm: 3×CO2) were set up, and nitrate and phosphate were added at the start of the experiment in order to induce a phytoplankton bloom. Despite similar responses of total particulate P concentration and phosphate turnover time at the three different pCO2 levels, the size distribution of particulate P and 33PO4 uptake suggested that phosphate transferred to the >10 μm fraction was greater in the 3×CO2 mesocosm during the first 6-10 days when phosphate concentration was high. During the period of phosphate depletion (after Day 12), specific phosphate affinity and specific alkaline phosphatase activity (APA) suggested a P-deficiency (i.e. suboptimal phosphate supply) but not a P-limitation for the phytoplankton and bacterial community at the three different pCO2 levels. Although specific phosphate affinity and specific APA tended to be higher in 3×CO2 than in 2×CO2 and 1×CO2 mesocosms during the phosphate depletion period, no statistical differences were found. Responses of specific glucose affinity for bacteria were similar at the three different pCO2 levels. Measured specific glucose affinities were consistently much lower than the theoretical maximum predicted from the diffusion-limited model, suggesting that bacterial growth was not limited by the availability of labile dissolved organic carbon. These results suggest that availability of phosphate and glucose was similar at the three different pCO2 levels.

Plasmodium vivax trophozoite-stage proteomes

PubMed Central

Anderson, D.C.; Lapp, Stacey A.; Akinyi, Sheila; Meyer, Esmeralda V.S.; Barnwell, John W.; Korir-Morrison, Cindy; Galinski, Mary R.

2015-01-01

Plasmodium vivax is the causative infectious agent of 80–300 million annual cases of malaria. Many aspects of this parasite’s biology remain unknown. To further elucidate the interaction of P. vivax with its Saimiri boliviensis host, we obtained detailed proteomes of infected red blood cells, representing the trophozoite-enriched stage of development. Data from two of three biological replicate proteomes, emphasized here, were analyzed using five search engines, which enhanced identifications and resulted in the most comprehensive P. vivax proteomes to date, with 1375 P. vivax and 3209 S. boliviensis identified proteins. Ribosome subunit proteins were noted for both P. vivax and S. boliviensis, consistent with P. vivax’s known reticulocyte host–cell specificity. A majority of the host and pathogen proteins identified belong to specific functional categories, and several parasite gene families, while 33% of the P. vivax proteins have no reported function. Hemoglobin was significantly oxidized in both proteomes, and additional protein oxidation and nitration was detected in one of the two proteomes. Detailed analyses of these post-translational modifications are presented. The proteins identified here significantly expand the known P. vivax proteome and complexity of available host protein functionality underlying the host–parasite interactive biology, and reveal unsuspected oxidative modifications that may impact protein function. Biological significance Plasmodium vivax malaria is a serious neglected disease, causing an estimated 80 to 300 million cases annually in 95 countries. Infection can result in significant morbidity and possible death. P. vivax, unlike the much better-studied Plasmodium falciparum species, cannot be grown in long-term culture, has a dormant form in the liver called the hypnozoite stage, has a reticulocyte host–cell preference in the blood, and creates caveolae vesicle complexes at the surface of the infected reticulocyte membranes. Studies of stage-specific P. vivax expressed proteomes have been limited in scope and focused mainly on pathogen proteins, thus limiting understanding of the biology of this pathogen and its host interactions. Here three P. vivax proteomes are reported from biological replicates based on purified trophozoite-infected reticulocytes from different Saimiri boliviensis infections (the main non-human primate experimental model for P. vivax biology and pathogenesis). An in-depth analysis of two of the proteomes using 2D LC/MS/MS and multiple search engines identified 1375 pathogen proteins and 3209 host proteins. Numerous functional categories of both host and pathogen proteins were identified, including several known P. vivax protein family members (e.g., PHIST, eTRAMP and VIR), and 33% of protein identifications were classified as hypothetical. Ribosome subunit proteins were noted for both P. vivax and S. boliviensis, consistent with this parasite species’ known reticulocyte host–cell specificity. In two biological replicates analyzed for post-translational modifications, hemoglobin was extensively oxidized, and various other proteins were also oxidized or nitrated in one of the two replicates. The cause of such protein modification remains to be determined but could include oxidized heme and oxygen radicals released from the infected red blood cell’s parasite-induced acidic digestive vacuoles. In any case, the data suggests the presence of distinct infection-specific conditions whereby both the pathogen and host infected red blood cell proteins may be subject to significant oxidative stress. PMID:25545414

Anti-tumor function of double-promoter regulated adenovirus carrying SEA gene, in the treatment of bladder cancer.

PubMed

Hu, Jianpeng; Xuan, Xujun; Han, Conghui; Hao, Lin; Zhang, Peiying; Chen, Meng; He, Houguang; Fan, Tao; Dong, Binzheng

2012-03-01

To construct an adenovirus carrying SEA gene and regulated by telomerase reverse transcriptase (hTERT) and hypoxia-inducible factor (HIF) promoters and investigate its anti-tumor function in vitro, as well as its role in lymphocyte production. hTERT and HIF genes were cloned into adenovirus E1A and E1B shuttle plasmids. The control vector for SEA gene expression is under the regulation of CMV and SV40 promoters. Double regulation was obtained through homologous recombination. The positive clones of replicable adenovirus H2-SEA-Ad were selected by plaque assay. The adenovirus was purified, titrated, and DNA was verified by PCR. The obtained virus was used to infect EJ bladder tumor cells and the SEA Mrna, and protein expression was measured by RT-PCR, western blot, and immunofluorescence microscopy, respectively. Co-culture of lymphocytes and tumor cells was observed dynamically under microscope. The construction of shuttle plasmid p315-CSS-SEA was confirmed by PCR and DNA sequencing. Insertion of superantigen SEA gene in adenovirus (H2-SEA-Ad.SEA) was obtained by homologous recombination. In lymphocytes and tumor cell co-culture, the number of viable tumor cells in test groups was significantly lower than that in control group after 12, 24, and 48 h of treatment. Production of interleukin-2, interleukin-4, and tumor necrosis factor were higher in test groups than in control group. Expression of SEA gene in bladder tumor cells by adenoviral vector caused reduced tumor cell proliferation, as well as stimulation of inflammatory cytokine productions in co-cultures with lymphocytes.

Effects of Carbon in Flooded Paddy Soils: Implications for Microbial Activity and Arsenic Mobilization

NASA Astrophysics Data System (ADS)

Avancha, S.; Boye, K.

2014-12-01

In the Mekong delta in Cambodia, naturally occurring arsenic (originating from erosion in the Himalaya Mountains) in paddy soils is mobilized during the seasonal flooding. As a consequence, rice grown on the flooded soils may take up arsenic and expose people eating the rice to this carcinogenic substance. Microbial activity will enhance or decrease the mobilization of arsenic depending on their metabolic pathways. Among the microbes naturally residing in the soil are denitrifying bacteria, sulfate reducers, metal reducers (Fe, Mn), arsenic reducers, methanogens, and fermenters, whose activity varies based on the presence of oxygen. The purpose of the experiment was to assess how different amendments affect the microbial activity and the arsenic mobilization during the transition from aerobic to anaerobic metabolism after flooding of naturally contaminated Cambodian soil. In a batch experiment, we investigated how the relative metabolic rate of naturally occurring microbes could vary with different types of organic carbon. The experiment was designed to measure the effects of various sources of carbon (dried rice straw, charred rice straw, manure, and glucose) on the microbial activity and arsenic release in an arsenic-contaminated paddy soil from Cambodia under flooded conditions. All amendments were added based on the carbon content in order to add 0.036 g of carbon per vial. The soil was flooded with a 10mM TRIS buffer solution at pH 7.04 in airtight 25mL serum vials and kept at 25 °C. We prepared 14 replicates per treatment to sample both gas and solution. On each sampling point, the solution replicates were sampled destructively. The gas replicates continued on and were sampled for both gas and solution on the final day of the experiment. We measured pH, total arsenic, methane, carbon dioxide, and nitrous oxide at 8 hours, 1.5 days, 3.33 days, and 6.33 days from the start of the experiment.

E2F1 and E2F2 prevent replicative stress and subsequent p53-dependent organ involution.

PubMed

Iglesias-Ara, A; Zenarruzabeitia, O; Buelta, L; Merino, J; Zubiaga, A M

2015-10-01

Tissue homeostasis requires tight regulation of cellular proliferation, differentiation and apoptosis. E2F1 and E2F2 transcription factors share a critical role in tissue homeostasis, since their combined inactivation results in overall organ involution, specially affecting the pancreatic gland, which subsequently triggers diabetes. We have examined the mechanism by which these E2Fs regulate tissue homeostasis. We show that pancreas atrophy in E2F1/E2F2 double-knockout (DKO) mice is associated with mitochondrial apoptosis and activation of the p53 pathway in young animals, before the development of diabetes. A deregulated expression of E2F target genes was detected in pancreatic cells of young DKO animals, along with unscheduled DNA replication and activation of a DNA damage response. Importantly, suppression of DNA replication in vivo with aphidicolin led to a significant inhibition of the p53 pathway in DKO pancreas, implying a causal link between DNA replication stress and p53 activation in this model. We further show that activation of the p53 pathway has a key role in the aberrant phenotype of DKO mice, since targeted inactivation of p53 gene abrogated cellular apoptosis and prevented organ involution and insulin-dependent diabetes in mice lacking E2F1/E2F2. Unexpectedly, p53 inactivation unmasked oncogenic features of E2F1/E2F2-depleted cells, as evidenced by an accelerated tumor development in triple-knockout mice compared with p53(-/-) mice. Collectively, our data reveal a role for E2F1 and E2F2 as suppressors of replicative stress in differentiating cells, and uncover the existence of a robust E2F-p53 regulatory axis to enable tissue homeostasis and prevent tumorigenesis. These findings have implications in the design of approaches targeting E2F for cancer therapy.

E2F1 and E2F2 prevent replicative stress and subsequent p53-dependent organ involution

PubMed Central

Iglesias-Ara, A; Zenarruzabeitia, O; Buelta, L; Merino, J; Zubiaga, A M

2015-01-01

Tissue homeostasis requires tight regulation of cellular proliferation, differentiation and apoptosis. E2F1 and E2F2 transcription factors share a critical role in tissue homeostasis, since their combined inactivation results in overall organ involution, specially affecting the pancreatic gland, which subsequently triggers diabetes. We have examined the mechanism by which these E2Fs regulate tissue homeostasis. We show that pancreas atrophy in E2F1/E2F2 double-knockout (DKO) mice is associated with mitochondrial apoptosis and activation of the p53 pathway in young animals, before the development of diabetes. A deregulated expression of E2F target genes was detected in pancreatic cells of young DKO animals, along with unscheduled DNA replication and activation of a DNA damage response. Importantly, suppression of DNA replication in vivo with aphidicolin led to a significant inhibition of the p53 pathway in DKO pancreas, implying a causal link between DNA replication stress and p53 activation in this model. We further show that activation of the p53 pathway has a key role in the aberrant phenotype of DKO mice, since targeted inactivation of p53 gene abrogated cellular apoptosis and prevented organ involution and insulin-dependent diabetes in mice lacking E2F1/E2F2. Unexpectedly, p53 inactivation unmasked oncogenic features of E2F1/E2F2-depleted cells, as evidenced by an accelerated tumor development in triple-knockout mice compared with p53−/− mice. Collectively, our data reveal a role for E2F1 and E2F2 as suppressors of replicative stress in differentiating cells, and uncover the existence of a robust E2F-p53 regulatory axis to enable tissue homeostasis and prevent tumorigenesis. These findings have implications in the design of approaches targeting E2F for cancer therapy. PMID:25656653

Warming and Acidification Induced Mass Mortality of a Coastal Keystone predator

NASA Astrophysics Data System (ADS)

Melzner, F.; Findeisen, U.

2016-02-01

The Baltic Sea is characterized by low salinity and pronounced fluctuations in pCO2. On-line monitoring of pCO2 in 2014 in Kiel Fjord demonstrated occurrence of peak values of >2,000 µatm in summer and autumn and average values >750 µatm. We assessed the impacts of elevated temperature (ambient temperature, ambient +3°C) and pCO2 (500, 1,500, 2,400 µatm) on the keystone species Asterias rubens in a fully crossed long - term experiment (N=5 replicate tanks each, 1 year duration). During spring and early summer (February - June), high temperature animals ingested significantly more food and spawned significantly earlier (April 30th) than ambient acclimated animals (May 23rd). Elevated pCO2 led to comparatively minor reductions in food intake and scope for growth during that period. During summer (June - August), elevated temperature >25°C caused negative energy budgets and >95% mortality in the warm acclimated groups, while mortality was low in the ambient temperature groups. Our results indicate that A. rubens may benefit from increased temperature during colder months, yet dramatically suffer during summer heat waves in warm years. Meaningful experimental approaches to assess species vulnerability to climate change need to encompass all seasons and realistic abiotic stressor levels.

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDermott, Jason E.; Mitchell, Hugh D.; Gralinski, Lisa E.

The complex interplay between viral replication and host immune response during infection remains poorly understood. While many viruses are known to employ antiimmune strategies to facilitate their replication, highly pathogenic virus infections can also cause an excessive immune response that exacerbates, rather than reduces pathogenicity. To investigate this dichotomy in severe acute respiratory syndrome coronavirus (SARS-CoV), we developed a transcriptional network model of SARS-CoV infection in mice and used the model to prioritize candidate regulatory targets for further investigation. We validated our predictions in 18 different knockout (KO) mouse strains, showing that network topology provides significant predictive power to identifymore » genes that are important for viral infection. We identified a novel player in the immune response to virus infection, Kepi, an inhibitory subunit of the protein phosphatase 1 (PP1) complex, which protects against SARS-CoV pathogenesis. We also found that receptors for the proinflammatory cytokine, tumor necrosis factor alpha (TNFα), promote pathogenesis through a parallel feed-forward circuit that promotes inflammation. These results are consistent with previous studies showing the role of over-stimulation of the inflammatory response to SARS-CoV in pathogenesis. We conclude that the critical balance between immune response and inflammation can be manipulated to improve the outcome of the infection. Further, our study provides two potential therapeutic strategies for mitigating the effects of SARS-CoV infection, and may provide insight into treatment strategies for Middle East Respiratory Syndrome Coronavirus (MERS-CoV).« less

Cystatin C and Risk of Diabetes and the Metabolic Syndrome - Biomarker and Genotype Association Analyses.

PubMed

Magnusson, Martin; Molvin, John; Engström, Gunnar; Svensson-Färbom, Patrik; Persson, Margaretha; Christensson, Anders; Nilsson, Peter; Melander, Olle

2016-01-01

We recently reported a relationship between plasma levels of cystatin C and incidence of the metabolic syndrome (MetS) among the first 2,369 subjects who participated in the re-examination study of the population-based Malmö and Diet Cancer Cardiovascular cohort (MDC-CC-re-exam). In this study we aimed to replicate these results and also investigate if cystatin C was causally associated with MetS and diabetes. We estimated the effect size of the strongest GWAS derived cystatin C SNP (major allele of rs13038305) on plasma cystatin C in the now completed MDC-CC-re-exam (n = 3,734) and thereafter examined the association between plasma cystatin C (403 cases of diabetes and 2665 controls) as well as rs13038305 (235 cases and 2425 controls) with incident diabetes. The association of rs13038305 and incident MetS (511 cases of MetS and 1980 controls) was similarly investigated in the whole MDC-CC-re-exam. We also attempted to replicate our previously shown association of cystatin C with incident MetS in subjects from the MDC-CC-re-exam (147 cases and 711 controls) that were not included in our previous report. In the entire MDC-CC-re-exam, each copy of the major allele of rs13038305 was associated with approximately 0.30 standard deviation (SD) higher plasma concentration of cystatin C (β = 0.33, p = 4.2E-28) in age and sex adjusted analysis. Cystatin C in plasma was not associated with incident diabetes after adjustment for known diabetes risk factors (OR per 1 SD increment 0.99 (0.86-1.13), p = 0.842). In the replication cohort of MDC-CC-re-exam, the OR (95% CI) for incident MetS in subjects belonging to quartiles 1, 2, 3 and 4 of plasma cystatin C levels was 1.00 (reference), 1.21 (0.70-2.07), 1.62 (0.95-2.78) and 1.72 (1.01-2.93) (ptrend = 0.026) in age and sex adjusted analysis. In the entire MDC-CC-re-exam the odds ratio for incident MetS and diabetes per copy of the major rs13038305 allele was 1.13, (0.95-1.34), p = 0.160 and 1.07, 95% CI 0.89-1.30, p = 0.478, respectively. We were able to replicate our previously shown association between high levels of cystatin C and increased risk of future development of MetS. However, a causal involvement of cystatin C in the etiology of MetS or diabetes seems unlikely since genetic elevation of plasma cystatin C was not significantly related to incidence of these diseases.

Au-HKUST-1 Composite Nanocapsules: Synthesis with a Coordination Replication Strategy and Catalysis on CO Oxidation.

PubMed

Liu, Yongxin; Zhang, Jiali; Song, Lingxiao; Xu, Wenyuan; Guo, Zanru; Yang, Xiaomin; Wu, Xiaoxin; Chen, Xi

2016-09-07

A novel coordination replication of Cu2O redox-template strategy is reported to efficiently fabricate Au-HKUST-1 composite nanocapsule, with a HKUST-1 sandwich shell and an embedded Au nanoparticles layer. The novel synthesis procedure involves forming Au nanoparticles on the surface of Cu2O, transforming partial Cu2O into HKUST-1 shell via coordination replication, and removing the residual Cu2O by acid. The as-prepared Au-HKUST-1 composite nanocapsules displayed high catalytic activity on CO oxidation.

Blood pressure loci identified with a gene-centric array.

PubMed

Johnson, Toby; Gaunt, Tom R; Newhouse, Stephen J; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W; Tzoulaki, Ioanna; O'Brien, Eoin T; Poulter, Neil R; Sever, Peter; Shields, Denis C; Thom, Simon; Wannamethee, Sasiwarang G; Whincup, Peter H; Brown, Morris J; Connell, John M; Dobson, Richard J; Howard, Philip J; Mein, Charles A; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Davey Smith, George; Day, Ian N M; Lawlor, Debbie A; Goodall, Alison H; Fowkes, F Gerald; Abecasis, Gonçalo R; Elliott, Paul; Gateva, Vesela; Braund, Peter S; Burton, Paul R; Nelson, Christopher P; Tobin, Martin D; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-François; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sõber, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S; Hastie, Claire E; Hedner, Thomas; Lee, Wai K; Melander, Olle; Wahlstrand, Björn; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A; Palmen, Jutta; Chen, Li; Stewart, Alexandre F R; Wells, George A; Westra, Harm-Jan; Wolfs, Marcel G M; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Maris; Kuh, Diana; Humphries, Steve E; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V; Dominiczak, Anna F; Farrall, Martin; Hingorani, Aroon D; Samani, Nilesh J; Caulfield, Mark J; Munroe, Patricia B

2011-12-09

Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies. Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

PubMed Central

Menachery, Vineet D.; Mitchell, Hugh D.; Cockrell, Adam S.; Gralinski, Lisa E.; Yount, Boyd L.; Graham, Rachel L.; McAnarney, Eileen T.; Douglas, Madeline G.; Scobey, Trevor; Beall, Anne; Dinnon, Kenneth; Kocher, Jacob F.; Hale, Andrew E.; Stratton, Kelly G.; Waters, Katrina M.

