Lysine acetylation stoichiometry and proteomics analyses reveal pathways regulated by sirtuin 1 in human cells.

PubMed

Gil, Jeovanis; Ramírez-Torres, Alberto; Chiappe, Diego; Luna-Peñaloza, Juan; Fernandez-Reyes, Francis C; Arcos-Encarnación, Bolivar; Contreras, Sandra; Encarnación-Guevara, Sergio

2017-11-03

Lysine acetylation is a widespread posttranslational modification affecting many biological pathways. Recent studies indicate that acetylated lysine residues mainly exhibit low acetylation occupancy, but challenges in sample preparation and analysis make it difficult to confidently assign these numbers, limiting understanding of their biological significance. Here, we tested three common sample preparation methods to determine their suitability for assessing acetylation stoichiometry in three human cell lines, identifying the acetylation occupancy in more than 1,300 proteins from each cell line. The stoichiometric analysis in combination with quantitative proteomics also enabled us to explore their functional roles. We found that higher abundance of the deacetylase sirtuin 1 (SIRT1) correlated with lower acetylation occupancy and lower levels of ribosomal proteins, including those involved in ribosome biogenesis and rRNA processing. Treatment with the SIRT1 inhibitor EX-527 confirmed SIRT1's role in the regulation of pre-rRNA synthesis and processing. Specifically, proteins involved in pre-rRNA transcription, including subunits of the polymerase I and SL1 complexes and the RNA polymerase I-specific transcription initiation factor RRN3, were up-regulated after SIRT1 inhibition. Moreover, many protein effectors and regulators of pre-rRNA processing needed for rRNA maturation were also up-regulated after EX-527 treatment with the outcome that pre-rRNA and 28S rRNA levels also increased. More generally, we found that SIRT1 inhibition down-regulates metabolic pathways, including glycolysis and pyruvate metabolism. Together, these results provide the largest data set thus far of lysine acetylation stoichiometry (available via ProteomeXchange with identifier PXD005903) and set the stage for further biological investigations of this central posttranslational modification. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Splicing Factor 2-Associated Protein p32 Participates in Ribosome Biogenesis by Regulating the Binding of Nop52 and Fibrillarin to Preribosome Particles*

PubMed Central

Yoshikawa, Harunori; Komatsu, Wataru; Hayano, Toshiya; Miura, Yutaka; Homma, Keiichi; Izumikawa, Keiichi; Ishikawa, Hideaki; Miyazawa, Naoki; Tachikawa, Hiroyuki; Yamauchi, Yoshio; Isobe, Toshiaki; Takahashi, Nobuhiro

2011-01-01

Ribosome biogenesis starts with transcription of the large ribosomal RNA precursor (47S pre-rRNA), which soon combines with numerous factors to form the 90S pre-ribosome in the nucleolus. Although the subsequent separation of the pre-90S particle into pre-40S and pre-60S particles is critical for the production process of mature small and large ribosomal subunits, its molecular mechanisms remain undetermined. Here, we present evidence that p32, fibrillarin (FBL), and Nop52 play key roles in this separation step. Mass-based analyses combined with immunoblotting showed that p32 associated with 155 proteins including 31 rRNA-processing factors (of which nine were components of small subunit processome, and six were those of RIX1 complex), 13 chromatin remodeling components, and six general transcription factors required for RNA polymerase III-mediated transcription. Of these, a late rRNA-processing factor Nop52 interacted directly with p32. Immunocytochemical analyses demonstrated that p32 colocalized with an early rRNA-processing factor FBL or Nop52 in the nucleolus and Cajal bodies, but was excluded from the nucleolus after actinomycin D treatment. p32 was present in the pre-ribosomal fractions prepared by cell fractionation or separated by ultracentrifugation of the nuclear extract. p32 also associated with pre-rRNAs including 47S/45S and 32S pre-rRNAs. Furthermore, knockdown of p32 with a small interfering RNA slowed the early processing from 47S/45S pre-rRNAs to 18S rRNA and 32S pre-rRNA. Finally, Nop52 was found to compete with FBL for binding to p32 probably in the nucleolus. Given the fact that FBL and Nop52 are associated with pre-ribosome particles distinctly different from each other, we suggest that p32 is a new rRNA maturation factor involved in the remodeling from pre-90S particles to pre-40S and pre-60S particles that requires the exchange of FBL for Nop52. PMID:21536856

Aggregation of Ribosomal Protein S6 at Nucleolus Is Cell Cycle-Controlled and Its Function in Pre-rRNA Processing Is Phosphorylation Dependent.

PubMed

Zhang, Duo; Chen, Hui-Peng; Duan, Hai-Feng; Gao, Li-Hua; Shao, Yong; Chen, Ke-Yan; Wang, You-Liang; Lan, Feng-Hua; Hu, Xian-Wen

2016-07-01

Ribosomal protein S6 (rpS6) has long been regarded as one of the primary r-proteins that functions in the early stage of 40S subunit assembly, but its actual role is still obscure. The correct forming of 18S rRNA is a key step in the nuclear synthesis of 40S subunit. In this study, we demonstrate that rpS6 participates in the processing of 30S pre-rRNA to 18S rRNA only when its C-terminal five serines are phosphorylated, however, the process of entering the nucleus and then targeting the nucleolus does not dependent its phosphorylation. Remarkably, we also find that the aggregation of rpS6 at the nucleolus correlates to the phasing of cell cycle, beginning to concentrate in the nucleolus at later S phase and disaggregate at M phase. J. Cell. Biochem. 117: 1649-1657, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Lack of WDR36 leads to preimplantation embryonic lethality in mice and delays the formation of small subunit ribosomal RNA in human cells in vitro.