2017-01-01

ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation. In vitro replication attenuation also extends to in vivo models, allowing use of dORF3-5 as a live attenuated vaccine platform. Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. PMID:28830941

Primary Severe Acute Respiratory Syndrome Coronavirus Infection Limits Replication but Not Lung Inflammation upon Homologous Rechallenge

PubMed Central

Clay, Candice; Donart, Nathan; Fomukong, Ndingsa; Knight, Jennifer B.; Lei, Wanli; Price, Lance; Hahn, Fletcher; Van Westrienen, Jesse

2012-01-01

Our knowledge regarding immune-protective and immunopathogenic events in severe acute respiratory syndrome coronavirus (SARS-CoV) infection is limited, and little is known about the dynamics of the immune response at the primary site of disease. Here, an African green monkey (AGM) model was used to elucidate immune mechanisms that facilitate viral clearance but may also contribute to persistent lung inflammation following SARS-CoV infection. During primary infection, SARS-CoV replicated in the AGM lung for up to 10 days. Interestingly, lung inflammation was more prevalent following viral clearance, as leukocyte numbers peaked at 14 days postinfection (dpi) and remained elevated at 28 dpi compared to those of mock-infected controls. Lung macrophages but not dendritic cells were rapidly activated, and both cell types had high activation marker expression at late infection time points. Lung proinflammatory cytokines were induced at 1 to 14 dpi, but most returned to baseline by 28 dpi except interleukin 12 (IL-12) and gamma interferon. In SARS-CoV homologous rechallenge studies, 11 of the 12 animals were free of replicating virus at day 5 after rechallenge. However, incidence and severity of lung inflammation was not reduced despite the limited viral replication upon rechallenge. Evaluating the role of antibodies in immune protection or potentiation revealed a progressive increase in anti-SARS-CoV antibodies in lung and serum that did not correlate temporally or spatially with enhanced viral replication. This study represents one of the first comprehensive analyses of lung immunity, including changes in leukocyte populations, lung-specific cytokines, and antibody responses following SARS-CoV rechallenge in AGMs. PMID:22345460

Function of BRCA1 at a DNA Replication Origin

DTIC Science & Technology

2004-07-01

origin of Epstein-Barr Virus DNA replication (Ori P). OriP replicates once and only once per cell cycle in synchrony with the cellular genome, and is...modifications, and to investigate its function at OriP in DNA replication and plasmid maintenance. We propose that these studies will provide valuable...information concerning the function of OriP at replication origins and in the control of DNA replication initiation and genome stability.

DNA replication initiator Cdc6 also regulates ribosomal DNA transcription initiation.

PubMed

Huang, Shijiao; Xu, Xiaowei; Wang, Guopeng; Lu, Guoliang; Xie, Wenbing; Tao, Wei; Zhang, Hongyin; Jiang, Qing; Zhang, Chuanmao

2016-04-01

RNA-polymerase-I-dependent ribosomal DNA (rDNA) transcription is fundamental to rRNA processing, ribosome assembly and protein synthesis. However, how this process is initiated during the cell cycle is not fully understood. By performing a proteomic analysis of transcription factors that bind RNA polymerase I during rDNA transcription initiation, we identified that the DNA replication initiator Cdc6 interacts with RNA polymerase I and its co-factors, and promotes rDNA transcription in G1 phase in an ATPase-activity-dependent manner. We further showed that Cdc6 is targeted to the nucleolus during late mitosis and G1 phase in a manner that is dependent on B23 (also known as nucleophosmin, NPM1), and preferentially binds to the rDNA promoter through its ATP-binding domain. Overexpression of Cdc6 increases rDNA transcription, whereas knockdown of Cdc6 results in a decreased association of both RNA polymerase I and the RNA polymerase I transcription factor RRN3 with rDNA, and a reduction of rDNA transcription. Furthermore, depletion of Cdc6 impairs the interaction between RRN3 and RNA polymerase I. Taken together, our data demonstrate that Cdc6 also serves as a regulator of rDNA transcription initiation, and indicate a mechanism by which initiation of rDNA transcription and DNA replication can be coordinated in cells. © 2016. Published by The Company of Biologists Ltd.

Development of pH Sensitive Nanoparticles for Intestinal Drug Delivery Using Chemically Modified Guar Gum Co-Polymer.

PubMed

Varma, Vegesna Naga Sravan Kumar; Shivakumar, Hosakote Gurumalappa; Balamuralidhara, Veerna; Navya, Manne; Hani, Umme

2016-01-01

The aim of the research work was to chemically modify guargum (GG) as a pH sensitive co-polymer and formulating intestinal targeting ESO nanoparticles (NPs) using the synthesized co-polymer. Poly acrylamide-grafted-guar gum (PAAm-g-GG) co-polymer was synthesized by free radical polymerization. Chemical modification of PAAm-g-GG by alkaline hydrolysis results in formation of a pH-sensitive co-polymer. The effect of GG and acryl amide (AAm) on grafting was studied. Esomeprazole magnesium (ESO) loaded pH sensitive NPs were prepared by nano-emulsification polymer crosslinking method and characterized. Sixteen formulations were prepared and the concentration of process variables wasvaried to obtain nanoparticles of 200-600 nm. The NPs were found to be homogenous in size distribution. The encapsulation efficiency and drug loading ranged from 33.2% to 50.1% and 12.2% to 17.2% respectively. Particle size, encapsulation efficiency and drug loading increasedalong with co-polymer concentration. In-vitro release studies at pH 1.2 for 2 h, followed by pH 6.8 showed that environment pH significantly affected the drug release. SEM has shown that NPsare spherical with smooth surface. The pH sensitive PAAm-g-GGNPs resisted the initial release of the drug from the drug loaded NPs in acidic pH and delayed the release process to a longer period in alkaline environment.

Development of pH Sensitive Nanoparticles for Intestinal Drug Delivery Using Chemically Modified Guar Gum Co-Polymer

PubMed Central

Varma, Vegesna Naga Sravan Kumar; Shivakumar, Hosakote Gurumalappa; Balamuralidhara, Veerna; Navya, Manne; Hani, Umme

2016-01-01

The aim of the research work was to chemically modify guargum (GG) as a pH sensitive co-polymer and formulating intestinal targeting ESO nanoparticles (NPs) using the synthesized co-polymer. Poly acrylamide-grafted-guar gum (PAAm-g-GG) co-polymer was synthesized by free radical polymerization. Chemical modification of PAAm-g-GG by alkaline hydrolysis results in formation of a pH-sensitive co-polymer. The effect of GG and acryl amide (AAm) on grafting was studied. Esomeprazole magnesium (ESO) loaded pH sensitive NPs were prepared by nano-emulsification polymer crosslinking method and characterized. Sixteen formulations were prepared and the concentration of process variables wasvaried to obtain nanoparticles of 200-600 nm. The NPs were found to be homogenous in size distribution. The encapsulation efficiency and drug loading ranged from 33.2% to 50.1% and 12.2% to 17.2% respectively. Particle size, encapsulation efficiency and drug loading increasedalong with co-polymer concentration. In-vitro release studies at pH 1.2 for 2 h, followed by pH 6.8 showed that environment pH significantly affected the drug release. SEM has shown that NPsare spherical with smooth surface. The pH sensitive PAAm-g-GGNPs resisted the initial release of the drug from the drug loaded NPs in acidic pH and delayed the release process to a longer period in alkaline environment. PMID:27610149

40 CFR 98.172 - GHGs to report.

Code of Federal Regulations, 2010 CFR

2010-07-01

... combustion units include, but are not limited to, by-product recovery coke oven battery combustion stacks... except you must use the default CO2 emission factors for coke oven gas and blast furnace gas from Table C... flares according to the requirements in § 98.33(c)(2) using the emission factors for coke oven gas and...

Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer

PubMed Central

Turnbull, Clare; Rapley, Elizabeth A.; Seal, Sheila; Pernet, David; Renwick, Anthony; Hughes, Deborah; Ricketts, Michelle; Linger, Rachel; Nsengimana, Jeremie; Deloukas, Panagiotis; Huddart, Robert A.; Bishop, D Timothy; Easton, Douglas F.; Stratton, Michael R.; Rahman, Nazneen

2013-01-01

We conducted a genome-wide association study for testicular germ cell tumor genotyping 298,782 SNPs in 979 cases and 4,947 controls from the UK and replicating associations in a further 664 cases and 3,456 controls. We identified three novel susceptibility loci, two of which include genes that are involved in telomere regulation. We identified two independent signals within the TERT-CLPTM1L locus on chromosome 5 which has been associated with multiple other cancers (rs4635969, OR=1.54 (95%CI 1.33-1.79), P=1.14×10−23 and rs2736100, OR 1.33 (1.18-1.50) P=7.55 ×10−15). We also identified a locus on chromosome 12 (rs2900333, OR=1.27 (95%CI 1.12-1.44), P=6.16×10−10) that contains ATF7IP, a regulator of TERT expression. Finally we identified a locus on chromosome 9 (rs755383, OR=1.37 (95%CI 1.21-1.55), P=1.12×10−23) containing the sex determination gene DMRT1, which has been linked with teratoma susceptibility in mice. PMID:20543847

Exogenous ACE2 Expression Allows Refractory Cell Lines To Support Severe Acute Respiratory Syndrome Coronavirus Replication

PubMed Central

Mossel, Eric C.; Huang, Cheng; Narayanan, Krishna; Makino, Shinji; Tesh, Robert B.; Peters, C. J.

2005-01-01

Of 30 cell lines and primary cells examined, productive severe acute respiratory syndrome coronavirus (Urbani strain) (SARS-CoV) infection after low-multiplicity inoculation was detected in only six: three African green monkey kidney epithelial cell lines (Vero, Vero E6, and MA104), a human colon epithelial line (CaCo-2), a porcine kidney epithelial line [PK(15)], and mink lung epithelial cells (Mv 1 Lu). SARS-CoV produced a lytic infection in Vero, Vero E6, and MA104 cells, but there was no visible cytopathic effect in Caco-2, Mv 1 Lu, or PK(15) cells. Multistep growth kinetics were identical in Vero E6 and MA104 cells, with maximum titer reached 24 h postinoculation (hpi). Virus titer was maximal 96 hpi in CaCo-2 cells, and virus was continually produced from infected CaCo-2 cells for at least 6 weeks after infection. CaCo-2 was the only human cell type of 13 tested that supported efficient SARS-CoV replication. Expression of the SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), resulted in SARS-CoV replication in all refractory cell lines examined. Titers achieved were variable and dependent upon the method of ACE2 expression. PMID:15731278

Microfossil evidence for trophic changes during the Eocene-Oligocene transition in the South Atlantic (ODP Site 1263, Walvis Ridge)

NASA Astrophysics Data System (ADS)

Bordiga, M.; Henderiks, J.; Tori, F.; Monechi, S.; Fenero, R.; Legarda-Lisarri, A.; Thomas, E.

2015-09-01

The biotic response of calcareous nannoplankton to environmental and climatic changes during the Eocene-Oligocene transition was investigated at a high resolution at Ocean Drilling Program (ODP) Site 1263 (Walvis Ridge, southeast Atlantic Ocean) and compared with a lower-resolution benthic foraminiferal record. During this time interval, global climate, which had been warm under high levels of atmospheric CO2 (pCO2) during the Eocene, transitioned into the cooler climate of the Oligocene, at overall lower pCO2. At Site 1263, the absolute nannofossil abundance (coccoliths per gram of sediment; N g-1) and the mean coccolith size decreased distinctly after the E-O boundary (EOB; 33.89 Ma), mainly due to a sharp decline in abundance of large-sized Reticulofenestra and Dictyococcites, occurring within a time span of ~ 47 kyr. Carbonate dissolution did not vary much across the EOB; thus, the decrease in abundance and size of nannofossils may reflect an overall decrease in their export production, which could have led to variations in the food availability for benthic foraminifers. The benthic foraminiferal assemblage data are consistent with a global decline in abundance of rectilinear species with complex apertures in the latest Eocene (~ 34.5 Ma), potentially reflecting changes in the food source, i.e., phytoplankton. This was followed by a transient increased abundance of species indicative of seasonal delivery of food to the sea floor (Epistominella spp.; ~ 33.9-33.4 Ma), with a short peak in overall food delivery at the EOB (buliminid taxa; ~ 33.8 Ma). Increased abundance of Nuttallides umbonifera (at ~ 33.3 Ma) indicates the presence of more corrosive bottom waters and possibly the combined arrival of less food at the sea floor after the second step of cooling (Step 2). The most important changes in the calcareous nannofossil and benthic communities occurred ~ 120 kyr after the EOB. There was no major change in nannofossil abundance or assemblage composition at Site 1263 after Step 2 although benthic foraminifera indicate more corrosive bottom waters during this time. During the onset of latest-Eocene-earliest-Oligocene climate change, marine phytoplankton thus showed high sensitivity to fast-changing conditions as well as to a possibly enhanced, pulsed nutrient supply and to the crossing of a climatic threshold (e.g., pCO2 decline, high-latitude cooling and changes in ocean circulation).

A Re-Examination of Global Suppression of RNA Interference by HIV-1

PubMed Central

Sanghvi, Viraj R.; Steel, Laura F.

2011-01-01

The nature of the interaction between replicating HIV-1 and the cellular RNAi pathway has been controversial, but it is clear that it can be complex and multifaceted. It has been proposed that the interaction is bi-directional, whereby cellular silencing pathways can restrict HIV-1 replication, and in turn, HIV-1 can suppress silencing pathways. Overall suppression of RNAi has been suggested to occur via direct binding and inhibition of Dicer by the HIV-1 Tat protein or through sequestration of TRBP, a Dicer co-factor, by the structured TAR element of HIV-1 transcripts. The role of Tat as an inhibitor of Dicer has been questioned and our results support and extend the conclusion that Tat does not inhibit RNAi that is mediated by either exogenous or endogenous miRNAs. Similarly, we find no suppression of silencing pathways in cells with replicating virus, suggesting that viral products such as the TAR RNA elements also do not reduce the efficacy of cellular RNA silencing. However, knockdown of Dicer does allow increased viral replication and this occurs at a post-transcriptional level. These results support the idea that although individual miRNAs can act to restrict HIV-1 replication, the virus does not counter these effects through a global suppression of RNAi synthesis or processing. PMID:21386885

Testing the Intervention Effect in Single-Case Experiments: A Monte Carlo Simulation Study

ERIC Educational Resources Information Center

Heyvaert, Mieke; Moeyaert, Mariola; Verkempynck, Paul; Van den Noortgate, Wim; Vervloet, Marlies; Ugille, Maaike; Onghena, Patrick

2017-01-01

This article reports on a Monte Carlo simulation study, evaluating two approaches for testing the intervention effect in replicated randomized AB designs: two-level hierarchical linear modeling (HLM) and using the additive method to combine randomization test "p" values (RTcombiP). Four factors were manipulated: mean intervention effect,…

The Effect of Aquatic Vegetation on Water Quality in the Everglades Agricultural Area Canals

NASA Astrophysics Data System (ADS)

Gomez, S. M.; Bhadha, J. H.; Lang, T. A.; Josan, M. S.; Daroub, S. H.

2011-12-01

The canals in the Everglades Agricultural Area contain an abundance of floating aquatic vegetation (FAV) and submerged aquatic vegetation (SAV). These FAV flourish in waters with high phosphorus (P) concentrations and prevent the co-precipitation of P with the limestone bedrock (CaCO3). To test the effects of FAV and SAV and the presence of sediments on water quality in the canals, a lysimeter study was set up and stocked with FAV (water lettuce) and SAV (filamentous algae). There were four treatments with four replicates Treatment one contained limerock, sediment from the canals, and FAV. Treatment two contained limerock, sediment, and SAV. Treatment three contained limerock and FAV, while treatment four had limerock and SAV. After 7 days, the buckets were drained and replaced the water with new, high P canal water. Water samples were taken at 0, 0.25, 1, 3, and 7 days after each weekly water exchange. To test water quality soluble reactive P, total P, total dissolved P, Ca, and total organic carbon were analyzed. The impact of FAV and SAV and canal sediments on water quality will be discussed. We hypothesize water lettuce treatments will initially result in a reduction in P-concentration in all species, but will only serve as a short-term sink because of their high turn-over rate and production of labile high-P sediment (floc). In addition, we hypothesize the treatments with no sediment will have more P reduction because of the availability for P to co-precipitate with CaCO3.

GENETIC MODIFIERS OF LIVER DISEASE IN CYSTIC FIBROSIS

PubMed Central

Bartlett, Jaclyn R.; Friedman, Kenneth J.; Ling, Simon C.; Pace, Rhonda G.; Bell, Scott C.; Bourke, Billy; Castaldo, Giuseppe; Castellani, Carlo; Cipolli, Marco; Colombo, Carla; Colombo, John L.; Debray, Dominique; Fernandez, Adriana; Lacaille, Florence; Macek, Milan; Rowland, Marion; Salvatore, Francesco; Taylor, Christopher J.; Wainwright, Claire; Wilschanski, Michael; Zemková, Dana; Hannah, William B.; Phillips, M. James; Corey, Mary; Zielenski, Julian; Dorfman, Ruslan; Wang, Yunfei; Zou, Fei; Silverman, Lawrence M.; Drumm, Mitchell L.; Wright, Fred A.; Lange, Ethan M.; Durie, Peter R.; Knowles, Michael R.

2013-01-01

Context A subset (~3–5%) of patients with cystic fibrosis (CF) develops severe liver disease (CFLD) with portal hypertension. Objective To assess whether any of 9 polymorphisms in 5 candidate genes (SERPINA1, ACE, GSTP1, MBL2, and TGFB1) are associated with severe liver disease in CF patients. Design, Setting, and Participants A 2-stage design was used in this case–control study. CFLD subjects were enrolled from 63 U.S., 32 Canadian, and 18 CF centers outside of North America, with the University of North Carolina at Chapel Hill (UNC) as the coordinating site. In the initial study, we studied 124 CFLD patients (enrolled 1/1999–12/2004) and 843 CF controls (patients without CFLD) by genotyping 9 polymorphisms in 5 genes previously implicated as modifiers of liver disease in CF. In the second stage, the SERPINA1 Z allele and TGFB1 codon 10 genotype were tested in an additional 136 CFLD patients (enrolled 1/2005–2/2007) and 1088 CF controls. Main Outcome Measures We compared differences in distribution of genotypes in CF patients with severe liver disease versus CF patients without CFLD. Results The initial study showed CFLD to be associated with the SERPINA1 (also known as α1-antiprotease and α1-antitrypsin) Z allele (P value=3.3×10−6; odds ratio (OR) 4.72, 95% confidence interval (CI) 2.31–9.61), and with transforming growth factor β-1 (TGFB1) codon 10 CC genotype (P=2.8×10−3; OR 1.53, CI 1.16–2.03). In the replication study, CFLD was associated with the SERPINA1 Z allele (P=1.4×10−3; OR 3.42, CI 1.54–7.59), but not with TGFB1 codon 10. A combined analysis of the initial and replication studies by logistic regression showed CFLD to be associated with SERPINA1 Z allele (P=1.5×10−8; OR 5.04, CI 2.88–8.83). Conclusion The SERPINA1 Z allele is a risk factor for liver disease in CF. Patients who carry the Z allele are at greater odds (OR ~5) to develop severe liver disease with portal hypertension. PMID:19738092

IL-33 and soluble ST2 levels as novel predictors for remission and progression of carotid plaque in early rheumatoid arthritis: A prospective study.

PubMed

Shen, Jiayun; Shang, Qing; Wong, Chun-Kwok; Li, Edmund K; Wang, Shang; Li, Rui-Jie; Lee, Ka-Lai; Leung, Ying-Ying; Ying, King-Yee; Yim, Cheuk-Wan; Kun, Emily W; Leung, Moon-Ho; Li, Martin; Li, Tena K; Zhu, Tracy Y; Yu, Shui-Lian; Kuan, Woon-Pang; Yu, Cheuk-Man; Tam, Lai-Shan

2015-08-01

To study the association between the baseline IL-33 and soluble ST2 (sST2) levels with disease remission and progression of carotid atherosclerosis in early rheumatoid arthritis (ERA) patients. A total of 98 ERA patients were enrolled. Disease activity and the presence of carotid plaque were evaluated at baseline and 12 months later. Plasma IL-33 and sST2 levels were determined using enzyme-linked immunosorbent assay kits. Baseline IL-33 and sST2 levels were associated with inflammatory markers and cardiovascular (CV) risk factors. Overall, 44(45%), 18(18%), and 21(21%) patients achieved remission based on 28-joint disease activity score (DAS28), Boolean, and simplified disease activity score (SDAI) criteria at 12 months, respectively. Patients with detectable IL-33 at baseline were less likely to achieve DAS28 (P = 0.010) and SDAI remission (P = 0.021), while a lower baseline sST2 level was able to predict DAS28, Boolean, and SDAI remission (P = 0.005, 0.001, and <0.001, respectively). Using multivariate analysis, a lower baseline sST2 level independently predict Boolean (OR = 0.789; P = 0.005) and SDAI remission (0.812; P = 0.008). Regarding carotid atherosclerosis, 9/98(9.2%) patients had plaque progression at 12 months. Baseline IL-33 was detectable in 8/9(89%) and 42/83(51%) of patients with and without plaque progression respectively (P = 0.029). Baseline detectable IL-33 was an independent predictor for plaque progression after adjusting for traditional CV risk factors (P = 0.017). Lower baseline sST2 levels independently predict disease remission and baseline detectable IL-33 independently predicts carotid plaque progression in ERA patients. This study suggests that inflammation induced by the IL-33/ST2 axis may play a significant role in the development of cardiovascular disease in RA. Copyright © 2015 Elsevier Inc. All rights reserved.

Increasing pCO2 correlates with low concentrations of intracellular dimethylsulfoniopropionate in the sea anemone Anemonia viridis

PubMed Central

Borell, Esther M; Steinke, Michael; Horwitz, Rael; Fine, Maoz

2014-01-01

Marine anthozoans maintain a mutualistic symbiosis with dinoflagellates that are prolific producers of the algal secondary metabolite dimethylsulfoniopropionate (DMSP), the precursor of the climate-cooling trace gas dimethyl sulfide (DMS). Surprisingly, little is known about the physiological role of DMSP in anthozoans and the environmental factors that regulate its production. Here, we assessed the potential functional role of DMSP as an antioxidant and determined how future increases in seawater pCO2 may affect DMSP concentrations in the anemone Anemonia viridis along a natural pCO2 gradient at the island of Vulcano, Italy. There was no significant difference in zooxanthellae genotype and characteristics (density of zooxanthellae, and chlorophyll a) as well as protein concentrations between anemones from three stations along the gradient, V1 (3232 μatm CO2), V2 (682 μatm) and control (463 μatm), which indicated that A. viridis can acclimate to various seawater pCO2. In contrast, DMSP concentrations in anemones from stations V1 (33.23 ± 8.30 fmol cell−1) and V2 (34.78 ± 8.69 fmol cell−1) were about 35% lower than concentrations in tentacles from the control station (51.85 ± 12.96 fmol cell−1). Furthermore, low tissue concentrations of DMSP coincided with low activities of the antioxidant enzyme superoxide dismutase (SOD). Superoxide dismutase activity for both host (7.84 ± 1.37 U·mg−1 protein) and zooxanthellae (2.84 ± 0.41 U·mg−1 protein) at V1 was 40% lower than at the control station (host: 13.19 ± 1.42; zooxanthellae: 4.72 ± 0.57 U·mg−1 protein). Our results provide insight into coastal DMSP production under predicted environmental change and support the function of DMSP as an antioxidant in symbiotic anthozoans. PMID:24634728

Increasing pCO2 correlates with low concentrations of intracellular dimethylsulfoniopropionate in the sea anemone Anemonia viridis.

PubMed

Borell, Esther M; Steinke, Michael; Horwitz, Rael; Fine, Maoz

2014-02-01

Marine anthozoans maintain a mutualistic symbiosis with dinoflagellates that are prolific producers of the algal secondary metabolite dimethylsulfoniopropionate (DMSP), the precursor of the climate-cooling trace gas dimethyl sulfide (DMS). Surprisingly, little is known about the physiological role of DMSP in anthozoans and the environmental factors that regulate its production. Here, we assessed the potential functional role of DMSP as an antioxidant and determined how future increases in seawater pCO2 may affect DMSP concentrations in the anemone Anemonia viridis along a natural pCO2 gradient at the island of Vulcano, Italy. There was no significant difference in zooxanthellae genotype and characteristics (density of zooxanthellae, and chlorophyll a) as well as protein concentrations between anemones from three stations along the gradient, V1 (3232 μatm CO2), V2 (682 μatm) and control (463 μatm), which indicated that A. viridis can acclimate to various seawater pCO2. In contrast, DMSP concentrations in anemones from stations V1 (33.23 ± 8.30 fmol cell(-1)) and V2 (34.78 ± 8.69 fmol cell(-1)) were about 35% lower than concentrations in tentacles from the control station (51.85 ± 12.96 fmol cell(-1)). Furthermore, low tissue concentrations of DMSP coincided with low activities of the antioxidant enzyme superoxide dismutase (SOD). Superoxide dismutase activity for both host (7.84 ± 1.37 U·mg(-1) protein) and zooxanthellae (2.84 ± 0.41 U·mg(-1) protein) at V1 was 40% lower than at the control station (host: 13.19 ± 1.42; zooxanthellae: 4.72 ± 0.57 U·mg(-1) protein). Our results provide insight into coastal DMSP production under predicted environmental change and support the function of DMSP as an antioxidant in symbiotic anthozoans.

No effect of skin temperature on human ventilation response to hypercapnia during light exercise with a normothermic core temperature.

PubMed

Greiner, Jesse G; Clegg, Miriam E; Walsh, Michael L; White, Matthew D

2010-05-01

Hyperthermia potentiates the influence of CO(2) on pulmonary ventilation (.V(E)). It remains to be resolved how skin and core temperatures contribute to the elevated exercise ventilation response to CO(2). This study was conducted to assess the influences of mean skin temperature (_T(SK)) and end-tidal PCO(2) (P(ET)CO(2)) on .V(E) during submaximal exercise with a normothermic esophageal temperature (T(ES)). Five males and three females who were 1.76 +/- 0.11 m tall (mean +/- SD), 75.8 +/- 15.6 kg in weight and 22.0 +/- 2.2 years of age performed three 1 h exercise trials in a climatic chamber with the relative humidity (RH) held at 31.5 +/- 9.5% and the ambient temperature (T (AMB)) maintained at one of 25, 30, or 35 degrees C. In each trial, the volunteer breathed eucapnic air for 5 min during a rest period and subsequently cycle ergometer exercised at 50 W until T (ES) stabilized at approximately 37.1 +/- 0.4 degrees C. Once T (ES) stabilized in each trial, the volunteer breathed hypercapnic air twice for approximately 5 min with P(ET)CO(2) elevated by approximately +4 or +7.5 mmHg. The significantly (P < 0.05) different increases of P(ET)CO(2) of +4.20 +/- 0.49 and +7.40 +/- 0.51 mmHg gave proportionately larger increases in .V(E) of 10.9 +/- 3.6 and 15.2 +/- 3.6 L min(-1) (P = 0.001). This hypercapnia-induced hyperventilation was uninfluenced by varying the _T(SK) to three significantly different levels (P < 0.001) of 33.2 +/- 1.2 degrees C, to 34.5 +/- 0.8 degrees C to 36.4 +/- 0.5 degrees C. In conclusion, the results support that skin temperature between approximately 33 and approximately 36 degrees C has neither effect on pulmonary ventilation nor on hypercapnia-induced hyperventilation during a light exercise with a normothermic core temperature.

Environmental stress cracking performance of polyether and PDMS-based polyurethanes in an in vitro oxidation model.

PubMed

Gallagher, Genevieve; Padsalgikar, Ajay; Tkatchouk, Ekaterina; Jenney, Chris; Iacob, Ciprian; Runt, James

2017-08-01

Environmental stress cracking (ESC) was replicated in vitro on Optim™ (OPT) insulation, a polydimethylsiloxane-based polyurethane utilized clinically in cardiac leads, using a Zhao-type oxidation model. OPT performance was compared to that of two industry standard polyether urethanes: Pellethane ® 80A (P80A), and Pellethane ® 55D (P55D). Clinically relevant specimen configurations and strain states were utilized: low-voltage cardiac lead segments were held in a U-shape by placing them inside of vials. To study whether aging conditions impacted ESC formation, half of the samples were subjected to a pretreatment in human plasma for 7 days at 37°C; all samples were then aged in oxidative solutions containing 0.9% NaCl, 20% H 2 O 2 , and either 0 or 0.1M CoCl 2 , with or without glass wool for 72 days at 37°C. Visual and SEM inspection revealed significant surface cracking consistent with ESC on all P80A and P55D samples. Sixteen of twenty P80A and 10/20 P55D samples also exhibited breaches. Seven of 20 OPT samples exhibited shallow surface cracking consistent with ESC. ATR-FTIR confirmed surface changes consistent with oxidation for all materials. The number average molecular weight decreased an average of 31% for OPT, 86% for P80A, and 56% for P55D samples. OPT outperformed P80A and P55D in this Zhao-type in vitro ESC model. An aging solution of 0.9% NaCl, 20% H 2 O 2 , and 0.1M CoCl 2 , with glass wool provided the best combination of ESC replication and ease of use. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1544-1558, 2017. © 2016 Wiley Periodicals, Inc.

Association of three genetic loci with uric acid concentration and risk of gout: a genome-wide association study.

PubMed

Dehghan, Abbas; Köttgen, Anna; Yang, Qiong; Hwang, Shih-Jen; Kao, Wh Linda; Rivadeneira, Fernando; Boerwinkle, Eric; Levy, Daniel; Hofman, Albert; Astor, Brad C; Benjamin, Emelia J; van Duijn, Cornelia M; Witteman, Jacqueline C; Coresh, Josef; Fox, Caroline S

2008-12-06

Hyperuricaemia, a highly heritable trait, is a key risk factor for gout. We aimed to identify novel genes associated with serum uric acid concentration and gout. Genome-wide association studies were done for serum uric acid in 7699 participants in the Framingham cohort and in 4148 participants in the Rotterdam cohort. Genome-wide significant single nucleotide polymorphisms (SNPs) were replicated in white (n=11 024) and black (n=3843) individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). The SNPs that reached genome-wide significant association with uric acid in either the Framingham cohort (p<5.0 x 10(-8)) or the Rotterdam cohort (p<1.0 x 10(-7)) were evaluated with gout. The results obtained in white participants were combined using meta-analysis. Three loci in the Framingham cohort and two in the Rotterdam cohort showed genome-wide association with uric acid. Top SNPs in each locus were: missense rs16890979 in SLC2A9 (p=7.0 x 10(-168) and 2.9 x 10(-18) for white and black participants, respectively); missense rs2231142 in ABCG2 (p=2.5 x 10(-60) and 9.8 x 10(-4)), and rs1165205 in SLC17A3 (p=3.3 x 10(-26) and 0.33). All SNPs were direction-consistent with gout in white participants: rs16890979 (OR 0.59 per T allele, 95% CI 0.52-0.68, p=7.0 x 10(-14)), rs2231142 (1.74, 1.51-1.99, p=3.3 x 10(-15)), and rs1165205 (0.85, 0.77-0.94, p=0.002). In black participants of the ARIC study, rs2231142 was direction-consistent with gout (1.71, 1.06-2.77, p=0.028). An additive genetic risk score of high-risk alleles at the three loci showed graded associations with uric acid (272-351 mumol/L in the Framingham cohort, 269-386 mumol/L in the Rotterdam cohort, and 303-426 mumol/L in white participants of the ARIC study) and gout (frequency 2-13% in the Framingham cohort, 2-8% in the Rotterdam cohort, and 1-18% in white participants in the ARIC study). We identified three genetic loci associated with uric acid concentration and gout. A score based on genes with a putative role in renal urate handling showed a substantial risk for gout.

Genetic Association Analysis of Functional Impairment in Chronic Obstructive Pulmonary Disease

PubMed Central

Hersh, Craig P.; DeMeo, Dawn L.; Lazarus, Ross; Celedón, Juan C.; Raby, Benjamin A.; Benditt, Joshua O.; Criner, Gerard; Make, Barry; Martinez, Fernando J.; Scanlon, Paul D.; Sciurba, Frank C.; Utz, James P.; Reilly, John J.; Silverman, Edwin K.

2006-01-01

Rationale: Patients with severe chronic obstructive pulmonary disease (COPD) may have varying levels of disability despite similar levels of lung function. This variation may reflect different COPD subtypes, which may have different genetic predispositions. Objectives: To identify genetic associations for COPD-related phenotypes, including measures of exercise capacity, pulmonary function, and respiratory symptoms. Methods: In 304 subjects from the National Emphysema Treatment Trial, we genotyped 80 markers in 22 positional and/or biologically plausible candidate genes. Regression models were used to test for association, using a test–replication approach to guard against false-positive results. For significant associations, effect estimates were recalculated using the entire cohort. Positive associations with dyspnea were confirmed in families from the Boston Early-Onset COPD Study. Results: The test–replication approach identified four genes—microsomal epoxide hydrolase (EPHX1), latent transforming growth factor-β binding protein-4 (LTBP4), surfactant protein B (SFTPB), and transforming growth factor-β1 (TGFB1)—that were associated with COPD-related phenotypes. In all subjects, single-nucleotide polymorphisms (SNPs) in EPHX1 (p ⩽ 0.03) and in LTBP4 (p ⩽ 0.03) were associated with maximal output on cardiopulmonary exercise testing. Markers in LTBP4 (p ⩽ 0.05) and SFTPB (p = 0.005) were associated with 6-min walk test distance. SNPs in EPHX1 were associated with carbon monoxide diffusing capacity (p ⩽ 0.04). Three SNPs in TGFB1 were associated with dyspnea (p ⩽ 0.002), one of which replicated in the family study (p = 0.02). Conclusions: Polymorphisms in several genes seem to be associated with COPD-related traits other than FEV1. These associations may identify genes in pathways important for COPD pathogenesis. PMID:16456143

A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism

PubMed Central

Phakthanakanok, Krongsakda; Ratanakhanokchai, Khanok; Kyu, Khin Lay; Sompornpisut, Pornthep; Watts, Aaron; Pinitglang, Surapong

2009-01-01

Background SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Understanding the binding mode of SARS CoVMpro with a specific substrate is useful and contributes to structural-based drug design. The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach. Results The one turn α-helix chain (residues 47–54) of the SARS CoVMpro was directly involved in the induced-fit model of the enzyme-substrate complex. The S3 subsite of the enzyme had a negatively charged region due to the presence of Glu47. During MD simulations, Glu47 of the enzyme was shown to play a key role in electrostatic bonding with the P3Lys of the octapeptide. Conclusion MD simulations were carried out on the SARS CoVMpro-octapeptide complex. The hypothesis proposed that Glu47 of SARS CoVMpro is an important residue in the S3 subsite and is involved in binding with P3Lys of the octapeptide. PMID:19208150

Viral DNA Replication Orientation and hnRNPs Regulate Transcription of the Human Papillomavirus 18 Late Promoter.

PubMed

Wang, Xiaohong; Liu, Haibin; Ge, Hui; Ajiro, Masahiko; Sharma, Nishi R; Meyers, Craig; Morozov, Pavel; Tuschl, Thomas; Klar, Amar; Court, Donald; Zheng, Zhi-Ming

2017-05-30

The life cycle of human papillomaviruses (HPVs) is tightly linked to keratinocyte differentiation. Although expression of viral early genes is initiated immediately upon virus infection of undifferentiated basal cells, viral DNA amplification and late gene expression occur only in the mid to upper strata of the keratinocytes undergoing terminal differentiation. In this report, we show that the relative activity of HPV18 TATA-less late promoter P 811 depends on its orientation relative to that of the origin (Ori) of viral DNA replication and is sensitive to the eukaryotic DNA polymerase inhibitor aphidicolin. Additionally, transfected 70-nucleotide (nt)-long single-strand DNA oligonucleotides that are homologous to the region near Ori induce late promoter activity. We also found that promoter activation in raft cultures leads to production of the late promoter-associated, sense-strand transcription initiation RNAs (tiRNAs) and splice-site small RNAs (spliRNAs). Finally, a cis -acting AAGTATGCA core element that functions as a repressor to the promoter was identified. This element interacts with hnRNP D0B and hnRNP A/B factors. Point mutations in the core prevented binding of hnRNPs and increased the promoter activity. Confirming this result, knocking down the expression of both hnRNPs in keratinocytes led to increased promoter activity. Taking the data together, our study revealed the mechanism of how the HPV18 late promoter is regulated by DNA replication and host factors. IMPORTANCE It has been known for decades that the activity of viral late promoters is associated with viral DNA replication among almost all DNA viruses. However, the mechanism of how DNA replication activates the viral late promoter and what components of the replication machinery are involved remain largely unknown. In this study, we characterized the P 811 promoter region of HPV18 and demonstrated that its activation depends on the orientation of DNA replication. Using single-stranded oligonucleotides targeting the replication fork on either leading or lagging strands, we showed that viral lagging-strand replication activates the promoter. We also identified a transcriptional repressor element located upstream of the promoter transcription start site which interacts with cellular proteins hnRNP D0B and hnRNP A/B and modulates the late promoter activity. This is the first report on how DNA replication activates a viral late promoter. Copyright © 2017 Wang et al.

Genome-Wide Screen Reveals Valosin-Containing Protein Requirement for Coronavirus Exit from Endosomes

PubMed Central

Wong, Hui Hui; Kumar, Pankaj; Tay, Felicia Pei Ling; Moreau, Dimitri

2015-01-01

ABSTRACT Coronaviruses are RNA viruses with a large zoonotic reservoir and propensity for host switching, representing a real threat for public health, as evidenced by severe acute respiratory syndrome (SARS) and the emerging Middle East respiratory syndrome (MERS). Cellular factors required for their replication are poorly understood. Using genome-wide small interfering RNA (siRNA) screening, we identified 83 novel genes supporting infectious bronchitis virus (IBV) replication in human cells. Thirty of these hits can be placed in a network of interactions with viral proteins and are involved in RNA splicing, membrane trafficking, and ubiquitin conjugation. In addition, our screen reveals an unexpected role for valosin-containing protein (VCP/p97) in early steps of infection. Loss of VCP inhibits a previously uncharacterized degradation of the nucleocapsid N protein. This inhibition derives from virus accumulation in early endosomes, suggesting a role for VCP in the maturation of virus-loaded endosomes. The several host factors identified in this study may provide avenues for targeted therapeutics. IMPORTANCE Coronaviruses are RNA viruses representing a real threat for public health, as evidenced by SARS and the emerging MERS. However, cellular factors required for their replication are poorly understood. Using genome-wide siRNA screening, we identified novel genes supporting infectious bronchitis virus (IBV) replication in human cells. The several host factors identified in this study may provide directions for future research on targeted therapeutics. PMID:26311884

Adverse effects of ocean acidification on early development of squid (Doryteuthis pealeii).

PubMed

Kaplan, Maxwell B; Mooney, T Aran; McCorkle, Daniel C; Cohen, Anne L

2013-01-01

Anthropogenic carbon dioxide (CO2) is being absorbed into the ocean, altering seawater chemistry, with potentially negative impacts on a wide range of marine organisms. The early life stages of invertebrates with internal and external aragonite structures may be particularly vulnerable to this ocean acidification. Impacts to cephalopods, which form aragonite cuttlebones and statoliths, are of concern because of the central role they play in many ocean ecosystems and because of their importance to global fisheries. Atlantic longfin squid (Doryteuthis pealeii), an ecologically and economically valuable taxon, were reared from eggs to hatchlings (paralarvae) under ambient and elevated CO2 concentrations in replicated experimental trials. Animals raised under elevated pCO2 demonstrated significant developmental changes including increased time to hatching and shorter mantle lengths, although differences were small. Aragonite statoliths, critical for balance and detecting movement, had significantly reduced surface area and were abnormally shaped with increased porosity and altered crystal structure in elevated pCO2-reared paralarvae. These developmental and physiological effects could alter squid paralarvae behavior and survival in the wild, directly and indirectly impacting marine food webs and commercial fisheries.

Adverse Effects of Ocean Acidification on Early Development of Squid (Doryteuthis pealeii)

PubMed Central

Kaplan, Maxwell B.; Mooney, T. Aran; McCorkle, Daniel C.; Cohen, Anne L.