PubMed

Gallenberger, Martin; Meinel, Dominik M; Kroeber, Markus; Wegner, Michael; Milkereit, Philipp; Bösl, Michael R; Tamm, Ernst R

2011-02-01

Mutations in WD repeat domain 36 gene (WDR36) play a causative role in some forms of primary open-angle glaucoma, a leading cause of blindness worldwide. WDR36 is characterized by the presence of multiple WD40 repeats and shows homology to Utp21, an essential protein component of the yeast small subunit (SSU) processome required for maturation of 18S rRNA. To clarify the functional role of WDR36 in the mammalian organism, we generated and investigated mutant mice with a targeted deletion of Wdr36. In parallel experiments, we used RNA interference to deplete WDR36 mRNA in mouse embryos and cultured human trabecular meshwork (HTM-N) cells. Deletion of Wdr36 in the mouse caused preimplantation embryonic lethality, and essentially similar effects were observed when WDR36 mRNA was depleted in mouse embryos by RNA interference. Depletion of WDR36 mRNA in HTM-N cells caused apoptotic cell death and upregulation of mRNA for BAX, TP53 and CDKN1A. By immunocytochemistry, staining for WDR36 was observed in the nucleolus of cells, which co-localized with that of nucleolar proteins such as nucleophosmin and PWP2. In addition, recombinant and epitope-tagged WDR36 localized to the nucleolus of HTM-N cells. By northern blot analysis, a substantial decrease in 21S rRNA, the precursor of 18S rRNA, was observed following knockdown of WDR36. In addition, metabolic-labeling experiments consistently showed a delay of 18S rRNA maturation in WDR36-depleted cells. Our results provide evidence that WDR36 is an essential protein in mammalian cells which is involved in the nucleolar processing of SSU 18S rRNA.

The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA

PubMed Central

Sloan, Katherine E.; Bohnsack, Markus T.; Schneider, Claudia; Watkins, Nicholas J.

2014-01-01

During eukaryotic ribosome biogenesis, three of the mature ribosomal (r)RNAs are released from a single precursor transcript (pre-rRNA) by an ordered series of endonucleolytic cleavages and exonucleolytic processing steps. Production of the 18S rRNA requires the removal of the 5′ external transcribed spacer (5′ETS) by endonucleolytic cleavages at sites A0 and A1/site 1. In metazoans, an additional cleavage in the 5′ETS, at site A′, upstream of A0, has also been reported. Here, we have investigated how A′ processing is coordinated with assembly of the early preribosomal complex. We find that only the tUTP (UTP-A) complex is critical for A′ cleavage, while components of the bUTP (UTP-B) and U3 snoRNP are important, but not essential, for efficient processing at this site. All other factors involved in the early stages of 18S rRNA processing that were tested here function downstream from this processing step. Interestingly, we show that the RNA surveillance factors XRN2 and MTR4 are also involved in A′ cleavage in humans. A′ cleavage is largely bypassed when XRN2 is depleted, and we also discover that A′ cleavage is not always the initial processing event in all cell types. Together, our data suggest that A′ cleavage is not a prerequisite for downstream pre-rRNA processing steps and may, in fact, represent a quality control step for initial pre-rRNA transcripts. Furthermore, we show that components of the RNA surveillance machinery, including the exosome and TRAMP complexes, also play key roles in the recycling of excised spacer fragments and degradation of aberrant pre-rRNAs in human cells. PMID:24550520

Biosynthesis of ribosomal RNA in nucleoli regulates pluripotency and differentiation ability of pluripotent stem cells.

PubMed

Watanabe-Susaki, Kanako; Takada, Hitomi; Enomoto, Kei; Miwata, Kyoko; Ishimine, Hisako; Intoh, Atsushi; Ohtaka, Manami; Nakanishi, Mahito; Sugino, Hiromu; Asashima, Makoto; Kurisaki, Akira

2014-12-01

Pluripotent stem cells have been shown to have unique nuclear properties, for example, hyperdynamic chromatin and large, condensed nucleoli. However, the contribution of the latter unique nucleolar character to pluripotency has not been well understood. Here, we show that fibrillarin (FBL), a critical methyltransferase for ribosomal RNA (rRNA) processing in nucleoli, is one of the proteins highly expressed in pluripotent embryonic stem (ES) cells. Stable expression of FBL in ES cells prolonged the pluripotent state of mouse ES cells cultured in the absence of leukemia inhibitory factor (LIF). Analyses using deletion mutants and a point mutant revealed that the methyltransferase activity of FBL regulates stem cell pluripotency. Knockdown of this gene led to significant delays in rRNA processing, growth inhibition, and apoptosis in mouse ES cells. Interestingly, both partial knockdown of FBL and treatment with actinomycin D, an inhibitor of rRNA synthesis, induced the expression of differentiation markers in the presence of LIF and promoted stem cell differentiation into neuronal lineages. Moreover, we identified p53 signaling as the regulatory pathway for pluripotency and differentiation of ES cells. These results suggest that proper activity of rRNA production in nucleoli is a novel factor for the regulation of pluripotency and differentiation ability of ES cells. © 2014 AlphaMed Press.

CRM1 and its ribosome export adaptor NMD3 localize to the nucleolus and affect rRNA synthesis.

PubMed

Bai, Baoyan; Moore, Henna M; Laiho, Marikki

2013-01-01

CRM1 is an export factor that together with its adaptor NMD3 transports numerous cargo molecules from the nucleus to cytoplasm through the nuclear pore. Previous studies have suggested that CRM1 and NMD3 are detected in the nucleolus. However, their localization with subnucleolar domains or participation in the activities of the nucleolus are unclear. We demonstrate here biochemically and using imaging analyses that CRM1 and NMD3 co-localize with nucleolar marker proteins in the nucleolus. In particular, their nucleolar localization is markedly increased by inhibition of RNA polymerase I (Pol I) transcription by actinomycin D or by silencing Pol I catalytic subunit, RPA194. We show that CRM1 nucleolar localization is dependent on its activity and the expression of NMD3, whereas NMD3 nucleolar localization is independent of CRM1. This suggests that NMD3 provides nucleolar tethering of CRM1. While inhibition of CRM1 by leptomycin B inhibited processing of 28S ribosomal (r) RNA, depletion of NMD3 did not, suggesting that their effects on 28S rRNA processing are distinct. Markedly, depletion of NMD3 and inhibition of CRM1 reduced the rate of pre-47S rRNA synthesis. However, their inactivation did not lead to nucleolar disintegration, a hallmark of Pol I transcription stress, suggesting that they do not directly regulate transcription. These results indicate that CRM1 and NMD3 have complex functions in pathways that couple rRNA synthetic and processing engines and that the rRNA synthesis rate may be adjusted according to proficiency in rRNA processing and export.

Ribosomal RNA and ribosomal proteins in corynebacteria.

PubMed

Martín, Juan F; Barreiro, Carlos; González-Lavado, Eva; Barriuso, Mónica

2003-09-04

Ribosomal RNAs (rRNAs) (16S, 23S, 5S) encoded by the rrn operons and ribosomal proteins play a very important role in the formation of ribosomes and in the control of translation. Five copies of the rrn operon were reported by hybridization studies in Brevibacterium (Corynebacterium) lactofermentum but the genome sequence of Corynebacterium glutamicum provided evidence for six rrn copies. All six copies of the C. glutamicum 16S rRNA have a size of 1523 bp and each of the six copies of the 5S contain 120 bp whereas size differences are found between the six copies of the 23S rRNA. The anti-Shine-Dalgarno sequence at the 3'-end of the 16S rRNA was 5'-CCUCCUUUC-3'. Each rrn operon is transcribed as a large precursor rRNA (pre-rRNA) that is processed by RNaseIII and other RNases at specific cleavage boxes that have been identified in the C. glutamicum pre-rRNA. A secondary structure of the C. glutamicum 16S rRNA is proposed. The 16S rRNA sequence has been used as a molecular evolution clock allowing the deduction of a phylogenetic tree of all Corynebacterium species. In C. glutamicum, there are 11 ribosomal protein gene clusters encoding 42 ribosomal proteins. The organization of some of the ribosomal protein gene cluster is identical to that of Escherichia coli whereas in other clusters the organization of the genes is rather different. Some specific ribosomal protein genes are located in a different cluster in C. glutamicum when compared with E. coli, indicating that the control of expression of these genes is different in E. coli and C. glutamicum.

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.

PubMed

Santiago-Rodriguez, Tasha M; Fornaciari, Gino; Luciani, Stefania; Dowd, Scot E; Toranzos, Gary A; Marota, Isolina; Cano, Raul J

2016-11-01

Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome

PubMed Central

Kharde, Satyavati; Ahmed, Yasar Luqman; Stier, Gunter; Kunze, Ruth; Sinning, Irmgard

2017-01-01

In eukaryotes, ribosome assembly is a highly complex process that involves more than 200 assembly factors that ensure the folding, modification and processing of the different rRNA species as well as the timely association of ribosomal proteins. One of these factors, Mpp10 associates with Imp3 and Imp4 to form a complex that is essential for the normal production of the 18S rRNA. Here we report the crystal structure of a complex between Imp4 and a short helical element of Mpp10 to a resolution of 1.88 Å. Furthermore, we extend the interaction network of Mpp10 and characterize two novel interactions. Mpp10 is able to bind the ribosome biogenesis factor Utp3/Sas10 through two conserved motifs in its N-terminal region. In addition, Mpp10 interacts with the ribosomal protein S5/uS7 using a short stretch within an acidic loop region. Thus, our findings reveal that Mpp10 provides a platform for the simultaneous interaction with multiple proteins in the 90S pre-ribosome. PMID:28813493

The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity.

PubMed

Andrade, José M; Dos Santos, Ricardo F; Chelysheva, Irina; Ignatova, Zoya; Arraiano, Cecília M

2018-06-01

Ribosome biogenesis is a complex process involving multiple factors. Here, we show that the widely conserved RNA chaperone Hfq, which can regulate sRNA-mRNA basepairing, plays a critical role in rRNA processing and ribosome assembly in Escherichia coli Hfq binds the 17S rRNA precursor and facilitates its correct processing and folding to mature 16S rRNA Hfq assists ribosome assembly and associates with pre-30S particles but not with mature 30S subunits. Inactivation of Hfq strikingly decreases the pool of mature 70S ribosomes. The reduction in ribosome levels depends on residues located in the distal face of Hfq but not on residues found in the proximal and rim surfaces which govern interactions with the sRNAs. Our results indicate that Hfq-mediated regulation of ribosomes is independent of its function as sRNA-regulator. Furthermore, we observed that inactivation of Hfq compromises translation efficiency and fidelity, both features of aberrantly assembled ribosomes. Our work expands the functions of the Sm-like protein Hfq beyond its function in small RNA-mediated regulation and unveils a novel role of Hfq as crucial in ribosome biogenesis and translation. © 2018 The Authors.

Nuclear ribosome biogenesis mediated by the DIM1A rRNA dimethylase is required for organized root growth and epidermal patterning in Arabidopsis.