2013-01-01

Anthropogenic carbon dioxide (CO2) is being absorbed into the ocean, altering seawater chemistry, with potentially negative impacts on a wide range of marine organisms. The early life stages of invertebrates with internal and external aragonite structures may be particularly vulnerable to this ocean acidification. Impacts to cephalopods, which form aragonite cuttlebones and statoliths, are of concern because of the central role they play in many ocean ecosystems and because of their importance to global fisheries. Atlantic longfin squid (Doryteuthis pealeii), an ecologically and economically valuable taxon, were reared from eggs to hatchlings (paralarvae) under ambient and elevated CO2 concentrations in replicated experimental trials. Animals raised under elevated pCO2 demonstrated significant developmental changes including increased time to hatching and shorter mantle lengths, although differences were small. Aragonite statoliths, critical for balance and detecting movement, had significantly reduced surface area and were abnormally shaped with increased porosity and altered crystal structure in elevated pCO2-reared paralarvae. These developmental and physiological effects could alter squid paralarvae behavior and survival in the wild, directly and indirectly impacting marine food webs and commercial fisheries. PMID:23741298

Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158

PubMed Central

Boer, D. Roeland; Ruiz-Masó, José Angel; Rueda, Manuel; Petoukhov, Maxim V.; Machón, Cristina; Svergun, Dmitri I.; Orozco, Modesto; del Solar, Gloria; Coll, Miquel

2016-01-01

DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii) sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation. PMID:26875695

Person-job and person-organization fits: Co-op fits in an aerospace engineering environment

NASA Astrophysics Data System (ADS)

Urban, Anthony John, Jr.

This dissertation research was a replication of a quantitative study completed by Dr. Cynthia Shantz at Wayne State University during 2003. The intent of the research was to investigate the fits of college students who participated in cooperative academic-work programs (co-ops) to employment positions within aerospace engineering. The objective of investigating person-job (P-J) and person-organization (P-O) fits was to determine if variables could be identified that indicated an individual's aptitude to complete successfully aerospace engineering standard work. Research participants were co-op employees who were surveyed during their employment to identify indications of their fits into their organization and job assignments. Dr. Shantz's research led to the thought employment success might increase when P-J and P-O fits increase. For example, reduced initial training investments and increased employee retention might result with improved P-O and P-J fits. Research data were gathered from surveys of co-ops who worked at a Connecticut aerospace engineering company. Data were collected by distributing invitations to co-ops to participate in three online surveys over a 9-11 week period. Distribution of survey invitations was accomplished through the Human Resources Department to ensure that respondent identities were maintained private. To protect anonymity and privacy further, no identifying information about individuals or the company is published. However, some demographic information was collected to ensure that correlations were based on valid and reliable data and research and analysis methods. One objective of this research was to determine if co-op characteristics could be correlated with successful employment in an aerospace engineering environment. A second objective was to determine if P-J and P-O fits vary over time as co-ops become increasing familiar with their assignments, organization, and environment. Understanding and incorporating the use P-J and P-O fits characteristics in the employment preparation and screening process may benefit aerospace engineering companies, co-ops, and academia through gains realized in reduced employment recruitment time and retention cost, student improvement in preparation to fit into aerospace engineering environments, and increases in pre- and post-graduation job placement rates.

Role of Chromatin assembly factor 1 in DNA replication of Plasmodium falciparum.

PubMed

Gupta, Mohit Kumar; Agarawal, Meetu; Banu, Khadija; Reddy, K Sony; Gaur, Deepak; Dhar, Suman Kumar

2018-01-01

Nucleosome assembly in P. falciparum could be the key process in maintaining its genomic integrity as DNA replicates more than once per cell cycle during several stages of its life cycle. Here, we report the functional characterization of P. falciparum chromatin assembly factor 1 (CAF1), which interacts with several proteins namely PfCAF2, Histones, PfHP1 and others. Consistent with the above findings, we demonstrate the presence of PfCAF1 at the telomeric repeat regions, central and subtelomeric var genes of multiple var gene family along with PfHP1. Further, we report the upregulation of PfCAF1 after treatment with genotoxic agents like MMS and HU. Together, these findings establish role of PfCAF1 in heterochromatin maintenance and as histone chaperone in nucleosome assembly and DNA damage repair. Copyright © 2017 Elsevier Inc. All rights reserved.

Blocking the interaction between HIV-1 integrase and human LEDGF/p75: mutational studies, virtual screening and molecular dynamics simulations.

PubMed

Reddy, Karnati Konda; Singh, Poonam; Singh, Sanjeev Kumar

2014-03-04

HIV-1 integrase (IN) mediates integration of viral cDNA into the host cell genome, an essential step in the retroviral life cycle. The human lens epithelium-derived growth factor (LEDGF/p75) is a co-factor of HIV-1 IN that plays a crucial role in viral integration. Because of its crucial role in early steps of HIV replication, the IN-LEDGF/p75 interaction represents an attractive target for anti-HIV drug discovery. In this study, the IN-LEDGF/p75 interaction was studied by in silico mutational studies and molecular dynamics simulations. The results showed that all of the key residues in the LEDGF/p75 binding pocket of IN protein are important for stabilization of the complex. Structure-based virtual screening against HIV-1 IN using the ChemBridge database was performed through three different protocols of docking simulations with varying precisions and computational intensities. Six compounds based on the docking score, binding affinity and pharmacokinetic parameters were selected and an analysis of the interactions with key amino acid residues of IN was carried out. Subsequently, molecular dynamics simulations of these compounds in the LEDGF/p75 binding site of IN were carried out in order to study the stability of complexes and their hydrogen bonding interactions. IN residues Glu170, His171, and Thr174 in chain A as well as Gln95 and Thr125 in chain B were discovered to play important roles in the binding of compounds. These findings could be helpful for blocking IN-LEDGF/p75 interaction, and provide a method for avoiding viral resistance and cross-resistance.

Cell-Free and Cell-Based Approaches to Explore the Roles of Host Membranes and Lipids in the Formation of Viral Replication Compartment Induced by Tombusviruses.

PubMed

Nagy, Peter D; Pogany, Judit; Xu, Kai

2016-03-03

Plant positive strand RNA viruses are intracellular infectious agents that take advantage of cellular lipids and membranes to support replication and protect viral RNA from degradation by host antiviral responses. In this review, we discuss how Tomato bushy stunt virus (TBSV) co-opts lipid transfer proteins and modulates lipid metabolism and transport to facilitate the assembly of the membrane-bound viral replicase complexes within intricate replication compartments. Identification and characterization of the proviral roles of specific lipids and proteins involved in lipid metabolism based on results from yeast (Saccharomyces cerevisiae) model host and cell-free approaches are discussed. The review also highlights the advantage of using liposomes with chemically defined composition to identify specific lipids required for TBSV replication. Remarkably, all the known steps in TBSV replication are dependent on cellular lipids and co-opted membranes.

Contributions to accelerating atmospheric CO2 growth from economic activity, carbon intensity, and efficiency of natural sinks.

PubMed

Canadell, Josep G; Le Quéré, Corinne; Raupach, Michael R; Field, Christopher B; Buitenhuis, Erik T; Ciais, Philippe; Conway, Thomas J; Gillett, Nathan P; Houghton, R A; Marland, Gregg

2007-11-20

The growth rate of atmospheric carbon dioxide (CO(2)), the largest human contributor to human-induced climate change, is increasing rapidly. Three processes contribute to this rapid increase. Two of these processes concern emissions. Recent growth of the world economy combined with an increase in its carbon intensity have led to rapid growth in fossil fuel CO(2) emissions since 2000: comparing the 1990s with 2000-2006, the emissions growth rate increased from 1.3% to 3.3% y(-1). The third process is indicated by increasing evidence (P = 0.89) for a long-term (50-year) increase in the airborne fraction (AF) of CO(2) emissions, implying a decline in the efficiency of CO(2) sinks on land and oceans in absorbing anthropogenic emissions. Since 2000, the contributions of these three factors to the increase in the atmospheric CO(2) growth rate have been approximately 65 +/- 16% from increasing global economic activity, 17 +/- 6% from the increasing carbon intensity of the global economy, and 18 +/- 15% from the increase in AF. An increasing AF is consistent with results of climate-carbon cycle models, but the magnitude of the observed signal appears larger than that estimated by models. All of these changes characterize a carbon cycle that is generating stronger-than-expected and sooner-than-expected climate forcing.

Contributions to accelerating atmospheric CO2 growth from economic activity, carbon intensity, and efficiency of natural sinks

PubMed Central

Canadell, Josep G.; Le Quéré, Corinne; Raupach, Michael R.; Field, Christopher B.; Buitenhuis, Erik T.; Ciais, Philippe; Conway, Thomas J.; Gillett, Nathan P.; Houghton, R. A.; Marland, Gregg

2007-01-01

The growth rate of atmospheric carbon dioxide (CO2), the largest human contributor to human-induced climate change, is increasing rapidly. Three processes contribute to this rapid increase. Two of these processes concern emissions. Recent growth of the world economy combined with an increase in its carbon intensity have led to rapid growth in fossil fuel CO2 emissions since 2000: comparing the 1990s with 2000–2006, the emissions growth rate increased from 1.3% to 3.3% y−1. The third process is indicated by increasing evidence (P = 0.89) for a long-term (50-year) increase in the airborne fraction (AF) of CO2 emissions, implying a decline in the efficiency of CO2 sinks on land and oceans in absorbing anthropogenic emissions. Since 2000, the contributions of these three factors to the increase in the atmospheric CO2 growth rate have been ≈65 ± 16% from increasing global economic activity, 17 ± 6% from the increasing carbon intensity of the global economy, and 18 ± 15% from the increase in AF. An increasing AF is consistent with results of climate–carbon cycle models, but the magnitude of the observed signal appears larger than that estimated by models. All of these changes characterize a carbon cycle that is generating stronger-than-expected and sooner-than-expected climate forcing. PMID:17962418

Surface Charge Development on Transition Metal Sulfides: An Electrokinetic Study

NASA Astrophysics Data System (ADS)

Bebie, Joakim; Schoonen, Martin A. A.; Fuhrmann, Mark; Strongin, Daniel R.

1998-02-01

The isoelectric points, pH i.e.p., of ZnS, PbS, CuFeS 2, FeS, FeS 2, NiS 2, CoS 2, and MnS 2 in NaCl supported electrolyte solutions are estimated to be between pH 3.3 and 0.6, with most of the isoelectric points below pH 2. The first electrokinetic measurements on NiS 2, CoS 2, and MnS 2 are reported here. Below pH i.e.p. the metal-sulfide surfaces are positively charged, above pH i.e.p. the surfaces are negatively charged. The addition of Me 2+ ions shifts the pH i.e.p. and changes the pH dependence considerably. The isoelectric points of the measured transition metal sulfides in the absence of metal ions or dissolved sulfide (H 2S or HS -) are in agreement with those found in earlier studies. The pH range of observed isoelectric points for metal sulfides (0.6-3.3) is compared to the considerably wider pH i.e.p. range (2-12) found for oxides. The correlation between pH i.e.p. and the electronegativities of the metal sulfides suggests that all metal sulfides will have an isoelectric point between pH 0.6 and 3.3. Compared to metal oxides, sulfides exhibit an isoelectric point that is largely independent of the nature of the metal cation in the solid.

Thermogravimetric analysis and fast pyrolysis of Milkweed.

PubMed

Kim, Seung-Soo; Agblevor, Foster A

2014-10-01

Pyrolysis of Milkweed was carried out in a thermogravimetric analyzer and a bubbling fluidized bed reactor. Total liquid yield of Milkweed pyrolysis was between 40.74% and 44.19 wt% between 425 °C and 550 °C. The gas yield increased from 27.90 wt% to 33.33 wt% with increasing reaction temperature. The higher heating values (HHV) of the Milkweed bio-oil were relatively high (30.33-32.87 MJ/kg) and varied with reaction temperature, feeding rate and fluidization velocity. The selectivity for CO2 was highest within non-condensable gases, and the molar ratio of CO2/CO was about 3 at the different reaction conditions. The (13)C NMR analysis, of the bio-oil showed that the relative concentration carboxylic group and its derivatives was higher at 425 °C than 475 °C, which resulted in slightly higher oxygen content in bio-oil. The pH of aqueous phase obtained at 475 °C was 7.37 which is the highest reported for any lignocellulosic biomass pyrolysis oils. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification and replication of the interplay of four genetic high-risk variants for urinary bladder cancer

PubMed Central

Selinski, Silvia; Blaszkewicz, Meinolf; Ickstadt, Katja; Gerullis, Holger; Otto, Thomas; Roth, Emanuel; Volkert, Frank; Ovsiannikov, Daniel; Moormann, Oliver; Banfi, Gergely; Nyirady, Peter; Vermeulen, Sita H; Garcia-Closas, Montserrat; Figueroa, Jonine D; Johnson, Alison; Karagas, Margaret R; Kogevinas, Manolis; Malats, Nuria; Schwenn, Molly; Silverman, Debra T; Koutros, Stella; Rothman, Nathaniel; Kiemeney, Lambertus A; Hengstler, Jan G; Golka, Klaus

2017-01-01

Abstract Little is known whether genetic variants identified in genome-wide association studies interact to increase bladder cancer risk. Recently, we identified two- and three-variant combinations associated with a particular increase of bladder cancer risk in a urinary bladder cancer case–control series (Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), 1501 cases, 1565 controls). In an independent case–control series (Nijmegen Bladder Cancer Study, NBCS, 1468 cases, 1720 controls) we confirmed these two- and three-variant combinations. Pooled analysis of the two studies as discovery group (IfADo-NBCS) resulted in sufficient statistical power to test up to four-variant combinations by a logistic regression approach. The New England and Spanish Bladder Cancer Studies (2080 cases and 2167 controls) were used as a replication series. Twelve previously identified risk variants were considered. The strongest four-variant combination was obtained in never smokers. The combination of rs1014971[AA] near apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A (APOBEC3A) and chromobox homolog 6 (CBX6), solute carrier family 1s4 (urea transporter), member 1 (Kidd blood group) (SLC14A1) exon single nucleotide polymorphism (SNP) rs1058396[AG, GG], UDP glucuronosyltransferase 1 family, polypeptide A complex locus (UGT1A) intron SNP rs11892031[AA] and rs8102137[CC, CT] near cyclin E1 (CCNE1) resulted in an unadjusted odds ratio (OR) of 2.59 (95% CI = 1.93–3.47; P = 1.87 × 10−10), while the individual variant ORs ranged only between 1.11 and 1.30. The combination replicated in the New England and Spanish Bladder Cancer Studies (ORunadjusted = 1.60, 95% CI = 1.10–2.33; P = 0.013). The four-variant combination is relatively frequent, with 25% in never smoking cases and 11% in never smoking controls (total study group: 19% cases, 14% controls). In conclusion, we show that four high-risk variants can statistically interact to confer increased bladder cancer risk particularly in never smokers. PMID:29028944

Accessory proteins of SARS-CoV and other coronaviruses.

PubMed

Liu, Ding Xiang; Fung, To Sing; Chong, Kelvin Kian-Long; Shukla, Aditi; Hilgenfeld, Rolf

2014-09-01

The huge RNA genome of SARS coronavirus comprises a number of open reading frames that code for a total of eight accessory proteins. Although none of these are essential for virus replication, some appear to have a role in virus pathogenesis. Notably, some SARS-CoV accessory proteins have been shown to modulate the interferon signaling pathways and the production of pro-inflammatory cytokines. The structural information on these proteins is also limited, with only two (p7a and p9b) having their structures determined by X-ray crystallography. This review makes an attempt to summarize the published knowledge on SARS-CoV accessory proteins, with an emphasis on their involvement in virus-host interaction. The accessory proteins of other coronaviruses are also briefly discussed. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses" (see Introduction by Hilgenfeld and Peiris (2013)). Copyright © 2014 Elsevier B.V. All rights reserved.

DNA replication machinery is required for development in Drosophila.

PubMed

Kohzaki, Hidetsugu; Asano, Maki; Murakami, Yota

2018-01-01

 In Drosophila , some factors involved in chromosome replication seem to be involved in gene amplification and endoreplication, which are actively utilized in particular tissue development, but direct evidence has not been shown. Therefore, we examined the effect of depletion of replication factors on these processes. First, we confirmed RNAi knockdown can be used for the depletion of replication factors by comparing the phenotypes of RNAi knockdown and deletion or point mutants of the components of DNA licensing factor, MCM2, MCM4 and Cdt1. Next, we found that tissue-specific RNAi knockdown of replication factors caused tissue-specific defects, probably due to defects in DNA replication. In particular, we found that depletion inhibited gene amplification of the chorion gene in follicle cells and endoreplication in salivary glands, showing that chromosomal DNA replication factors are required for these processes. Finally, using RNAi, we screened the genes for chromosomal DNA replication that affected tissue development. Interestingly, wing specific knockdown of Mcm10 induced wing formation defects. These results suggest that some components of chromosomal replication machinery are directly involved in tissue development.

Synthesis and crystal structure of the solid solution Co3(SeO3)3-x(PO3OH)x(H2O) involving crystallographic split positions of Se4+ and P5+.

PubMed

Zimmermann, Iwan; Johnsson, Mats

2013-10-21

Three new cobalt selenite hydroxo-phosphates laying in the solid solution Co3(SeO3)3-x(PO3OH)x(H2O), with x = 0.8, x = 1.0, and x = 1.2 are reported. Single crystals were obtained by hydrothermal synthesis and the crystal structure was determined by single crystal X-ray diffraction. The structure can be described as a 3D framework having selenite and hydroxo-phosphate groups protruding into channels in the crystal structure. Se(4+) and P(5+) share a split position in the structure so that either SeO3 groups having a stereochemically active lone pair or tetrahedrally coordinated PO3OH groups are present. The OH-group is thus only present when the split position is occupied by P(5+). The crystal water is coordinated to a cobalt atom and TG and IR measurements show that the water and hydroxyl groups leave the structure at unusually high temperatures (>450 °C). Magnetic susceptibility measurements show antiferromagnetic coupling below 16 K and a magnetic moment of 4.02(3) μB per Co atom was observed.

Porcine circovirus type 2 induces the activation of nuclear factor kappa B by I{kappa}B{alpha} degradation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei Li; Kwang, Jimmy; Wang Jin

The transcription factor NF-{kappa}B is commonly activated upon virus infection and a key player in the induction and regulation of the host immune response. The present study demonstrated for the first time that porcine circovirus type 2 (PCV2), which is the primary causative agent of an emerging swine disease, postweaning multisystemic wasting syndrome, can activate NF-{kappa}B in PCV2-infected PK15 cells. In PCV2-infected cells, NF-{kappa}B was activated concomitantly with viral replication, which was characterized by increased DNA binding activity, translocation of NF-{kappa}B p65 from the cytoplasm to the nucleus, as well as degradation and phosphorylation of I{kappa}B{alpha} protein. We further demonstratedmore » PCV2-induced activation of NF-{kappa}B and colocalization of p65 nuclear translocation with virus replication in cultured cells. Treatment of cells with CAPE, a selective inhibitor of NF-{kappa}B activation, reduced virus protein expression and progeny production followed by decreasing PCV2-induced apoptotic caspase activity, indicating the involvement of this transcription factor in induction of cell death. Taken together, these data suggest that NF-{kappa}B activation is important for PCV2 replication and contributes to virus-mediated changes in host cells. The results presented here provide a basis for understanding molecular mechanism of PCV2 infection.« less

Influenza A Virus M2 Ion Channel Activity Is Essential for Efficient Replication in Tissue Culture

PubMed Central

Takeda, Makoto; Pekosz, Andrew; Shuck, Kevin; Pinto, Lawrence H.; Lamb, Robert A.

2002-01-01

The amantadine-sensitive ion channel activity of influenza A virus M2 protein was discovered through understanding the two steps in the virus life cycle that are inhibited by the antiviral drug amantadine: virus uncoating in endosomes and M2 protein-mediated equilibration of the intralumenal pH of the trans Golgi network. Recently it was reported that influenza virus can undergo multiple cycles of replication without M2 ion channel activity (T. Watanabe, S. Watanabe, H. Ito, H. Kida, and Y. Kawaoka, J. Virol. 75:5656–5662, 2001). An M2 protein containing a deletion in the transmembrane (TM) domain (M2-del29–31) has no detectable ion channel activity, yet a mutant virus was obtained containing this deletion. Watanabe and colleagues reported that the M2-del29–31 virus replicated as efficiently as wild-type (wt) virus. We have investigated the effect of amantadine on the growth of four influenza viruses: A/WSN/33; N31S-M2WSN, a mutant in which an asparagine residue at position 31 in the M2 TM domain was replaced with a serine residue; MUd/WSN, which possesses seven RNA segments from WSN plus the RNA segment 7 derived from A/Udorn/72; and A/Udorn/72. N31S-M2WSN was amantadine sensitive, whereas A/WSN/33 was amantadine resistant, indicating that the M2 residue N31 is the sole determinant of resistance of A/WSN/33 to amantadine. The growth of influenza viruses inhibited by amantadine was compared to the growth of an M2-del29–31 virus. We found that the M2-del29–31 virus was debilitated in growth to an extent similar to that of influenza virus grown in the presence of amantadine. Furthermore, in a test of biological fitness, it was found that wt virus almost completely outgrew M2-del29–31 virus in 4 days after cocultivation of a 100:1 ratio of M2-del29–31 virus to wt virus, respectively. We conclude that the M2 ion channel protein, which is conserved in all known strains of influenza virus, evolved its function because it contributes to the efficient replication of the virus in a single cycle. PMID:11773413

End-Tidal Carbon Dioxide Measurement during Pediatric Polysomnography: Signal Quality, Association with Apnea Severity, and Prediction of Neurobehavioral Outcomes.

PubMed

Paruthi, Shalini; Rosen, Carol L; Wang, Rui; Weng, Jia; Marcus, Carole L; Chervin, Ronald D; Stanley, Jeffrey J; Katz, Eliot S; Amin, Raouf; Redline, Susan

2015-11-01

To identify the role of end-tidal carbon dioxide (EtCO2) monitoring during polysomnography in evaluation of children with obstructive sleep apnea syndrome (OSAS), including the correlation of EtCO2 with other measures of OSAS and prediction of changes in cognition and behavior after adenotonsillectomy. Analysis of screening and endpoint data from the Childhood Adenotonsillectomy Trial, a randomized, controlled, multicenter study comparing early adenotonsillectomy (eAT) to watchful waiting/supportive care (WWSC) in children with OSAS. Multisite clinical referral settings. Children, ages 5.0 to 9.9 y with suspected sleep apnea. eAT or WWSC. Quality EtCO2 waveforms were present for ≥ 75% of total sleep time (TST) in 876 of 960 (91.3%) screening polysomnograms. Among the 322 children who were randomized, 55 (17%) met pediatric criteria for hypoventilation. The mean TST with EtCO2 > 50 mmHg was modestly correlated with apnea-hypopnea index (AHI) (r = 0.33; P < 0.0001) and with oxygen saturation ≤ 92% (r = 0.26; P < 0.0001). After adjusting for AHI, obesity, and other factors, EtCO2 > 50 mmHg was higher in African American children than others. The TST with EtCO2 > 50 mmHg decreased significantly more after eAT than WWSC. In adjusted analyses, baseline TST with EtCO2 > 50 mmHg did not predict postoperative changes in cognitive and behavioral measurements. Among children with suspected obstructive sleep apnea syndrome, overnight end-tidal carbon dioxide (EtCO2) levels are weakly to modestly correlated with other polysomnographic indices and therefore provide independent information on hypoventilation. EtCO2 levels improve with adenotonsillectomy but are not as responsive as AHI and do not provide independent prediction of cognitive or behavioral response to surgery. Childhood Adenotonsillectomy Study for Children with OSAS (CHAT). ClinicalTrials.gov Identifier #NCT00560859. © 2015 Associated Professional Sleep Societies, LLC.

HIV-1 protease inhibitor mutations affect the development of HIV-1 resistance to the maturation inhibitor bevirimat.

PubMed

Fun, Axel; van Maarseveen, Noortje M; Pokorná, Jana; Maas, Renée Em; Schipper, Pauline J; Konvalinka, Jan; Nijhuis, Monique

2011-08-24

Maturation inhibitors are an experimental class of antiretrovirals that inhibit Human Immunodeficiency Virus (HIV) particle maturation, the structural rearrangement required to form infectious virus particles. This rearrangement is triggered by the ordered cleavage of the precursor Gag polyproteins into their functional counterparts by the viral enzyme protease. In contrast to protease inhibitors, maturation inhibitors impede particle maturation by targeting the substrate of protease (Gag) instead of the protease enzyme itself. Direct cross-resistance between protease and maturation inhibitors may seem unlikely, but the co-evolution of protease and its substrate, Gag, during protease inhibitor therapy, could potentially affect future maturation inhibitor therapy. Previous studies showed that there might also be an effect of protease inhibitor resistance mutations on the development of maturation inhibitor resistance, but the exact mechanism remains unclear. We used wild-type and protease inhibitor resistant viruses to determine the impact of protease inhibitor resistance mutations on the development of maturation inhibitor resistance. Our resistance selection studies demonstrated that the resistance profiles for the maturation inhibitor bevirimat are more diverse for viruses with a mutated protease compared to viruses with a wild-type protease. Viral replication did not appear to be a major factor during emergence of bevirimat resistance. In all in vitro selections, one of four mutations was selected: Gag V362I, A364V, S368N or V370A. The impact of these mutations on maturation inhibitor resistance and viral replication was analyzed in different protease backgrounds. The data suggest that the protease background affects development of HIV-1 resistance to bevirimat and the replication profiles of bevirimat-selected HIV-1. The protease-dependent bevirimat resistance and replication levels can be explained by differences in CA/p2 cleavage processing by the different proteases. These findings highlight the complicated interactions between the viral protease and its substrate. By providing a better understanding of these interactions, we aim to help guide the development of second generation maturation inhibitors.

Evaluation of a Novel Tc-99m Labelled Vitamin B12 Derivative for Targeting Escherichia coli and Staphylococcus aureus In Vitro and in an Experimental Foreign-Body Infection Model.

PubMed

Baldoni, Daniela; Waibel, Robert; Bläuenstein, Peter; Galli, Filippo; Iodice, Violetta; Signore, Alberto; Schibli, Roger; Trampuz, Andrej

2015-12-01

Vitamin B12 (cyanocobalamin, Cbl) is accumulated by rapidly replicating prokaryotic and eukaryotic cells. We investigated the potential of a Tc-99m labelled Cbl derivative ([(99m)Tc]PAMA(4)-Cbl) for targeting infections caused by Escherichia coli and Staphylococcus aureus. In vitro binding assays were followed by biodistribution studies in a mouse model of foreign body infection. E. coli (ATCC 25922) and S. aureus (ATCC 43335) were used as test strains. [(57)Co]Cbl, [(67)Ga]citrate and [(99m)Tc]DTPA served as reference compounds. The in vitro competitive binding of [(57)Co]Cbl or [(99m)Tc]PAMA(4)-Cbl, and unlabeled Cbl, to viable or killed bacteria, was evaluated at 37 and 4 °C. A cage mouse model of infection was used for biodistribution of intravenous [(57)Co]Cbl and [(99m)Tc]PAMA(4)-Cbl in cage and dissected tissues of infected and non-infected mice. Maximum binding (mean ± SD) of [(57)Co]Cbl to viable E. coli was 81.7 ± 2.6 % and to S. aureus 34.0 ± 6.7 %, at 37 °C; no binding occurred to heat-killed bacteria. Binding to both test strains was displaced by 100- to 1000-fold excess of unlabeled Cbl. The in vitro binding of [(99m)Tc]PAMA(4)-Cbl was 100-fold and 3-fold lower than the one of [(57)Co]Cbl for E. coli and S. aureus, respectively. In vivo, [(99m)Tc]PAMA(4)-Cbl showed peak percentage of injected dose (% ID) values between 1.33 and 2.3, at 30 min post-injection (p.i.). Significantly higher retention occurred in cage fluids infected with S. aureus at 4 h and with E. coli at 8 h p.i. than in non-infected animals. Accumulation into infected cages was also higher than the one of [(99m)Tc]DTPA, which showed similar biodistribution in infected and sterile mice. [(57)Co]Cbl gradually accumulated in cages with peaks % ID between 3.58 and 4.83 % achieved from 24 to 48 h. Discrimination for infection occurred only in E. coli-infected mice, at 72 h p.i. [(67)Ga]citrate, which showed a gradual accumulation into cage fluids during 12 h, was discriminative for infection from 48 to 72 h p.i. (P < 0.05). Cbl displayed rapid and specific in vitro binding to test strains. [(99m)Tc]PAMA(4)-Cbl was rapidly cleared from most tissues and discriminated between sterile and infected cages, being a promising candidate for imaging infections in humans.

Systemic Candidiasis in Extremely Low Birthweight (ELBW) Neonates Despite the Routine Use of Topical Miconazole Prophylaxis: Trends, Risk Factors and Outcomes over an 11-Year Period.

PubMed

Sriram, Bhavani; Agarwal, Pratibha K; Tee, Nancy W S; Rajadurai, Victor S

2014-05-01

This study aims to determine the incidence, trends of systemic candidiasis and meningitis in extremely low birthweight (ELBW) neonates (<1000 gms) despite the routine use of topical miconazole prophylaxis and to compare the risk factors, adverse outcomes and comorbidities with controls. Retrospective cohort study of ELBW neonates with systemic candidiasis and meningitis over an 11-year period (1997 to 2007). Matched case control analyses were performed to determine the risk factors and comorbidities which were severe intraventricular haemorrhage (IVH), severe retinopathy of prematurity (ROP), patent ductus arteriosus (PDA) requiring treatment, necrotising enterocolitis (NEC), chronic lung disease (CLD) and cholestatic jaundice. Mortality and end organ involvement secondary to systemic candidiasis were identified as adverse outcomes. Of the 757 ELBW neonates, 51 (6.7%) had evidence of systemic candidiasis with a significant 3-fold increase in trend noted in 2007 as compared against 1997 (12.1% vs 3.8%) (RR 1.2, 95% CI, 1.06 to 1.36, P <0.001). This corresponds to a significant increasing trend of preceding or co-existent bacterial blood stream infections (BSI) in neonates with systemic candidiasis (0% in 1997 vs 7.1% in 2007, RR 1.40, 95% CI, 1.04 to 1.25, P = 0.005). On logistic regression analysis, decreasing gestational age was an independent risk factor for systemic candidiasis (OR 2.0, 95% CI, 1.52 to 2.63, P <0.001). Candida meningitis was detected in 4/38 (10.5%) and end organ involvement in 17 (33%). The organisms isolated were Candida parapsilosis 31 (61%), Candida albicans 17 (33%) and Candida glabrata 3 (5.8%). Significantly higher mortality was seen in cases when compared to controls 10/51 (19.6%) vs 76/706 (10.7%) (OR 2.02, 95% CI, 1.02 to 4.40, P <0.001). Increasing trend in the incidence of systemic candidiasis despite routine use of topical miconazole prophylaxis is of concern and future studies comparing the use of systemic fl uconazole versus oral nystatin may need to be considered.

Expression of the myeloid-associated marker CD33 is not an exclusive factor for leukemic plasmacytoid dendritic cells.

PubMed

Garnache-Ottou, Francine; Chaperot, Laurence; Biichle, Sabeha; Ferrand, Christophe; Remy-Martin, Jean-Paul; Deconinck, Eric; de Tailly, Patrick Darodes; Bulabois, Bénédicte; Poulet, Jacqueline; Kuhlein, Emilienne; Jacob, Marie-Christine; Salaun, Véronique; Arock, Michel; Drenou, Bernard; Schillinger, Françoise; Seilles, Estelle; Tiberghien, Pierre; Bensa, Jean-Claude; Plumas, Joel; Saas, Philippe

2005-02-01

A new entity of acute leukemia coexpressing CD4(+)CD56(+) markers without any other lineage-specific markers has been identified recently as arising from lymphoid-related plasmacytoid dendritic cells (pDCs). In our laboratory, cells from a patient with such CD4(+)CD56(+) lineage-negative leukemia were unexpectedly found to also express the myeloid marker CD33. To confirm the diagnosis of pDC leukemia despite the CD33 expression, we demonstrated that the leukemic cells indeed exhibited pDC phenotypic and functional properties. In 7 of 8 other patients with CD4(+)CD56(+) pDC malignancies, we were able to confirm that the tumor cells expressed CD33 although with variable expression levels. CD33 expression was shown by flow cytometry, reverse transcriptase-polymerase chain reaction, and immunoblot analysis. Furthermore, CD33 monoclonal antibody stimulation of purified CD4(+)CD56(+) leukemic cells led to cytokine secretion, thus confirming the presence of a functional CD33 on these leukemic cells. Moreover, we found that circulating pDCs in healthy individuals also weakly express CD33. Overall, our results demonstrate that the expression of CD33 on CD4(+)CD56(+) lineage-negative cells should not exclude the diagnosis of pDC leukemia and underline that pDC-specific markers should be used at diagnosis for CD4(+)CD56(+) malignancies.

An improved biosensor for acetaldehyde determination using a bienzymatic strategy at poly(neutral red) modified carbon film electrodes.

PubMed

Ghica, Mariana Emilia; Pauliukaite, Rasa; Marchand, Nicolas; Devic, Eric; Brett, Christopher M A

2007-05-15

Improved biosensors for acetaldehyde determination have been developed using a bienzymatic strategy, based on a mediator-modified carbon film electrode and co-immobilisation of NADH oxidase and aldehyde dehydrogenase. Modification of the carbon film electrode with poly(neutral red) mediator resulted in a sensitive, low-cost and reliable NADH detector. Immobilisation of the enzymes was performed using encapsulation in a sol-gel matrix or cross-linking with glutaraldehyde. The bienzymatic biosensors were characterized by studying the influence of pH, applied potential and co-factors. The sol-gel and glutaraldehyde biosensors showed a linear response up to 60 microM and 100 microM, respectively, with detection limits of 2.6 microM and 3.3 microM and sensitivities were 1.7 microA mM(-1) and 5.6 microA mM(-1). The optimised biosensors showed good stability and good selectivity and have been tested for application for the determination of acetaldehyde in natural samples such as wine.

Expression of CD33 is a predictive factor for effect of gemtuzumab ozogamicin at different doses in adult acute myeloid leukaemia.

PubMed

Khan, N; Hills, R K; Virgo, P; Couzens, S; Clark, N; Gilkes, A; Richardson, P; Knapper, S; Grimwade, D; Russell, N H; Burnett, A K; Freeman, S D

2017-05-01

It remains unclear in adult acute myeloid leukaemia (AML) whether leukaemic expression of CD33, the target antigen for gemtuzumab ozogamicin (GO), adds prognostic information on GO effectiveness at different doses. CD33 expression quantified in 1583 patients recruited to UK-NCRI-AML17 (younger adults) and UK-NCRI-AML16 (older adults) trials was correlated with clinical outcomes and benefit from GO including a dose randomisation. CD33 expression associated with genetic subgroups, including lower levels in both adverse karyotype and core-binding factor (CBF)-AML, but was not independently prognostic. When comparing GO versus no GO (n=393, CBF-AMLs excluded) by stratified subgroup-adjusted analysis, patients with lowest quartile (Q1) %CD33-positivity had no benefit from GO (relapse risk, HR 2.41 (1.27-4.56), P=0.009 for trend; overall survival, HR 1.52 (0.92-2.52)). However, from the dose randomisation (NCRI-AML17, n=464, CBF-AMLs included), 6 mg/m 2 GO only had a relapse benefit without increased early mortality in CD33-low (Q1) patients (relapse risk HR 0.64 (0.36-1.12) versus 1.70 (0.99-2.92) for CD33-high, P=0.007 for trend). Thus CD33 expression is a predictive factor for GO effect in adult AML; although GO does not appear to benefit the non-CBF AML patients with lowest CD33 expression a higher GO dose may be more effective for CD33-low but not CD33-high younger adults.

Rheumatoid arthritis association at 6q23

PubMed Central

Thomson, Wendy; Barton, Anne; Ke, Xiayi; Eyre, Steve; Hinks, Anne; Bowes, John; Donn, Rachelle; Symmons, Deborah; Hider, Samantha; Bruce, Ian N; Wilson, Anthony G; Marinou, Ioanna; Morgan, Ann; Emery, Paul; Carter, Angela; Steer, Sophia; Hocking, Lynne; Reid, David M; Wordsworth, Paul; Harrison, Pille; Strachan, David; Worthington, Jane

2009-01-01

The Wellcome Trust Case Control Consortium (WTCCC) identified nine single SNPs putatively associated with rheumatoid arthritis at P = 1 × 10 -5 - 5 × 10-7 in a genome-wide association screen. One, rs6920220, was unequivocally replicated (trend P = 1.1 × 10-8) in a validation study, as described here. This SNP maps to 6q23, between the genes oligodendrocyte lineage transcription factor 3 (OLIG3) and tumor necrosis factor-α-induced protein 3 (TNFAIP3). PMID:17982455

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus.

PubMed

McDermott, Jason E; Mitchell, Hugh D; Gralinski, Lisa E; Eisfeld, Amie J; Josset, Laurence; Bankhead, Armand; Neumann, Gabriele; Tilton, Susan C; Schäfer, Alexandra; Li, Chengjun; Fan, Shufang; McWeeney, Shannon; Baric, Ralph S; Katze, Michael G; Waters, Katrina M

2016-09-23

The complex interplay between viral replication and host immune response during infection remains poorly understood. While many viruses are known to employ anti-immune strategies to facilitate their replication, highly pathogenic virus infections can also cause an excessive immune response that exacerbates, rather than reduces pathogenicity. To investigate this dichotomy in severe acute respiratory syndrome coronavirus (SARS-CoV), we developed a transcriptional network model of SARS-CoV infection in mice and used the model to prioritize candidate regulatory targets for further investigation. We validated our predictions in 18 different knockout (KO) mouse strains, showing that network topology provides significant predictive power to identify genes that are important for viral infection. We identified a novel player in the immune response to virus infection, Kepi, an inhibitory subunit of the protein phosphatase 1 (PP1) complex, which protects against SARS-CoV pathogenesis. We also found that receptors for the proinflammatory cytokine tumor necrosis factor alpha (TNFα) promote pathogenesis, presumably through excessive inflammation. The current study provides validation of network modeling approaches for identifying important players in virus infection pathogenesis, and a step forward in understanding the host response to an important infectious disease. The results presented here suggest the role of Kepi in the host response to SARS-CoV, as well as inflammatory activity driving pathogenesis through TNFα signaling in SARS-CoV infections. Though we have reported the utility of this approach in bacterial and cell culture studies previously, this is the first comprehensive study to confirm that network topology can be used to predict phenotypes in mice with experimental validation.

A replicated field intervention study evaluating the impact of a highly adjustable chair and office ergonomics training on visual symptoms☆

PubMed Central

Menéndez, Cammie Chaumont; Amick, Benjamin C.; Robertson, Michelle; Bazzani, Lianna; DeRango, Kelly; Rooney, Ted; Moore, Anne

2016-01-01

Objective Examine the effects of two office ergonomics interventions in reducing visual symptoms at a private sector worksite. Methods A quasi-experimental study design evaluated the effects of a highly adjustable chair with office ergonomics training intervention (CWT group) and the training only (TO group) compared with no intervention (CO group). Data collection occurred 2 and 1 month(s) pre-intervention and 2, 6 and 12 months post-intervention. During each data collection period, a work environment and health questionnaire (covariates) and daily health diary (outcomes) were completed. Multilevel statistical models tested hypotheses. Results Both the training only intervention (p < 0.001) and the chair with training intervention (p = 0.01) reduced visual symptoms after 12 months. Conclusion The office ergonomics training alone and coupled with a highly adjustable chair reduced visual symptoms. In replicating results from a public sector worksite at a private sector worksite the external validity of the interventions is strengthened, thus broadening its generalizability. PMID:22030069

A replicated field intervention study evaluating the impact of a highly adjustable chair and office ergonomics training on visual symptoms.

PubMed

Menéndez, Cammie Chaumont; Amick, Benjamin C; Robertson, Michelle; Bazzani, Lianna; DeRango, Kelly; Rooney, Ted; Moore, Anne

2012-07-01

Examine the effects of two office ergonomics interventions in reducing visual symptoms at a private sector worksite. A quasi-experimental study design evaluated the effects of a highly adjustable chair with office ergonomics training intervention (CWT group) and the training only (TO group) compared with no intervention (CO group). Data collection occurred 2 and 1 month(s) pre-intervention and 2, 6 and 12 months post-intervention. During each data collection period, a work environment and health questionnaire (covariates) and daily health diary (outcomes) were completed. Multilevel statistical models tested hypotheses. Both the training only intervention (p<0.001) and the chair with training intervention (p=0.01) reduced visual symptoms after 12 months. The office ergonomics training alone and coupled with a highly adjustable chair reduced visual symptoms. In replicating results from a public sector worksite at a private sector worksite the external validity of the interventions is strengthened, thus broadening its generalizability. Published by Elsevier Ltd.