PubMed

Wieckowski, Yana; Schiefelbein, John

2012-07-01

Position-dependent patterning of hair and non-hair cells in the Arabidopsis thaliana root epidermis is a powerful system to study the molecular basis of cell fate specification. Here, we report an epidermal patterning mutant affecting the ADENOSINE DIMETHYL TRANSFERASE 1A (DIM1A) rRNA dimethylase gene, predicted to participate in rRNA posttranscriptional processing and base modification. Consistent with a role in ribosome biogenesis, DIM1A is preferentially expressed in regions of rapid growth, and its product is nuclear localized with nucleolus enrichment. Furthermore, DIM1A preferentially accumulates in the developing hair cells, and the dim1A point mutant alters the cell-specific expression of the transcriptional regulators GLABRA2, CAPRICE, and WEREWOLF. Together, these findings suggest that establishment of cell-specific gene expression during root epidermis development is dependent upon proper ribosome biogenesis, possibly due to the sensitivity of the cell fate decision to relatively small differences in gene regulatory activities. Consistent with its effect on the predicted S-adenosyl-l-Met binding site, dim1A plants lack the two 18S rRNA base modifications but exhibit normal pre-rRNA processing. In addition to root epidermal defects, the dim1A mutant exhibits abnormal root meristem division, leaf development, and trichome branching. Together, these findings provide new insights into the importance of rRNA base modifications and translation regulation for plant growth and development.

Nuclear Ribosome Biogenesis Mediated by the DIM1A rRNA Dimethylase Is Required for Organized Root Growth and Epidermal Patterning in Arabidopsis[C][W

PubMed Central

Wieckowski, Yana; Schiefelbein, John

2012-01-01

Position-dependent patterning of hair and non-hair cells in the Arabidopsis thaliana root epidermis is a powerful system to study the molecular basis of cell fate specification. Here, we report an epidermal patterning mutant affecting the ADENOSINE DIMETHYL TRANSFERASE 1A (DIM1A) rRNA dimethylase gene, predicted to participate in rRNA posttranscriptional processing and base modification. Consistent with a role in ribosome biogenesis, DIM1A is preferentially expressed in regions of rapid growth, and its product is nuclear localized with nucleolus enrichment. Furthermore, DIM1A preferentially accumulates in the developing hair cells, and the dim1A point mutant alters the cell-specific expression of the transcriptional regulators GLABRA2, CAPRICE, and WEREWOLF. Together, these findings suggest that establishment of cell-specific gene expression during root epidermis development is dependent upon proper ribosome biogenesis, possibly due to the sensitivity of the cell fate decision to relatively small differences in gene regulatory activities. Consistent with its effect on the predicted S-adenosyl-l-Met binding site, dim1A plants lack the two 18S rRNA base modifications but exhibit normal pre-rRNA processing. In addition to root epidermal defects, the dim1A mutant exhibits abnormal root meristem division, leaf development, and trichome branching. Together, these findings provide new insights into the importance of rRNA base modifications and translation regulation for plant growth and development. PMID:22829145

The Treacher Collins syndrome (TCOF1) gene product is involved in pre-rRNA methylation.

PubMed

Gonzales, Bianca; Henning, Dale; So, Rolando B; Dixon, Jill; Dixon, Michael J; Valdez, Benigno C

2005-07-15

Treacher Collins syndrome (TCS) is characterized by defects in craniofacial development, which results from mutations in the TCOF1 gene. TCOF1 encodes the nucleolar phosphoprotein treacle, which interacts with upstream binding factor (UBF) and affects transcription of the ribosomal DNA gene. The present study shows participation of treacle in the 2'-O-methylation of pre-rRNA. Antisense-mediated down-regulation of treacle expression in Xenopus laevis oocytes reduced 2'-O-methylation of pre-rRNA. Analysis of RNA isolated from wild-type and Tcof1+/- heterozygous mice embryos from strains that exhibit a lethal phenotype showed significant reduction in 2'-O-methylation at nucleotide C463 of 18S rRNA. The level of pseudouridylation of U1642 of 18S rRNA from the same RNA samples was not affected suggesting specificity. There is no significant difference in rRNA methylation between wild-type and heterozygous embryos of DBA x BALB/c mice, which have no obvious craniofacial phenotype. The function of treacle in pre-rRNA methylation is most likely mediated by its direct physical interaction with NOP56, a component of the ribonucleoprotein methylation complex. Although treacle co-localizes with UBF throughout mitosis, it co-localizes with NOP56 and fibrillarin, a putative methyl transferase, only during telophase when rDNA gene transcription and pre-rRNA methylation are known to commence. These observations suggest that treacle might link RNA polymerase I-catalyzed transcription and post-transcriptional modification of pre-rRNA. We hypothesize that haploinsufficiency of treacle in TCS patients results in inhibition of production of properly modified mature rRNA in addition to inhibition of rDNA gene transcription, which consequently affects proliferation and proper differentiation of specific embryonic cells during development.

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

PubMed

Oh, Jeongsu; Choi, Chi-Hwan; Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

2016-01-01

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr.

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment

PubMed Central

Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

2016-01-01

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology–a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr. PMID:26954507

IL8 and IL16 levels indicate serum and plasma quality.

PubMed

Kofanova, Olga; Henry, Estelle; Quesada, Rocio Aguilar; Bulla, Alexandre; Linares, Hector Navarro; Lescuyer, Pierre; Shea, Kathi; Stone, Mars; Tybring, Gunnel; Bellora, Camille; Betsou, Fay

2018-02-09

Longer pre-centrifugation times alter the quality of serum and plasma samples. Markers for such delays in sample processing and hence for the sample quality, have been identified. Twenty cytokines in serum, EDTA plasma and citrate plasma samples were screened for changes in concentration induced by extended blood pre-centrifugation delays at room temperature. The two cytokines that showed the largest changes were further validated for their "diagnostic performance" in identifying serum or plasma samples with extended pre-centrifugation times. In this study, using R&D Systems ELISA kits, EDTA plasma samples and serum samples with a pre-centrifugation delay longer than 24 h had an IL16 concentration higher than 313 pg/mL, and an IL8 concentration higher than 125 pg/mL, respectively. EDTA plasma samples with a pre-centrifugation delay longer than 48 h had an IL16 concentration higher than 897 pg/mL, citrate plasma samples had an IL8 concentration higher than 21.5 pg/mL and serum samples had an IL8 concentration higher than 528 pg/mL. These robust and accurate tools, based on simple and commercially available ELISA assays can greatly facilitate qualification of serum and plasma legacy collections with undocumented pre-analytics.