Replication of the association of BDNF and MC4R variants with dietary intake in the Diabetes Prevention Program

PubMed Central

McCaffery, Jeanne M.; Jablonski, Kathleen A.; Franks, Paul W.; Delahanty, Linda M.; Aroda, Vanita; Marrero, David; Hamman, Richard F.; Horton, Edward S.; Dagogo-Jack, Samuel; Wylie-Rosett, Judith; Barrett-Connor, Elizabeth; Kitabchi, Abbas; Knowler, William C.; Wing, Rena R.; Florez, Jose C.

2016-01-01

OBJECTIVES Genome-wide association studies (GWAS) have identified consistent associations with obesity, with a number of studies implicating eating behavior as a primary mechanism. Few studies have replicated genetic associations with dietary intake. This study evaluates the association between obesity susceptibility loci and dietary intake. METHODS Data were obtained as part of the Diabetes Prevention Program (DPP), a clinical trial of diabetes prevention in persons at high risk of diabetes. The association of 31 GWAS-identified obesity risk alleles with dietary intake, measured through a food frequency questionnaire, was investigated in 3,180 participants from DPP at baseline. Results The minor allele at BDNF, identified as protective against obesity, was associated with lower total caloric intake (β=−106.06, SE=33.13; P=0.0014) at experiment-wide statistical significance (P=0.0016), while association of MC4R rs571312 with higher caloric intake reached nominal significance (β = 61.32, SE=26.24; P=0.0194). Among non-Hispanic White participants, the association of BDNF rs2030323 with total caloric intake was stronger (β=−151.99, SE=30.09; P<0.0001), and association of FTO rs1421085 with higher caloric intake (β=56.72, SE=20.69; P=0.0061) and percentage fat intake (β=0.37, SE=0.08; P=0.0418) was also observed. Conclusions These results demonstrate with the strength of independent replication that BDNF rs2030323 is associated with 100 – 150 greater total caloric intake per allele, with additional contributions of MC4R and, in non-Hispanic White individuals, FTO. As it has been argued that an additional 100 kcals per day could account for the trends in weight gain, prevention focusing on genetic profiles with high dietary intake may help to quell adverse obesity trends. Clinical Trial registration: ClinicalTrials.gov, NCT00004992 PMID:27551991

Novel genome-wide association study-based candidate loci for differentiated thyroid cancer risk.

PubMed

Figlioli, Gisella; Köhler, Aleksandra; Chen, Bowang; Elisei, Rossella; Romei, Cristina; Cipollini, Monica; Cristaudo, Alfonso; Bambi, Franco; Paolicchi, Elisa; Hoffmann, Per; Herms, Stefan; Kalemba, Michał; Kula, Dorota; Pastor, Susana; Marcos, Ricard; Velázquez, Antonia; Jarząb, Barbara; Landi, Stefano; Hemminki, Kari; Försti, Asta; Gemignani, Federica

2014-10-01

Genome-wide association studies (GWASs) on differentiated thyroid cancer (DTC) have identified robust associations with single nucleotide polymorphisms (SNPs) at 9q22.33 (FOXE1), 14q13.3 (NKX2-1), and 2q35 (DIRC3). Our recently published GWAS suggested additional susceptibility loci specific for the high-incidence Italian population. The purpose of this study was to identify novel Italian-specific DTC risk variants based on our GWAS and to test them further in low-incidence populations. We investigated 45 SNPs selected from our GWAS first in an Italian population. SNPs that showed suggestive evidence of association were investigated in the Polish and Spanish cohorts. The combined analysis of the GWAS and the Italian replication study (2260 case patients and 2218 control subjects) provided strong evidence of association with rs10136427 near BATF (odds ratio [OR] =1.40, P = 4.35 × 10(-7)) and rs7267944 near DHX35 (OR = 1.39, P = 2.13 × 10(-8)). A possible role in DTC susceptibility in the Italian populations was also found for rs13184587 (ARSB) (P = 8.54 × 10(-6)) and rs1220597 (SPATA13) (P = 3.25 × 10(-6)). Only the associations between rs10136427 and rs7267944 and DTC risk were replicated in the Polish and the Spanish populations with little evidence of population heterogeneity (GWAS and all replications combined, OR = 1.30, P = 9.30 × 10(-7) and OR = 1.32, P = 1.34 × 10(-8), respectively). In silico analyses provided new insights into the possible functional consequences of the SNPs that showed the strongest association with DTC. Our findings provide evidence for novel DTC susceptibility variants. Further studies are warranted to identify the specific genetic variants responsible for the observed associations and to functionally validate our in silico predictions.

Large-Scale Gene-Centric Analysis Identifies Novel Variants for Coronary Artery Disease

PubMed Central

2011-01-01

Coronary artery disease (CAD) has a significant genetic contribution that is incompletely characterized. To complement genome-wide association (GWA) studies, we conducted a large and systematic candidate gene study of CAD susceptibility, including analysis of many uncommon and functional variants. We examined 49,094 genetic variants in ∼2,100 genes of cardiovascular relevance, using a customised gene array in 15,596 CAD cases and 34,992 controls (11,202 cases and 30,733 controls of European descent; 4,394 cases and 4,259 controls of South Asian origin). We attempted to replicate putative novel associations in an additional 17,121 CAD cases and 40,473 controls. Potential mechanisms through which the novel variants could affect CAD risk were explored through association tests with vascular risk factors and gene expression. We confirmed associations of several previously known CAD susceptibility loci (eg, 9p21.3:p<10−33; LPA:p<10−19; 1p13.3:p<10−17) as well as three recently discovered loci (COL4A1/COL4A2, ZC3HC1, CYP17A1:p<5×10−7). However, we found essentially null results for most previously suggested CAD candidate genes. In our replication study of 24 promising common variants, we identified novel associations of variants in or near LIPA, IL5, TRIB1, and ABCG5/ABCG8, with per-allele odds ratios for CAD risk with each of the novel variants ranging from 1.06–1.09. Associations with variants at LIPA, TRIB1, and ABCG5/ABCG8 were supported by gene expression data or effects on lipid levels. Apart from the previously reported variants in LPA, none of the other ∼4,500 low frequency and functional variants showed a strong effect. Associations in South Asians did not differ appreciably from those in Europeans, except for 9p21.3 (per-allele odds ratio: 1.14 versus 1.27 respectively; P for heterogeneity = 0.003). This large-scale gene-centric analysis has identified several novel genes for CAD that relate to diverse biochemical and cellular functions and clarified the literature with regard to many previously suggested genes. PMID:21966275

Epidermal regulation of dermal fibroblast activity.

PubMed

Garner, W L

1998-07-01

Although the association between delayed burn wound healing and subsequent hypertrophic scar formation is well-established, the mechanism for this relationship is unknown. Unhealed burn wounds lack an epidermis, suggesting a possible regulatory role for the epidermis in controlling dermal fibroblast matrix synthesis. Therefore, we examined the effect of epidermal cells and media conditioned by epidermal cells on fibroblast collagen synthesis and replication. Purified fibroblast and keratinocyte cell strains were developed from discarded normal adult human skin. Conditioned media were created by incubation of cytokine-free and serum-free medium with either confluent fibroblast or keratinocyte cultures for 18 hours (n = 3). Nearly confluent fibroblast cultures were exposed for 48 hours to graded concentrations of either unconditioned medium (control), conditioned medium, or varying numbers of keratinocytes. Replication was quantified by the incorporation of 3H-thymidine. Collagen synthesis was measured by the incorporation of 3H-proline into collagenase-sensitive protein. Data were compared using analysis of variance (ANOVA) and linear regression. Keratinocyte conditioned medium induced a significant increase in replication (n = 3) (p = 0.004) and a decrease in collagen synthesis (n = 6) (p < 0.001). In contrast, neither fibroblast conditioned medium nor control medium had an effect on fibroblast replication or collagen synthesis. Co-culture of fibroblast with a graded number of keratinocytes similarly decreased collagen synthesis (n = 6) (p < 0.001). Dermal fibroblast collagen synthesis appears to be regulated by a soluble keratinocyte product. This result suggests a mechanism for the clinical observation that unhealed burn wounds, which lack the epidermis, demonstrate excess collagen production and scar. Clinical strategies to decrease hypertrophic scar should include an attempt at early wound closure with skin grafting or the application of cultured epithelial autografts.

Daclatasvir inhibits hepatitis C virus NS5A motility and hyper-accumulation of phosphoinositides

PubMed Central

Chukkapalli, Vineela; Berger, Kristi L.; Kelly, Sean M.; Thomas, Meryl; Deiters, Alexander; Randall, Glenn

2014-01-01

Combinations of direct-acting antivirals (DAAs) against the hepatitis C virus (HCV) have the potential to revolutionize the HCV therapeutic regime. An integral component of DAA combination therapies are HCV NS5A inhibitors. It has previously been proposed that NS5A DAAs inhibit two functions of NS5A: RNA replication and virion assembly. In this study, we characterize the impact of a prototype NS5A DAA, daclatasvir (DCV), on HCV replication compartment formation. DCV impaired HCV replicase localization and NS5A motility. In order to characterize the mechanism behind altered HCV replicase localization, we examined the impact of DCV on the interaction of NS5A with its essential cellular cofactor, phosphatidylinositol-4-kinase III α (PI4KA). We observed that DCV does not inhibit PI4KA directly, nor does it impair early events of the NS5A-PI4KA interaction that can occur when NS5A is expressed alone. NS5A functions that are unaffected by DCV include PI4KA binding, as determined by co-immunoprecipitation, and a basal accumulation of the PI4KA product, PI4P. However, DCV impairs late steps in PI4KA activation that requires NS5A expressed in the context of the HCV polyprotein. These NS5A functions include hyper-stimulation of PI4P levels and appropriate replication compartment formation. The data are most consistent with a model wherein DCV inhibits conformational changes in the NS5A protein or protein complex formations that occur in the context of HCV polyprotein expression and stimulate PI4P hyper-accumulation and replication compartment formation. PMID:25546252

Imaging analysis of nuclear antiviral factors through direct detection of incoming adenovirus genome complexes.

PubMed

Komatsu, Tetsuro; Will, Hans; Nagata, Kyosuke; Wodrich, Harald

2016-04-22

Recent studies involving several viral systems have highlighted the importance of cellular intrinsic defense mechanisms through nuclear antiviral proteins that restrict viral propagation. These factors include among others components of PML nuclear bodies, the nuclear DNA sensor IFI16, and a potential restriction factor PHF13/SPOC1. For several nuclear replicating DNA viruses, it was shown that these factors sense and target viral genomes immediately upon nuclear import. In contrast to the anticipated view, we recently found that incoming adenoviral genomes are not targeted by PML nuclear bodies. Here we further explored cellular responses against adenoviral infection by focusing on specific conditions as well as additional nuclear antiviral factors. In line with our previous findings, we show that neither interferon treatment nor the use of specific isoforms of PML nuclear body components results in co-localization between incoming adenoviral genomes and the subnuclear domains. Furthermore, our imaging analyses indicated that neither IFI16 nor PHF13/SPOC1 are likely to target incoming adenoviral genomes. Thus our findings suggest that incoming adenoviral genomes may be able to escape from a large repertoire of nuclear antiviral mechanisms, providing a rationale for the efficient initiation of lytic replication cycle. Copyright © 2016 Elsevier Inc. All rights reserved.

Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic evidence for folate-pathway abnormalities.

PubMed

Naj, Adam C; Beecham, Gary W; Martin, Eden R; Gallins, Paul J; Powell, Eric H; Konidari, Ioanna; Whitehead, Patrice L; Cai, Guiqing; Haroutunian, Vahram; Scott, William K; Vance, Jeffery M; Slifer, Michael A; Gwirtsman, Harry E; Gilbert, John R; Haines, Jonathan L; Buxbaum, Joseph D; Pericak-Vance, Margaret A

2010-09-23

Genome-wide association studies (GWAS) of late-onset Alzheimer disease (LOAD) have consistently observed strong evidence of association with polymorphisms in APOE. However, until recently, variants at few other loci with statistically significant associations have replicated across studies. The present study combines data on 483,399 single nucleotide polymorphisms (SNPs) from a previously reported GWAS of 492 LOAD cases and 496 controls and from an independent set of 439 LOAD cases and 608 controls to strengthen power to identify novel genetic association signals. Associations exceeding the experiment-wide significance threshold (alpha=1.03x10(-7)) were replicated in an additional 1,338 cases and 2,003 controls. As expected, these analyses unequivocally confirmed APOE's risk effect (rs2075650, P=1.9x10(-36)). Additionally, the SNP rs11754661 at 151.2 Mb of chromosome 6q25.1 in the gene MTHFD1L (which encodes the methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like protein) was significantly associated with LOAD (P=4.70x10(-8); Bonferroni-corrected P=0.022). Subsequent genotyping of SNPs in high linkage disequilibrium (r2>0.8) with rs11754661 identified statistically significant associations in multiple SNPs (rs803424, P=0.016; rs2073067, P=0.03; rs2072064, P=0.035), reducing the likelihood of association due to genotyping error. In the replication case-control set, we observed an association of rs11754661 in the same direction as the previous association at P=0.002 (P=1.90x10(-10) in combined analysis of discovery and replication sets), with associations of similar statistical significance at several adjacent SNPs (rs17349743, P=0.005; rs803422, P=0.004). In summary, we observed and replicated a novel statistically significant association in MTHFD1L, a gene involved in the tetrahydrofolate synthesis pathway. This finding is noteworthy, as MTHFD1L may play a role in the generation of methionine from homocysteine and influence homocysteine-related pathways and as levels of homocysteine are a significant risk factor for LOAD development.

[Co-infections of HIV, syphilis and HSV-2 among men who have sex with men at the voluntary HIV counseling and testing clinics in Shanghai].

PubMed

Liu, Y; Tang, H F; Ning, Z; Zheng, H; He, N; Zhang, Y Y

2017-10-10

Objective: To understand the prevalence rates of HIV-syphilis and HIV-herpes simplex virus 2 (HSV-2) co-infections and related factors among men having sex with men (MSM) who had visited the voluntary HIV counseling and testing (VCT) clinics in Shanghai, China. Methods: 756 eligible MSM who attended the VCT clinics of Shanghai Municipality and Putuo district during March to August, 2015 were recruited to participate in a cross-sectional survey with questionnaire interview and blood testing for HIV, syphilis and HSV-2. Results: A total of 732 participants completed a valid questionnaire survey. The prevalence rates were 3.3 % (24/732) for HIV/Syphilis co-infection, 1.9 % (14/732) for HIV/HSV-2 co-infection, and 0.7 % (5/732) for HIV/Syphilis/HSV-2 co-infection, respectively. HIV prevalence appeared significantly higher among syphilis-infected participants (45.3 % , 24/53) than those without Syphilis (7.2 % , 61/679) (χ(2)=63.11, P <0.001), and was also significantly higher among HSV-2 infected participants (34.1 % , 14/41) than those without the HSV-2 infection (10.3 % , 71/691) (χ(2)=21.49, P <0.001). Results from the Multivariate regression analysis indicated that participants who were migrants ( OR =3.50, 95 %CI : 1.01-12.17), having had middle school or lower levels of education ( OR =4.46, 95 %CI : 1.54-12.87) or ever used illicit drugs ( OR =4.25, 95 %CI : 1.67-10.82, P =0.002) were under possible risks on HIV and Syphilis co-infection. Those participants who had high middle school or lower levels of education ( OR =6.87, 95 %CI : 1.86-25.42; OR =9.82, 95 %CI : 2.25-42.85) were under risk on HIV and HSV-2 co-infection. Conclusion: HIV/Syphilis and HIV/HSV-2 co-infection were seen among MSM who attended the VCT clinics in Shanghai that called for special attention, especially on migrants, those with low education or illicit drug users.

Action Mechanism of Chamaecyparis obtusa Oil on Hair Growth

PubMed Central

Park, Young-Ok; Kim, Su-Eun; Kim, Young-Chul

2013-01-01

This study was carried out to examine the action mechanism of Chamaecyparis obtusa oil (CO) on hair growth in C57BL/6 mice. For alkaline phosphatase (ALP) and γ-glutamyl transpeptidase (γ-GT) activities in the skin tissue, at week 4, the 3% minoxidil (MXD) and 3% CO treatment groups showed an ALP activity that was significantly higher by 85% (p < 0.001) and 48% (p < 0.05) and an γ-GT activity that was significantly higher by 294% (p < 0.01) and 254% (p < 0.05) respectively, as compared to the saline (SA) treatment group. For insulin-like growth factor-1 (IGF-1) mRNA expression in the skin tissue, at week 4, the MXD and CO groups showed a significantly higher expression by 204% (p < 0.05) and 426% (p < 0.01) respectively, as compared to the SA group. At week 4, vascular endothelial growth factor (VEGF) expression in the MXD and CO groups showed a significantly higher expression by 74% and 96% (p < 0.05) respectively, however, epidermal growth factor (EGF) expression in the MXD and CO groups showed a significantly lower expression by 66% and 61% (p < 0.05) respectively, as compared to the SA group. Stem cell factor (SCF) expression in the MXD and CO groups was observed by immunohistochemistry as significant in a part of the bulge around the hair follicle and in a part of the basal layer of the epidermis. Taking all the results together, on the basis of effects on ALP and γ-GT activity, and the expression of IGF-1, VEGF and SCF, which are related to the promotion of hair growth, it can be concluded that CO induced a proliferation and division of hair follicle cells and maintained the anagen phase. Because EGF expression was decreased significantly, CO could delay the transition to the catagen phase. PMID:24578794

Targeting Virus-host Interactions of HIV Replication.

PubMed

Weydert, Caroline; De Rijck, Jan; Christ, Frauke; Debyser, Zeger

2016-01-01

Cellular proteins that are hijacked by HIV in order to complete its replication cycle, form attractive new targets for antiretroviral therapy. In particular, the protein-protein interactions between these cellular proteins (cofactors) and viral proteins are of great interest to develop new therapies. Research efforts have led to the validation of different cofactors and some successes in therapeutic applications. Maraviroc, the first cofactor inhibitor approved for human medicinal use, provided a proof of concept. Furthermore, compounds developed as Integrase-LEDGF/p75 interaction inhibitors (LEDGINs) have advanced to early clinical trials. Other compounds targeting cofactors and cofactor-viral protein interactions are currently under development. Likewise, interactions between cellular restriction factors and their counteracting HIV protein might serve as interesting targets in order to impair HIV replication. In this respect, compounds targeting the Vif-APOBEC3G interaction have been described. In this review, we focus on compounds targeting the Integrase- LEDGF/p75 interaction, the Tat-P-TEFb interaction and the Vif-APOBEC3G interaction. Additionally we give an overview of currently discovered compounds presumably targeting cellular cofactor-HIV protein interactions.

Host iron redistribution as a risk factor for incident tuberculosis in HIV infection: an 11-year retrospective cohort study

PubMed Central

2013-01-01

Background Identifying people at higher risk of developing tuberculosis with human immunodeficiency virus (HIV) infection may improve clinical management of co-infections. Iron influences tuberculosis (TB) pathogenesis, but understanding the exact mechanisms of how and timing of when iron is involved remains challenging since biological samples are rarely available from the disease susceptibility period due to the difficulty in predicting in who and when, if ever, TB will develop. The objective of this research was to determine how host iron status measured at HIV diagnosis and genotypes related to host iron metabolism were associated with incident TB. Methods Archived clinical data, plasma and DNA were analyzed from 1139 adult participants in a large HIV-1, HIV-2 and dual seroprevalent cohort based at the Medical Research Council Laboratories in The Gambia. Incident pulmonary and/or extrapulmonary TB diagnoses a minimum of 28 days after HIV diagnosis were independently re-confirmed using available evidence (n=152). Multiple host iron status biomarkers, Haptoglobin and solute carrier family 11, member 1 (SLC11A1) genotypes were modeled to characterize how indicators of host iron metabolism were associated with TB susceptibility. Results Hemoglobin (incidence rate ratio, IRR=0.88, 95% CI=0.79-0.98), plasma transferrin (IRR=0.53, 0.33-0.84) and ferritin (IRR=1.26, 1.05-1.51) were significantly associated with TB after adjusting for TB susceptibility factors. While genotype associations were not statistically significant, SLC11A1 associations replicated similar directions as reported in HIV-seronegative meta-analyses. Conclusions Evidence of host iron redistribution at HIV diagnosis was associated with incident TB, and genetic influences on iron homeostasis may be involved. Low hemoglobin was associated with subsequent diagnosis of TB, but when considered in combination with additional iron status biomarkers, the collective findings point to a mechanism whereby anemia and iron redistribution are likely due to viral and/or bacteria-driven processes and the host immune response to infection. As a result, iron supplementation may not be efficacious or safe under these circumstances. Clinical and nutritional management of HIV and Mycobacterium tuberculosis co-infected individuals, especially in regions where food insecurity and malnutrition co-exist, may be further improved when the iron-related TB risk factors identified here are better understood and managed to favor host rather than pathogen outcomes. PMID:23360117

Expression profiling of colorectal cancer cells reveals inhibition of DNA replication licensing by extracellular calcium.

PubMed

Aggarwal, Abhishek; Schulz, Herbert; Manhardt, Teresa; Bilban, Martin; Thakker, Rajesh V; Kallay, Enikö

2017-06-01

Colorectal cancer is one of the most common cancers in industrialised societies. Epidemiological studies, animal experiments, and randomized clinical trials have shown that dietary factors can influence all stages of colorectal carcinogenesis, from initiation through promotion to progression. Calcium is one of the factors with a chemoprophylactic effect in colorectal cancer. The aim of this study was to understand the molecular mechanisms of the anti-tumorigenic effects of extracellular calcium ([Ca 2+ ] o ) in colon cancer cells. Gene expression microarray analysis of colon cancer cells treated for 1, 4, and 24h with 2mM [Ca 2+ ] o identified significant changes in expression of 1571 probe sets (ANOVA, p<10 -5 ). The main biological processes affected by [Ca 2+ ] o were DNA replication, cell division, and regulation of transcription. All factors involved in DNA replication-licensing were significantly downregulated by [Ca 2+ ] o . Furthermore, we show that the calcium-sensing receptor (CaSR), a G protein-coupled receptor is a mediator involved in this process. To test whether these results were physiologically relevant, we fed mice with a standard diet containing low (0.04%), intermediate (0.1%), or high (0.9%) levels of dietary calcium. The main molecules regulating replication licensing were inhibited also in vivo, in the colon of mice fed high calcium diet. We show that among the mechanisms behind the chemopreventive effect of [Ca 2+ ] o is inhibition of replication licensing, a process often deregulated in neoplastic transformation. Our data suggest that dietary calcium is effective in preventing replicative stress, one of the main drivers of cancer and this process is mediated by the calcium-sensing receptor. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Indexation of cardiac output to biometric parameters in critically ill patients: A systematic analysis of a transpulmonary thermodilution-derived database.

PubMed

Saugel, Bernd; Mair, Sebastian; Götz, Simon Q; Tschirdewahn, Julia; Frank, Johanna; Höllthaler, Josef; Schmid, Roland M; Huber, Wolfgang

2015-10-01

Cardiac output (CO) (liters per minute) is usually normalized (ie, indexed) to the patient's body surface area (BSA) resulting in the hemodynamic variable cardiac index (CI) (liters per minute per square meter). We aimed (1) to evaluate the impact of different body weight-based CO indexations on the resulting CI values and (2) to identify biometric parameters independently associated with CO in critically ill patients. The study is an analysis of a database containing transpulmonary thermodilution-derived hemodynamic variables of 234 medical intensive care unit patients. Cardiac index indexed to actual BSA was statistically significantly lower compared with CI indexed to predicted BSA in the totality of patients and in the subgroups of patients with body mass index greater than or equal to 25 kg/m(2) but less than 30 kg/m(2) and body mass index greater than or equal to 30 kg/m(2) (with a statistically significant difference in the proportion of low and high CI measurements). Multivariate analysis of the first CO measurement of each patient demonstrated that CO was independently associated with age (P < .001), height (P = .001), and actual body weight (BWact) (P = .030). Multivariate analysis of the mean of the patients' CO measurements confirmed age (P < .001), height (P = .001), and BWact (P < .001) as biometric factors independently associated with CO. Age was identified as the most important factor with each year of age decreasing CO by 66 mL/min (95% confidence interval, 47-86 mL/min). The indexation of CO to BSA is highly dependent on the body weight estimation formula used to calculate BSA. Cardiac output is independently associated with the biometric factors age, height, and BWact. These factors might be considered for indexation of CO. Copyright © 2015 Elsevier Inc. All rights reserved.

Selenium adsorption and speciation with Mg-FeCO₃ layered double hydroxides loaded cellulose fibre.

PubMed

Chen, Ming-Li; An, Myog-Il

2012-06-15

A novel adsorbent was developed by coating Mg-FeCO(3) layered double hydroxides (LDHs) on cellulose fibre. The LDHs take up significant amount of selenite and selenate in a wide pH range with similar sorption capacities (pH 3.8-8.0 for selenite and pH 5.8-7.0 for selenate). A mini-column packed with Mg-FeCO(3) LDHs layer coated cellulose fibre particles was incorporated into a sequential injection system for uptake of selenite at pH 6.0. The retained selenite was afterwards collected with 70 μ L of 0.8%(m/v) NaOH as eluent, followed by hydride generation and atomic fluorescence spectrometric detection. Total inorganic selenium was adsorbed at pH 6.0 by the LDHs-cellulose fibre mini-column after selenate was pre-reduced to selenite by 2.0 mol L(-1) HCl at 80°C, and selenium speciation was performed by difference. With a sample volume of 1.0 mL, an enrichment factor of 13.3 was derived with a detection limit of 11 ng L(-1) within a linear range of 0.04-4.0 μg L(-1). A relative standard deviation (RSD) of 3.3% (0.5 μg L(-1), n=11) was achieved. The procedure was validated by analyzing selenium in a certified reference material GBW 10010 (rice), and speciation of inorganic selenium in natural water samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Evaluation of photosynthetic efficacy and CO2 removal of microalgae grown in an enriched bicarbonate medium.

PubMed

Abinandan, S; Shanthakumar, S

2016-06-01

Bicarbonate species in the aqueous phase is the primary source for CO 2 for the growth of microalgae. The potential of carbon dioxide (CO 2 ) fixation by Chlorella pyrenoidosa in enriched bicarbonate medium was evaluated. In the present study, effects of parameters such as pH, sodium bicarbonate concentration and inoculum size were assessed for the removal of CO 2 by C. pyrenoidosa under mixotrophic condition. Central composite design tool from response surface methodology was used to validate statistical methods in order to study the influence of these parameters. The obtained results reveal that the maximum removal of CO 2 was attained at pH 8 with sodium bicarbonate concentration of 3.33 g/l, and inoculum size of 30 %. The experimental results were statistically significant with R 2 value of 0.9527 and 0.960 for CO 2 removal and accumulation of chlorophyll content, respectively. Among the various interactions, interactive effects between the parameters pH and inoculum size was statistically significant (P < 0.05) for CO 2 removal and chlorophyll accumulation. Based on the studies, the application of C. pyrenoidosa as a potential source for carbon dioxide removal at alkaline pH from bicarbonate source is highlighted.

α -unbound levels in 34Ar from 36Ar(p ,t )34Ar reaction measurements and implications for the astrophysical 30S(α ,p )33Cl reaction rate

NASA Astrophysics Data System (ADS)

Long, A. M.; Adachi, T.; Beard, M.; Berg, G. P. A.; Couder, M.; deBoer, R. J.; Dozono, M.; Görres, J.; Fujita, H.; Fujita, Y.; Hatanaka, K.; Ishikawa, D.; Kubo, T.; Matsubara, H.; Namiki, Y.; O'Brien, S.; Ohkuma, Y.; Okamura, H.; Ong, H. J.; Patel, D.; Sakemi, Y.; Shimbara, Y.; Suzuki, S.; Talwar, R.; Tamii, A.; Volya, A.; Wakasa, T.; Watanabe, R.; Wiescher, M.; Yamada, R.; Zenihiro, J.

2018-05-01

The 30S(α ,p )33Cl reaction has been identified in several type-1 x-ray burst (XRB) sensitivity studies as a significant reaction within the α p process, possibly influencing not only the abundances of burst ashes but also the bolometric shape of double-peaked light curves coming from certain XRB systems. Given the dearth of experimental data on the 30S(α ,p ) 33Cl reaction at burst temperatures, we have performed high energy-resolution forward-angle 36Ar(p ,t )34Ar measurements in order to identify levels in 34Ar that could appear as resonances in the 30S(α ,p )33Cl reaction. Energies of levels identified in this work, along with model-based assumptions for spin assignments and spectroscopic factors, were then used to determine a rate for the 30S(α ,p )33Cl reaction based on a narrow-resonance formalism. The rates determined in this work are then compared with two standard Hauser-Feshbach model predictions over a range of XRB temperatures.

P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance.

PubMed

Loll-Krippleber, Raphael; Brown, Grant W

2017-09-15

mRNA-processing (P-) bodies are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant downregulation of a network of genes critical for DNA replication stress resistance and leads to toxic acetaldehyde accumulation. Our data reveal the scope and the targets of regulation by P-body proteins during the DNA replication stress response.P-bodies form in response to stress and act as sites of mRNA storage and degradation. Here the authors identify the mRNA targets of P-bodies during DNA replication stress, and show that P-body proteins act to prevent toxic accumulation of these target transcripts.

Material-induced Senescence (MIS): Fluidity Induces Senescent Type Cell Death of Lung Cancer Cells via Insulin-Like Growth Factor Binding Protein 5.

PubMed

Mano, Sharmy Saimon; Uto, Koichiro; Ebara, Mitsuhiro

2017-01-01

Objective: We propose here material-induced senescence (MIS) as a new therapeutic concept that limits cancer progression by stable cell cycle arrest. This study examined for the first time the effect of material fluidity on cellular senescence in lung carcinoma using poly(ε-caprolactone- co -D, L-lactide) (P(CL- co -DLLA)) with tunable elasticity and fluidity. Methods: The fluidity was varied by chemically crosslinking the polymer networks: the crosslinked P(CL- co -DLLA) shows solid-like properties with a stiffness of 260 kPa, while the non-crosslinked polymer exists in a quasi-liquid state with loss and storage moduli of 33 kPa and 11 kPa, respectively. Results: We found that cancer cells growing on the non-crosslinked, fluidic substrate undergo a non-apoptotic form of cell death and the cell cycle was accumulated in a G0/G1 phase. Next, we investigated the expression of biomarkers that are associated with cancer pathways. The cancer cells on the fluidic substrate expressed several biomarkers associated with senescence such as insulin-like growth factor binding protein 5 (IGFBP5). This result indicates that when cancer cells sense fluidity in their surroundings, the cells express IGFBP5, which in turn triggers the expression of tumor suppressor protein 53 and initiates cell cycle arrest at the G1 phase followed by cellular senescence. Furthermore, the cancer cells on the fluidic substrate maintained their epithelial phenotype, suggesting that the cancer cells do not undergo epithelial to mesenchymal transition. Conclusion: By considering these results as the fundamental information for MIS, our system could be applied to induce senescence in treatment-resistant cancers such as metastatic cancer or cancer stem cells.

DNA Damage Signaling Is Induced in the Absence of Epstein-Barr Virus (EBV) Lytic DNA Replication and in Response to Expression of ZEBRA.

PubMed

Wang'ondu, Ruth; Teal, Stuart; Park, Richard; Heston, Lee; Delecluse, Henri; Miller, George

2015-01-01

Epstein Barr virus (EBV), like other oncogenic viruses, modulates the activity of cellular DNA damage responses (DDR) during its life cycle. Our aim was to characterize the role of early lytic proteins and viral lytic DNA replication in activation of DNA damage signaling during the EBV lytic cycle. Our data challenge the prevalent hypothesis that activation of DDR pathways during the EBV lytic cycle occurs solely in response to large amounts of exogenous double stranded DNA products generated during lytic viral DNA replication. In immunofluorescence or immunoblot assays, DDR activation markers, specifically phosphorylated ATM (pATM), H2AX (γH2AX), or 53BP1 (p53BP1), were induced in the presence or absence of viral DNA amplification or replication compartments during the EBV lytic cycle. In assays with an ATM inhibitor and DNA damaging reagents in Burkitt lymphoma cell lines, γH2AX induction was necessary for optimal expression of early EBV genes, but not sufficient for lytic reactivation. Studies in lytically reactivated EBV-positive cells in which early EBV proteins, BGLF4, BGLF5, or BALF2, were not expressed showed that these proteins were not necessary for DDR activation during the EBV lytic cycle. Expression of ZEBRA, a viral protein that is necessary for EBV entry into the lytic phase, induced pATM foci and γH2AX independent of other EBV gene products. ZEBRA mutants deficient in DNA binding, Z(R183E) and Z(S186E), did not induce foci of pATM. ZEBRA co-localized with HP1β, a heterochromatin associated protein involved in DNA damage signaling. We propose a model of DDR activation during the EBV lytic cycle in which ZEBRA induces ATM kinase phosphorylation, in a DNA binding dependent manner, to modulate gene expression. ATM and H2AX phosphorylation induced prior to EBV replication may be critical for creating a microenvironment of viral and cellular gene expression that enables lytic cycle progression.

Class I ADP-Ribosylation Factors Are Involved in Enterovirus 71 Replication

PubMed Central

Wang, Jianmin; Du, Jiang; Jin, Qi

2014-01-01

Enterovirus 71 is one of the major causative agents of hand, foot, and mouth disease in infants and children. Replication of enterovirus 71 depends on host cellular factors. The viral replication complex is formed in novel, cytoplasmic, vesicular compartments. It has not been elucidated which cellular pathways are hijacked by the virus to create these vesicles. Here, we investigated whether proteins associated with the cellular secretory pathway were involved in enterovirus 71 replication. We used a loss-of-function assay, based on small interfering RNA. We showed that enterovirus 71 RNA replication was dependent on the activity of Class I ADP-ribosylation factors. Simultaneous depletion of ADP-ribosylation factors 1 and 3, but not three others, inhibited viral replication in cells. We also demonstrated with various techniques that the brefeldin-A-sensitive guanidine nucleotide exchange factor, GBF1, was critically important for enterovirus 71 replication. Our results suggested that enterovirus 71 replication depended on GBF1-mediated activation of Class I ADP-ribosylation factors. These results revealed a connection between enterovirus 71 replication and the cellular secretory pathway; this pathway may represent a novel target for antiviral therapies. PMID:24911624

Reproductive outcomes after multiagent chemotherapy for high-risk gestational trophoblastic neoplasia.

PubMed

Wong, Jacqueline M K; Liu, Dachao; Lurain, John R

2014-01-01

To analyze the reproductive outcomes of women with high-risk gestational trophoblastic neoplasia (GTN) treated with multiagent EMA-CO chemotherapy. Of 212 patients treated with chemotherapy for GTN between 1986 and 2012, 65 (31%) could be contacted by telephone or mail and consented to participate in a questionnaire designed to assess their menstrual and reproduction outcomes. Twenty-four high-risk (HR) and 41 low-risk (LR) patients consented to the study. Fifteen (63%) HR and 34 (83%) LR women had not undergone hysterectomy (p = 0.08). Of the 12 HR and 33 LR women who could recall their menstrual history, all 12 (100%) HR and 32 (97%) LR women resumed menses after chemotherapy. Both groups also had a similar age of menopause (HR, 43.8 years; LR, 48.5 years) (p = 0.19). Although fewer women in the HR group desired to become pregnant after chemotherapy (HR 5/15 [33%] vs. LR 25/34 [74%]) (p = 0.01), 8 HR women (53%) and 29 LR women (85%) eventually became pregnant (p = 0.03), with equivalent live birth rates of 74% and 76%, respectively. Multiagent EMA-CO chemotherapy did not significantly alter menstrual or reproductive outcomes compared to single-agent methotrexate chemotherapy for GTN.

True and standardized total tract phosphorus digestibility in canola meals from Brassica napus black and Brassica juncea yellow fed to growing pigs.

PubMed

Adhikari, P A; Heo, J M; Nyachoti, C M

2015-01-01

The aim was to determine the true total tract digestibility (TTTD) and standardized total tract digestibility (STTD) of P in canola meals from Brassica napus black (BNB) and Brassica juncea yellow (BJY) fed to growing pigs. Fifty-four barrows with an initial BW of 19.9 ± 0.22 kg (mean ± SEM) were allocated in 3 consecutive blocks to 1 of 9 dietary treatments in a randomized complete block design to give 6 replicate pigs per diet. Dietary treatments were cornstarch based with increasing concentrations of P, that is, 0.8, 1.6, 2.4, and 3.3 g/kg (as-fed basis) from either BNB or BJY as the sole source of P and a gelatin-based P-free diet. Limestone was added to maintain a Ca:total P ratio of 1.2:1 in all diets. All diets contained titanium dioxide (3 g/kg) as an indigestible marker. Daily feed allowance was calculated to supply 2.6 times the maintenance energy requirement based on the BW at the beginning of each period and offered in 2 equal portions at 0800 and 1600 h as a dry mash. Pigs were individually housed in metabolism crates and fed experimental diets for 16 d, including 9 d for adaptation to feed and 5 d for total but separate collection of feces and urine. The apparent total tract digestibility values of P increased from 19.0 to 30.0% for BNB and from 17.3 to 28.3% for BJY as the dietary P content increased from 0.8 to 3.3 g/kg DM. The TTTD of P was determined using the regression analysis as dietary P content increased from 0.8 to 3.3 g/kg whereas the STTD of P was calculated for the diet with the highest P content (i.e., 3.3 g/kg, as-fed basis) using the P-free diet to estimate endogenous P losses (EPL). The total and basal EPL estimates obtained with regression analysis and the P-free diet were 665 ± 0.03 and 209 ± 96 mg/kg DMI, respectively. The TTTD of P was 33.3 and 32.0% in BNB and BJY, respectively. Respective STTD values were 31.0 and 28.3%. The results indicated that the TTTD and STTD of P were comparable in the 2 canola meals from BNB and BJY canola.

An Empirical Comparison of Competing Factor Structures for the Repeatable Battery for the Assessment of Neuropsychological Status: A Project FRONTIER Study†

PubMed Central

Torrence, Nicole D.; John, Samantha E.; Gavett, Brandon E.; O'Bryant, Sid E.

2016-01-01

The original factor structure of the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) has received little empirical support, but at least eight alternative factor structures have been identified in the literature. The current study used confirmatory factor analysis to compare the original RBANS model with eight alternatives, which were adjusted to include a general factor. Participant data were obtained from Project FRONTIER, an epidemiological study of rural health, and comprised 341 adults (229 women, 112 men) with mean age of 61.2 years (SD = 12.1) and mean education of 12.4 years (SD = 3.3). A bifactor version of the model proposed by Duff and colleagues provided the best fit to the data (CFI = 0.98; root-mean-squared error of approximation = 0.07), but required further modification to produce appropriate factor loadings. The results support the inclusion of a general factor and provide partial replication of the Duff and colleagues RBANS model. PMID:26429558

Mutagenesis of Dengue Virus Protein NS2A Revealed a Novel Domain Responsible for Virus-Induced Cytopathic Effect and Interactions between NS2A and NS2B Transmembrane Segments.