Willing to Wait: Elevated Reward-Processing EEG Activity Associated with a Greater Preference for Larger-But-Delayed Rewards

PubMed Central

Pornpattananangkul, Narun; Nusslock, Robin

2016-01-01

While almost everyone discounts the value of future rewards over immediate rewards, people differ in their so-called delay-discounting. One of the several factors that may explain individual differences in delay-discounting is reward-processing. To study individual-differences in reward-processing, however, one needs to consider the heterogeneity of neural-activity at each reward-processing stage. Here using EEG, we separated reward-related neural activity into distinct reward-anticipation and reward-outcome stages using time-frequency characteristics. Thirty-seven individuals completed a behavioral delay-discounting task. Reward-processing EEG activity was assessed using a separate reward-learning task, called a reward time-estimation task. During this task, participants were instructed to estimate time duration and were provided performance feedback on a trial-by-trial basis. Participants received monetary-reward for accurate-performance on Reward trials, but not on No-Reward trials. Reward trials, relative to No-Reward trials, enhanced EEG activity during both reward-anticipation stage (including, cued-locked delta power during cue-evaluation and pre-feedback alpha suppression during feedback-anticipation) and at the reward-outcome stage (including, feedback-locked delta, theta and beta power). Moreover, all of these EEG indices correlated with behavioral performance in the time-estimation task, suggesting their essential roles in learning and adjusting performance to maximize winnings in a reward-learning situation. Importantly, enhanced EEG power during Reward trials for 1) pre-feedback alpha suppression, 2) feedback-locked theta and 3) feedback-locked beta was associated with a greater preference for larger-but-delayed rewards. Results highlight the association between a stronger preference toward larger-but-delayed rewards and enhanced reward-processing. Moreover, our reward-processing EEG indices detail the specific stages of reward-processing where these associations occur. PMID:27477630

A Plant 5S Ribosomal RNA Mimic Regulates Alternative Splicing of Transcription Factor IIIA Pre-mRNAs

PubMed Central

Hammond, Ming C.; Wachter, Andreas; Breaker, Ronald R.

2009-01-01

Transcription factor IIIA (TFIIIA) is required for eukaryotic synthesis of 5S ribosomal RNA by RNA polymerase III. Here we report the discovery of a structured RNA element with striking resemblance to 5S rRNA that is conserved within TFIIIA precursor mRNAs (pre-mRNAs) from diverse plant lineages. TFIIIA protein expression is controlled by alternative splicing of the exon containing the plant 5S rRNA mimic (P5SM). P5SM triggers exon skipping upon binding of ribosomal protein L5, a natural partner of 5S rRNA, which demonstrates the functional adaptation of its structural mimicry. Since the exon-skipped splice product encodes full-length TFIIIA protein, these results reveal a ribosomal protein-mRNA interaction that is involved in 5S rRNA synthesis and has implications for cross-coordination of ribosomal components. This study also provides insight into the origin and function of a newfound class of structured RNA that regulates alternative splicing. PMID:19377483

The 28S–18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor

PubMed Central

Schnare, Murray N.; Collings, James C.; Spencer, David F.; Gray, Michael W.

2000-01-01

In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from ∼11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an ∼55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A′ pre-rRNA processing sites within the 5′ external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5′ ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C.fasciculata and Trypanosoma brucei involves 3′-terminal addition of three A residues that are not present in the corresponding DNA sequences. PMID:10982863

Pre-hospital Delay as Determinant of Ischemic Stroke Outcome in an Italian Cohort of Patients Not Receiving Thrombolysis.

PubMed

Denti, Licia; Artoni, Andrea; Scoditti, Umberto; Gatti, Elisa; Bussolati, Chiara; Ceda, Gian Paolo

2016-06-01

Pre-hospital delay in acute stroke is critical to the administration of thrombolysis and affects patients' clinical outcome. In this study, the impact of pre-hospital delay on the outcome of ischemic stroke was investigated in an Italian cohort of patients who did not receive thrombolysis. Data from a cohort of 1847 patients, suffering from first-ever ischemic stroke and referred to an in-hospital clinical pathway were analyzed retrospectively. The relationship between pre-hospital delay and 1-month mortality was assessed with adjustment for demographics, premorbid disability, and stroke severity, which was graded according to the Scandinavian Stroke Scale, with higher scores indicating less severity. Five hundred and twelve patients (27.7%) arrived at hospital within 2 hours of symptom onset. A significant correlation was found between early arrival and a reduced risk of 1-month mortality (hazard ratio .65; 95% confidence interval .48-.89; P = .02). There was a significant interaction (P = .01) between pre-hospital delay and the neurological score on mortality in the multivariate model, and the survival advantage of early admission was significant only for patients with scores on the Scandinavian Stroke Scale less than 18 (hazard ratio .54; 95% confidence interval .34-.85; P = .008). Our study suggests that reducing pre-hospital delay can increase the probability of survival in patients with ischemic stroke, especially those who are most severely affected. Even if the patients cannot benefit from thrombolysis, survival rates can be increased provided that they are managed according to standardized care processes. Copyright © 2016 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Willing to wait: Elevated reward-processing EEG activity associated with a greater preference for larger-but-delayed rewards.