PubMed

Wu, Ren-Huang; Tsai, Ming-Han; Tsai, Kuen-Nan; Tian, Jia Ni; Wu, Jian-Sung; Wu, Su-Ying; Chern, Jyh-Haur; Chen, Chun-Hong; Yueh, Andrew

2017-06-15

The NS2A protein of dengue virus (DENV) has eight predicted transmembrane segments (pTMS1 to -8) and participates in RNA replication, virion assembly, and host antiviral response. However, the roles of specific amino acid residues within the pTMS regions of NS2A during the viral life cycle are not clear. Here, we explore the function of DENV NS2A by introducing a series of alanine substitutions into the N-terminal half (pTMS1 to -4) of the protein in the context of a DENV infectious clone or subgenomic replicon. Six NS2A mutants (NM5, -7, -9, and -17 to -19) around pTMS1 and -2 displayed a novel phenotype showing a >1,000-fold reduction in virus yield, an absence of plaque formation despite wild-type-like replicon activity, and infectious-virus-like particle yields. HEK-293 cells infected with the six NS2A mutant viruses failed to cause a virus-induced cytopathic effect (CPE) by MitoCapture staining, cell proliferation, and lactate dehydrogenase release assays. Sequencing analyses of pseudorevertant viruses derived from lethal-mutant viruses revealed two consensus reversion mutations, leucine to phenylalanine at codon 181 (L181F) within pTMS7 of NS2A and isoleucine to threonine at codon 114 (I114T) within NS2B. The introduction of an NS2A-L181F mutation into the lethal (NM15, -16, -25, and -33) and CPE-defective (NM7, -9, and -19) mutants substantially rescued virus infectivity and virus-induced CPE, respectively, whereas the NS2B-L114T mutation rescued the NM16, -25, and -33 mutants. In conclusion, the results revealed the essential roles of the N-terminal half of NS2A in RNA replication and virus-induced CPE. Intramolecular interactions between pTMSs of NS2A and intermolecular interactions between the NS2A and NS2B proteins were also implicated. IMPORTANCE The characterization of the N-terminal (current study) and C-terminal halves of DENV NS2A is the most comprehensive mutagenesis study to date to investigate the function of NS2A during the flaviviral life cycle. A novel region responsible for virus-induced cytopathic effect (CPE) within pTMS1 and -2 of DENV NS2A was identified. Revertant genetics studies implied unexpected relationships between various pTMSs of DENV NS2A and NS2B. These results provide comprehensive information regarding the functions of DENV NS2A and the specific amino acids and transmembrane segments responsible for these functions. The positions and properties of the rescuing mutations were also revealed, providing important clues regarding the manner in which intramolecular or intermolecular interactions between the pTMSs of NS2A and NS2B regulate virus replication, assembly/secretion, and virus-induced CPE. These results expand the understanding of flavivirus replication. The knowledge may also facilitate studies of pathogenesis and novel vaccine and antiflaviviral drug development. Copyright © 2017 American Society for Microbiology.

Rapid Communication: Effect of machine, anatomical location, and replication on instrumental color of boneless pork loins.

PubMed

Barkley, K E; Fields, B; Dilger, A C; Boler, D D

2018-06-07

The objective was to determine the effect of machine, anatomical location and replication (multiple readings) on instrumental color and to characterize the amount of variation each factor contributed to overall color. Instrumental color was measured 3 times on the anterior and 3 times on the posterior end of 250 pork loins with 2 different Minolta CR-400 Chroma meter devices. Each Minolta was programed to use a D65 illuminant, 2º observer with an 8 mm aperture, and calibrated with white tiles specific to each machine. Therefore, a total of 12 instrumental color measurements were collected on each loin. The VARCOMP procedure in SAS was used to estimate the proportion of variation contributed by each factor to CIE L*, a*, b*, chroma and hue. Based on previous research, the average untrained consumer is able to distinguish between 3-L* units, 0.4-a* units, and 0.9-hue angle units. Loins evaluated with machine 1 were 0.71 L* units darker (P < 0.01), 1.09 b* units more yellow (P < 0.01), 0.47 chroma units more saturated (P < 0.01), and had a hue angle 5.12 units greater (P < 0.01) than when evaluated with machine 2 but did not differ (P = 0.24) in redness. The anterior portion of the loin was lighter, less red, more yellow, more saturated and had a greater hue angle than the posterior end (P < 0.01). All color trait values decreased (P < 0.01) as replication number increased. Inherent color differences among loins contributed the greatest proportion of variability for lightness (58%), redness (57%), yellowness (70%), saturation (70%) and hue angle (49%). Machine contributed 1% variability to lightness 3% to saturation, 23% to yellowness and 31% to hue angle (31%) but did not contribute to variability for redness. Anatomical location contributed 41% to lightness, 43% to redness, 7% to yellowness, 27% to saturation and 31% to hue angle. Replication did not contribute to total variation for any color traits, even though it did differ among measurements. Overall, there were differences in instrumental color values between the two machines tested but those differences were likely less than the threshold for detection by a consumer. Even so, inherent color differences between loins were a greater contributor to total variability than the differences between the 2 machines. Therefore, it is more important to define the location of measurements than replication or machine when using a Minolta CR-400 when performing color evaluations, assuming the settings are the same.

Virus-encoded miRNAs in Ebola virus disease.

PubMed

Duy, Janice; Honko, Anna N; Altamura, Louis A; Bixler, Sandra L; Wollen-Roberts, Suzanne; Wauquier, Nadia; O'Hearn, Aileen; Mucker, Eric M; Johnson, Joshua C; Shamblin, Joshua D; Zelko, Justine; Botto, Miriam A; Bangura, James; Coomber, Moinya; Pitt, M Louise; Gonzalez, Jean-Paul; Schoepp, Randal J; Goff, Arthur J; Minogue, Timothy D

2018-04-24

Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.

Genome-Wide Association Study Identifies Single Nucleotide Polymorphism in DYRK1A Associated with Replication of HIV-1 in Monocyte-Derived Macrophages

PubMed Central

Bol, Sebastiaan M.; Moerland, Perry D.; Limou, Sophie; van Remmerden, Yvonne; Coulonges, Cédric; van Manen, Daniëlle; Herbeck, Joshua T.; Fellay, Jacques; Sieberer, Margit; Sietzema, Jantine G.; van 't Slot, Ruben; Martinson, Jeremy; Zagury, Jean-François; Schuitemaker, Hanneke; van 't Wout, Angélique B.

2011-01-01

Background HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART), macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages. Methodology/Principal Findings Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96) or high (n = 96) p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.16×10−5). While the association was not genome-wide significant (p<1×10−7), we could replicate this association using monocyte-derived macrophages from an independent group of 31 individuals (p = 0.0034). Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.84×10−6). In addition, we found this SNP to be associated with HIV-1 disease progression in vivo in two independent cohort studies (p = 0.035 and p = 0.0048). Conclusions/Significance These findings suggest that the kinase DYRK1A is involved in the replication of HIV-1, in vitro in macrophages as well as in vivo. PMID:21364930

Physico-chemical factors influencing spore germination in cyanobacterium Fischerella muscicola.

PubMed

Mishra, Biranchi N; Kaushik, Manish S; Abraham, Gerard; Singh, Pawan K

2018-06-19

Spore (akinete) formation in the heterocystous and branched filamentous cyanobacterium Fischerella muscicola involves a significant increase in cell size and formation of several endospores in each of the cells. In present study, the physico-chemical factors (pH, light sources, nutrient deficiency, nitrogen sources, carbon sources, and growth hormones) affecting the germination of spores of F. muscicola were examined. Increase in spore germination frequency was detected above pH 8 with maximum germination (46.04%) recorded at pH 9, whereas a significant decrease in germination was observed at pH 6 when compared to control (pH 7.6). Spore germination was not observed at pH 5. Among light sources germination frequency followed the following order, that is, red light (39.9%) > white light (33.8%) > yellow light (3.4%) > green light (1.3%) whereas germination did not take place in dark and blue light. Ammonium chloride (NH 4 Cl) supported maximum (99.5%) germination frequency followed by calcium nitrate (Ca(NO 3 ) 2 ), potassium nitrate (KNO 3 ), and minimum germination was observed in urea. Nutrient (phosphorus, calcium, and magnesium) deficiency significantly enhanced the germination frequency with maximum increase in magnesium (Mg) deficient condition. Further, supplementation of carbon sources (glucose, fructose, and sodium acetate) and growth hormones (IAA and GA) also enhanced the germination frequency in this cyanobacterium. Therefore, it may be concluded that, those factors supporting higher germination frequency could be considered for successful production and use of this cyanobacterium in biofertilizer and other algal production technologies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of miR-33a-5P on ABCA1/G1-Mediated Cholesterol Efflux under Inflammatory Stress in THP-1 Macrophages

PubMed Central

Mao, Min; Lei, Han; Liu, Qing; Chen, Yaxi; Zhao, Lei; Li, Qing; Luo, Suxin; Zuo, Zhong; He, Quan; Huang, Wei; Zhang, Nan; Zhou, Chao; Ruan, Xiong Z.

2014-01-01

The present study is to investigate whether inflammatory cytokines inhibit ABCA1/ABCG1-mediated cholesterol efflux by regulating miR-33a-5P in THP-1 macrophages. We used interleukin-6 and tumor necrosis factor-alpha in the presence or absence of native low density lipoprotein (LDL) to stimulate THP-1 macrophages. THP-1 macrophages were infected by either control lentivirus vectors or lentivirus encoding miR-33a-5P or antisense miR-33a-5P. The effects of inflammatory cytokines, miR-33a-5P and antisense miR-33a-5P on intracellular lipids accumulation and intracellular cholesterol contents were assessed by oil red O staining and quantitative intracellular cholesterol assay. ApoA-I-mediated cholesterol efflux was examined using the fluorescent sterol (BODIPY-cholesterol). The gene and protein expressions of the molecules involved in cholesterol trafficking were examined using quantitative real-time polymerase chain reaction and Western blotting. Inflammatory cytokines or miR-33a-5P increased intracellular lipid accumulation and decreased apoA-I-mediated cholesterol efflux via decreasing the expression of ABCA1 and ABCG1 in the absence or presence of LDL in THP-1 macrophages. However, antisense miR-33a-5P reversed the effects of inflammatory cytokines on intracellular lipid accumulation, cholesterol efflux, and the expression of miR-33a-5P, ABCA1 and ABCG1 in the absence or presence of LDL in THP-1 macrophages. This study indicated that inflammatory cytokines inhibited ABCA1/ABCG1-mediated cholesterol efflux by up-regulating miR-33a-5P in THP-1 macrophages. PMID:25329888

Effects of miR-33a-5P on ABCA1/G1-mediated cholesterol efflux under inflammatory stress in THP-1 macrophages.

PubMed

Mao, Min; Lei, Han; Liu, Qing; Chen, Yaxi; Zhao, Lei; Li, Qing; Luo, Suxin; Zuo, Zhong; He, Quan; Huang, Wei; Zhang, Nan; Zhou, Chao; Ruan, Xiong Z

2014-01-01

The present study is to investigate whether inflammatory cytokines inhibit ABCA1/ABCG1-mediated cholesterol efflux by regulating miR-33a-5P in THP-1 macrophages. We used interleukin-6 and tumor necrosis factor-alpha in the presence or absence of native low density lipoprotein (LDL) to stimulate THP-1 macrophages. THP-1 macrophages were infected by either control lentivirus vectors or lentivirus encoding miR-33a-5P or antisense miR-33a-5P. The effects of inflammatory cytokines, miR-33a-5P and antisense miR-33a-5P on intracellular lipids accumulation and intracellular cholesterol contents were assessed by oil red O staining and quantitative intracellular cholesterol assay. ApoA-I-mediated cholesterol efflux was examined using the fluorescent sterol (BODIPY-cholesterol). The gene and protein expressions of the molecules involved in cholesterol trafficking were examined using quantitative real-time polymerase chain reaction and Western blotting. Inflammatory cytokines or miR-33a-5P increased intracellular lipid accumulation and decreased apoA-I-mediated cholesterol efflux via decreasing the expression of ABCA1 and ABCG1 in the absence or presence of LDL in THP-1 macrophages. However, antisense miR-33a-5P reversed the effects of inflammatory cytokines on intracellular lipid accumulation, cholesterol efflux, and the expression of miR-33a-5P, ABCA1 and ABCG1 in the absence or presence of LDL in THP-1 macrophages. This study indicated that inflammatory cytokines inhibited ABCA1/ABCG1-mediated cholesterol efflux by up-regulating miR-33a-5P in THP-1 macrophages.

Metalloporphyrin Co(III)TMPyP ameliorates acute, sublethal cyanide toxicity in mice.

PubMed

Benz, Oscar S; Yuan, Quan; Amoscato, Andrew A; Pearce, Linda L; Peterson, Jim

2012-12-17

The formation of Co(III)TMPyP(CN)(2) at pH 7.4 has been shown to be completely cooperative (α(H) = 2) with an association constant of 2.1 (±0.2) × 10(11). The kinetics were investigated by stopped-flow spectrophotometry and revealed a complicated net reaction exhibiting 4 phases at pH 7.4 under conditions where cyanide was in excess. The data suggest molecular HCN (rather than CN(-)) to be the attacking nucleophile around neutrality. The two slower phases do not seem to be present when cyanide is not in excess, and the other two phases have rates comparable to that observed for cobalamin, a known effective cyanide scavenger. Addition of bovine serum albumin (BSA) did not affect the cooperativity of cyanide binding to Co(III)TMPyP, only lowered the equilibrium constant slightly to 1.2 (±0.2) × 10(11) and had an insignificant effect on the observed rate. A sublethal mouse model was used to assess the effectiveness of Co(III)TMPyP as a potential cyanide antidote. The administration of Co(III)TMPyP to sodium cyanide intoxicated mice resulted in the time required for the surviving mice to right themselves from a supine position being significantly decreased (9 ± 2 min) compared to that of the controls (33 ± 2 min). All observations were consistent with the demonstrated antidotal activity of Co(III)TMPyP operating through a cyanide-binding (i.e., scavenging) mechanism.

A novel host factor for integration of mycobacteriophage L5

PubMed Central

Pedulla, Marisa L.; Lee, Mong Hong; Lever, Dawn C.; Hatfull, Graham F.

1996-01-01

Bacterial integration host factors (IHFs) play central roles in the cellular processes of recombination, DNA replication, transcription, and bacterial pathogenesis. We describe here a novel mycobacterial IHF (mIHF) of Mycobacterium smegmatis and Mycobacterium tuberculosis that stimulates integration of mycobacteriophage L5. mIHF is the product of a single gene and is unrelated at the sequence level to other integration host factors. By itself, mIHF does not bind preferentially to attP DNA, although it significantly alters the pattern of integrase (Int) binding, promoting the formation of specific integrase–mIHF–attP intasome complexes. PMID:8986825

Nonlinear, interacting responses to climate limit grassland production under global change.

PubMed

Zhu, Kai; Chiariello, Nona R; Tobeck, Todd; Fukami, Tadashi; Field, Christopher B

2016-09-20

Global changes in climate, atmospheric composition, and pollutants are altering ecosystems and the goods and services they provide. Among approaches for predicting ecosystem responses, long-term observations and manipulative experiments can be powerful approaches for resolving single-factor and interactive effects of global changes on key metrics such as net primary production (NPP). Here we combine both approaches, developing multidimensional response surfaces for NPP based on the longest-running, best-replicated, most-multifactor global-change experiment at the ecosystem scale-a 17-y study of California grassland exposed to full-factorial warming, added precipitation, elevated CO2, and nitrogen deposition. Single-factor and interactive effects were not time-dependent, enabling us to analyze each year as a separate realization of the experiment and extract NPP as a continuous function of global-change factors. We found a ridge-shaped response surface in which NPP is humped (unimodal) in response to temperature and precipitation when CO2 and nitrogen are ambient, with peak NPP rising under elevated CO2 or nitrogen but also shifting to lower temperatures. Our results suggest that future climate change will push this ecosystem away from conditions that maximize NPP, but with large year-to-year variability.

Does long-term elevation of CO{sub 2} concentration increase photosynthesis in forest floor vegetation? Indiana strawberry in a Maryland forest

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osborne, C.P.; Long, S.P.; Drake, B.G.

1997-05-01

As the partial pressure of CO{sub 2} (pCO{sub 2}) in the atmosphere rises, photorespiratory loss of carbon in C, photosynthesis will diminish and the net efficiency of light-limited photosynthetic carbon uptake should rise. Indiana strawberry (Duchesnea indica) growing on a Maryland forest floor was tested. Open-top chambers were used to elevate the pCO{sub 2} of a forest floor habitat to 67 Pa and were paired with control chambers with an ambient pCO{sub 2} of 38 Pa. After 3.5 years, D. indica leaves in the elevated pCO{sub 2} showed a significantly greater maximum quantum efficiency of net photosynthesis (by 22%) andmore » a lower light compensation point (by 42%) than leaves in the control chambers. The quantum efficiency to minimize photorespiration was the same for controls and plants grown at elevated pCO{sub 2}, showing the maximum efficiency of light-energy transduction into assimilated carbon was not altered by acclimation and the increase in light-limited photosynthesis at elevated pCO{sub 2} was a function of the decrease in photorespiration. Acclimation did decrease the ribulose-1,5-bisphosphate carboxylase/oxygenase and light-harvesting chlorophyll protein content of the leaf by more than 30%. These changes were associated with a decreased capacity for light-saturated, but not light-limited, photosynthesis. Leaves of D. indica grown and measured at elevated pCO{sub 2} showed greater light-saturated photosynthetic rates than leaves grown and measured at the current atmospheric pCO{sub 2}. In situ measurements under natural lighting showed large increases in leaf photosynthesis at elevated pCO{sub 2}, relative to controls, in both summer and fall. The increase in efficiency of light-limited photosynthesis with elevated pCO{sub 2} allowed positive net photosynthetic carbon uptake on days and at locations on the forest floor that light fluxes were insufficient for positive net photosynthesis in the current atmospheric pCO{sub 2}. 33 refs., 3 figs., 3 tabs.« less

Neutrality of the canonical NF-kappaB-dependent pathway for human and murine cytomegalovirus transcription and replication in vitro.

PubMed

Benedict, Chris A; Angulo, Ana; Patterson, Ginelle; Ha, Sukwon; Huang, Huang; Messerle, Martin; Ware, Carl F; Ghazal, Peter

2004-01-01

Cytomegalovirus (CMV) is known to rapidly induce activation of nuclear factor kappaB (NF-kappaB) after infection of fibroblast and macrophage cells. NF-kappaB response elements are present in the enhancer region of the CMV major immediate-early promoter (MIEP), and activity of the MIEP is strongly upregulated by NF-kappaB in transient-transfection assays. Here we investigate whether the NF-kappaB-dependent pathway is required for initiating or potentiating human and murine CMV replication in vitro. We show that expression of a dominant negative mutant of the inhibitor of NF-kappaB-alpha (IkappaBalphaM) does not alter the replication kinetics of human or mouse CMV in cultured cells. In addition, mouse embryo fibroblasts genetically deficient for p65/RelA actually showed elevated levels of MCMV replication. Mutation of all NF-kappaB response elements within the enhancer of the MIEP in a recombinant mouse CMV containing the human MIEP (hMCMV-ES), which we have previously shown to replicate in murine fibroblasts with kinetics equivalent to that of wild-type mouse CMV, did not negatively affect replication in fibroblasts. Taken together, these data show that, for CMV replication in cultured fibroblasts activation of the canonical NF-kappaB pathway and binding of NF-kappaB to the MIEP are dispensable, and in the case of p65 may even interfere, thus uncovering a previously unrecognized level of complexity in the host regulatory network governing MIE gene expression in the context of a viral infection.

Severe acute respiratory syndrome vaccine efficacy in ferrets: whole killed virus and adenovirus-vectored vaccines.

PubMed

See, Raymond H; Petric, Martin; Lawrence, David J; Mok, Catherine P Y; Rowe, Thomas; Zitzow, Lois A; Karunakaran, Karuna P; Voss, Thomas G; Brunham, Robert C; Gauldie, Jack; Finlay, B Brett; Roper, Rachel L

2008-09-01

Although the 2003 severe acute respiratory syndrome (SARS) outbreak was controlled, repeated transmission of SARS coronavirus (CoV) over several years makes the development of a SARS vaccine desirable. We performed a comparative evaluation of two SARS vaccines for their ability to protect against live SARS-CoV intranasal challenge in ferrets. Both the whole killed SARS-CoV vaccine (with and without alum) and adenovirus-based vectors encoding the nucleocapsid (N) and spike (S) protein induced neutralizing antibody responses and reduced viral replication and shedding in the upper respiratory tract and progression of virus to the lower respiratory tract. The vaccines also diminished haemorrhage in the thymus and reduced the severity and extent of pneumonia and damage to lung epithelium. However, despite high neutralizing antibody titres, protection was incomplete for all vaccine preparations and administration routes. Our data suggest that a combination of vaccine strategies may be required for effective protection from this pathogen. The ferret may be a good model for SARS-CoV infection because it is the only model that replicates the fever seen in human patients, as well as replicating other SARS disease features including infection by the respiratory route, clinical signs, viral replication in upper and lower respiratory tract and lung damage.