PubMed

Pornpattananangkul, Narun; Nusslock, Robin

2016-10-01

While almost everyone discounts the value of future rewards over immediate rewards, people differ in their so-called delay-discounting. One of the several factors that may explain individual differences in delay-discounting is reward-processing. To study individual-differences in reward-processing, however, one needs to consider the heterogeneity of neural-activity at each reward-processing stage. Here using EEG, we separated reward-related neural activity into distinct reward-anticipation and reward-outcome stages using time-frequency characteristics. Thirty-seven individuals first completed a behavioral delay-discounting task. Then reward-processing EEG activity was assessed using a separate reward-learning task, called a reward time-estimation task. During this EEG task, participants were instructed to estimate time duration and were provided performance feedback on a trial-by-trial basis. Participants received monetary-reward for accurate-performance on Reward trials, but not on No-Reward trials. Reward trials, relative to No-Reward trials, enhanced EEG activity during both reward-anticipation (including, cued-locked delta power during cue-evaluation and pre-feedback alpha suppression during feedback-anticipation) and reward-outcome (including, feedback-locked delta, theta and beta power) stages. Moreover, all of these EEG indices correlated with behavioral performance in the time-estimation task, suggesting their essential roles in learning and adjusting performance to maximize winnings in a reward-learning situation. Importantly, enhanced EEG power during Reward trials, as reflected by stronger 1) pre-feedback alpha suppression, 2) feedback-locked theta and 3) feedback-locked beta, was associated with a greater preference for larger-but-delayed rewards in a separate, behavioral delay-discounting task. Results highlight the association between a stronger preference toward larger-but-delayed rewards and enhanced reward-processing. Moreover, our reward-processing EEG indices detail the specific stages of reward-processing where these associations occur. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Intranuclear distribution of rat liver ribosomal RNA].

PubMed

Dabeva, M D; Todorov, B N; Khadzhiolova, A A

1976-03-01

A method is described for the isolation of pure liver nuclei with minimal cytoplasmic contaminants, loss of nuclear RNA and degradation of nuclear RNA. The RNA components are extracted in three distinct fractions by subsequent treatment with phenol at 4 degrees, 50 degrees and 85 degrees C. The total and 14C-orotate labelled RNA components in the three nuclear RNA fractions are characterized by nucleotide composition, poly(A)-RNA content and agar-gel electrophoresis. The results show that the RNA in three fractions correspond to the nucleosol, nucleolus and chromatin compartments of the nucleus. The nuclear HnRNA components are exclusively in the 85 degrees C RNA. Nuclear ribosomal RNA is extracted in the 4 degrees C and 50 degrees C RNA fractions. These two nuclear RNA fractions are distinct in constituent pre-rRNA species and the rate of labelling of their rRNA components. The amount of the pre-rRNA and rRNA species is determined. The results show that the nucleolus-nucleosol and nucleosol-cytoplasm transitions of ribosomal subparticles are markedly slower processes than the preceeding steps of ribosome biogenesis.

A Systematic Evaluation of Blood Serum and Plasma Pre-Analytics for Metabolomics Cohort Studies

PubMed Central

Jobard, Elodie; Trédan, Olivier; Postoly, Déborah; André, Fabrice; Martin, Anne-Laure; Elena-Herrmann, Bénédicte; Boyault, Sandrine

2016-01-01

The recent thriving development of biobanks and associated high-throughput phenotyping studies requires the elaboration of large-scale approaches for monitoring biological sample quality and compliance with standard protocols. We present a metabolomic investigation of human blood samples that delineates pitfalls and guidelines for the collection, storage and handling procedures for serum and plasma. A series of eight pre-processing technical parameters is systematically investigated along variable ranges commonly encountered across clinical studies. While metabolic fingerprints, as assessed by nuclear magnetic resonance, are not significantly affected by altered centrifugation parameters or delays between sample pre-processing (blood centrifugation) and storage, our metabolomic investigation highlights that both the delay and storage temperature between blood draw and centrifugation are the primary parameters impacting serum and plasma metabolic profiles. Storing the blood drawn at 4 °C is shown to be a reliable routine to confine variability associated with idle time prior to sample pre-processing. Based on their fine sensitivity to pre-analytical parameters and protocol variations, metabolic fingerprints could be exploited as valuable ways to determine compliance with standard procedures and quality assessment of blood samples within large multi-omic clinical and translational cohort studies. PMID:27929400

UBF complexes with phosphatidylinositol 4,5-bisphosphate in nucleolar organizer regions regardless of ongoing RNA polymerase I activity

PubMed Central

Sobol, Margarita; Yildirim, Sukriye; Philimonenko, Vlada V; Marášek, Pavel; Castaño, Enrique; Hozák, Pavel

2013-01-01

To maintain growth and division, cells require a large-scale production of rRNAs which occurs in the nucleolus. Recently, we have shown the interaction of nucleolar phosphatidylinositol 4,5-bisphosphate (PIP2) with proteins involved in rRNA transcription and processing, namely RNA polymerase I (Pol I), UBF, and fibrillarin. Here we extend the study by investigating transcription-related localization of PIP2 in regards to transcription and processing complexes of Pol I. To achieve this, we used either physiological inhibition of transcription during mitosis or inhibition by treatment the cells with actinomycin D (AMD) or 5,6-dichloro-1β-d-ribofuranosyl-benzimidazole (DRB). We show that PIP2 is associated with Pol I subunits and UBF in a transcription-independent manner. On the other hand, PIP2/fibrillarin colocalization is dependent on the production of rRNA. These results indicate that PIP2 is required not only during rRNA production and biogenesis, as we have shown before, but also plays a structural role as an anchor for the Pol I pre-initiation complex during the cell cycle. We suggest that throughout mitosis, PIP2 together with UBF is involved in forming and maintaining the core platform of the rDNA helix structure. Thus we introduce PIP2 as a novel component of the NOR complex, which is further engaged in the renewed rRNA synthesis upon exit from mitosis. PMID:24513678

Fast and secure handover of intra-ASN IEEE802.16 network by proposed certificate based pre-authentication

NASA Astrophysics Data System (ADS)

Sridevi, B.; Supriya, T. S.; Rajaram, S.

2013-01-01

The current generation of wireless networks has been designed predominantly to support voice and more recently data traffic. WiMAX is currently one of the hottest technologies in wireless. The main motive of the mobile technologies is to provide seamless cost effective mobility. But this is affected by Authentication cost and handover delay since on each handoff the Mobile Station (MS) has to undergo all steps of authentication. Pre-Authentication is used to reduce the handover delay and increase the speed of the Intra-ASN Handover. Proposed Pre-Authentication method is intended to reduce the authentication delay by getting pre authenticated by central authority called Pre Authentication Authority (PAA). MS requests PAA for Pre Authentication Certificate (PAC) before performing handoff. PAA verifies the identity of MS and provides PAC to MS and also to the neighboring target Base Stations (tBSs). MS having time bound PAC can skip the authentication process when recognized by target BS during handoff. It also prevents the DOS (Denial Of Service) attack and Replay attack. It has no wastage of unnecessary key exchange of the resources. The proposed work is simulated by NS2 model and by MATLAB.

Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae

PubMed Central

Hierlmeier, Thomas; Merl, Juliane; Sauert, Martina; Perez-Fernandez, Jorge; Schultz, Patrick; Bruckmann, Astrid; Hamperl, Stephan; Ohmayer, Uli; Rachel, Reinhard; Jacob, Anja; Hergert, Kristin; Deutzmann, Rainer; Griesenbeck, Joachim; Hurt, Ed; Milkereit, Philipp; Baßler, Jochen; Tschochner, Herbert

2013-01-01

Eukaryotic ribosome biogenesis requires more than 150 auxiliary proteins, which transiently interact with pre-ribosomal particles. Previous studies suggest that several of these biogenesis factors function together as modules. Using a heterologous expression system, we show that the large ribosomal subunit (LSU) biogenesis factor Noc1p of Saccharomyces cerevisiae can simultaneously interact with the LSU biogenesis factor Noc2p and Rrp5p, a factor required for biogenesis of the large and the small ribosomal subunit. Proteome analysis of RNA polymerase-I-associated chromatin and chromatin immunopurification experiments indicated that all members of this protein module and a specific set of LSU biogenesis factors are co-transcriptionally recruited to nascent ribosomal RNA (rRNA) precursors in yeast cells. Further ex vivo analyses showed that all module members predominantly interact with early pre-LSU particles after the initial pre-rRNA processing events have occurred. In yeast strains depleted of Noc1p, Noc2p or Rrp5p, levels of the major LSU pre-rRNAs decreased and the respective other module members were associated with accumulating aberrant rRNA fragments. Therefore, we conclude that the module exhibits several binding interfaces with pre-ribosomes. Taken together, our results suggest a co- and post-transcriptional role of the yeast Rrp5p–Noc1p–Noc2p module in the structural organization of early LSU precursors protecting them from non-productive RNase activity. PMID:23209026

Low levels of ribosomal RNA partly account for the very high photosynthetic phosphorus-use efficiency of Proteaceae species

PubMed Central

Sulpice, Ronan; Ishihara, Hirofumi; Schlereth, Armin; Cawthray, Gregory R; Encke, Beatrice; Giavalisco, Patrick; Ivakov, Alexander; Arrivault, StÉphanie; Jost, Ricarda; Krohn, Nicole; Kuo, John; Laliberté, Etienne; Pearse, Stuart J; Raven, John A; Scheible, Wolf-rüdiger; Teste, François; Veneklaas, Erik J; Stitt, Mark; Lambers, Hans

2014-01-01

Abstract Proteaceae species in south-western Australia occur on phosphorus- (P) impoverished soils. Their leaves contain very low P levels, but have relatively high rates of photosynthesis. We measured ribosomal RNA (rRNA) abundance, soluble protein, activities of several enzymes and glucose 6-phosphate (Glc6P) levels in expanding and mature leaves of six Proteaceae species in their natural habitat. The results were compared with those for Arabidopsis thaliana. Compared with A. thaliana, immature leaves of Proteaceae species contained very low levels of rRNA, especially plastidic rRNA. Proteaceae species showed slow development of the photosynthetic apparatus (‘delayed greening’), with young leaves having very low levels of chlorophyll and Calvin–Benson cycle enzymes. In mature leaves, soluble protein and Calvin–Benson cycle enzyme activities were low, but Glc6P levels were similar to those in A. thaliana. We propose that low ribosome abundance contributes to the high P efficiency of these Proteaceae species in three ways: (1) less P is invested in ribosomes; (2) the rate of growth and, hence, demand for P is low; and (3) the especially low plastidic ribosome abundance in young leaves delays formation of the photosynthetic machinery, spreading investment of P in rRNA. Although Calvin–Benson cycle enzyme activities are low, Glc6P levels are maintained, allowing their effective use. PMID:24895754

Low levels of ribosomal RNA partly account for the very high photosynthetic phosphorus-use efficiency of Proteaceae species.

PubMed

Sulpice, Ronan; Ishihara, Hirofumi; Schlereth, Armin; Cawthray, Gregory R; Encke, Beatrice; Giavalisco, Patrick; Ivakov, Alexander; Arrivault, Stéphanie; Jost, Ricarda; Krohn, Nicole; Kuo, John; Laliberté, Etienne; Pearse, Stuart J; Raven, John A; Scheible, Wolf-Rüdiger; Teste, François; Veneklaas, Erik J; Stitt, Mark; Lambers, Hans

2014-06-01

Proteaceae species in south-western Australia occur on phosphorus- (P) impoverished soils. Their leaves contain very low P levels, but have relatively high rates of photosynthesis. We measured ribosomal RNA (rRNA) abundance, soluble protein, activities of several enzymes and glucose 6-phosphate (Glc6P) levels in expanding and mature leaves of six Proteaceae species in their natural habitat. The results were compared with those for Arabidopsis thaliana. Compared with A. thaliana, immature leaves of Proteaceae species contained very low levels of rRNA, especially plastidic rRNA. Proteaceae species showed slow development of the photosynthetic apparatus (‘delayed greening’), with young leaves having very low levels of chlorophyll and Calvin-Benson cycle enzymes. In mature leaves, soluble protein and Calvin-Benson cycle enzyme activities were low, but Glc6P levels were similar to those in A. thaliana. We propose that low ribosome abundance contributes to the high P efficiency of these Proteaceae species in three ways: (1) less P is invested in ribosomes; (2) the rate of growth and, hence, demand for P is low; and (3) the especially low plastidic ribosome abundance in young leaves delays formation of the photosynthetic machinery, spreading investment of P in rRNA. Although Calvin-Benson cycle enzyme activities are low, Glc6P levels are maintained, allowing their effective use.

Beyond tRNA cleavage: novel essential function for yeast tRNA splicing endonuclease unrelated to tRNA processing

PubMed Central

Dhungel, Nripesh; Hopper, Anita K.

2012-01-01

Pre-tRNA splicing is an essential process in all eukaryotes. In yeast and vertebrates, the enzyme catalyzing intron removal from pre-tRNA is a heterotetrameric complex (splicing endonuclease [SEN] complex). Although the SEN complex is conserved, the subcellular location where pre-tRNA splicing occurs is not. In yeast, the SEN complex is located at the cytoplasmic surface of mitochondria, whereas in vertebrates, pre-tRNA splicing is nuclear. We engineered yeast to mimic the vertebrate cell biology and demonstrate that all three steps of pre-tRNA splicing, as well as tRNA nuclear export and aminoacylation, occur efficiently when the SEN complex is nuclear. However, nuclear pre-tRNA splicing fails to complement growth defects of cells with defective mitochondrial-located splicing, suggesting that the yeast SEN complex surprisingly serves a novel and essential function in the cytoplasm that is unrelated to tRNA splicing. The novel function requires all four SEN complex subunits and the catalytic core. A subset of pre-rRNAs accumulates when the SEN complex is restricted to the nucleus, indicating that the SEN complex moonlights in rRNA processing. Thus, findings suggest that selection for the subcellular distribution of the SEN complex may reside not in its canonical, but rather in a novel, activity. PMID:22391451

Terminator oligo blocking efficiently eliminates rRNA from Drosophila small RNA sequencing libraries.

PubMed

Wickersheim, Michelle L; Blumenstiel, Justin P

2013-11-01

A large number of methods are available to deplete ribosomal RNA reads from high-throughput RNA sequencing experiments. Such methods are critical for sequencing Drosophila small RNAs between 20 and 30 nucleotides because size selection is not typically sufficient to exclude the highly abundant class of 30 nucleotide 2S rRNA. Here we demonstrate that pre-annealing terminator oligos complimentary to Drosophila 2S rRNA prior to 5' adapter ligation and reverse transcription efficiently depletes 2S rRNA sequences from the sequencing reaction in a simple and inexpensive way. This depletion is highly specific and is achieved with minimal perturbation of miRNA and piRNA profiles.

Kinetic analysis of pre-ribosome structure in vivo

PubMed Central

Swiatkowska, Agata; Wlotzka, Wiebke; Tuck, Alex; Barrass, J. David; Beggs, Jean D.; Tollervey, David

2012-01-01

Pre-ribosomal particles undergo numerous structural changes during maturation, but their high complexity and short lifetimes make these changes very difficult to follow in vivo. In consequence, pre-ribosome structure and composition have largely been inferred from purified particles and analyzed in vitro. Here we describe techniques for kinetic analyses of the changes in pre-ribosome structure in living cells of Saccharomyces cerevisiae. To allow this, in vivo structure probing by DMS modification was combined with affinity purification of newly synthesized 20S pre-rRNA over a time course of metabolic labeling with 4-thiouracil. To demonstrate that this approach is generally applicable, we initially analyzed the accessibility of the region surrounding cleavage site D site at the 3′ end of the mature 18S rRNA region of the pre-rRNA. This revealed a remarkably flexible structure throughout 40S subunit biogenesis, with little stable RNA–protein interaction apparent. Analysis of folding in the region of the 18S central pseudoknot was consistent with previous data showing U3 snoRNA–18S rRNA interactions. Dynamic changes in the structure of the hinge between helix 28 (H28) and H44 of pre-18S rRNA were consistent with recently reported interactions with the 3′ guide region of U3 snoRNA. Finally, analysis of the H18 region indicates that the RNA structure matures early, but additional protection appears subsequently, presumably reflecting protein binding. The structural analyses described here were performed on total, affinity-purified, newly synthesized RNA, so many classes of RNA and RNA–protein complex are potentially amenable to this approach. PMID:23093724

Ribosomal RNA maturation in Schizosaccharomyces pombe is dependent on a large ribonucleoprotein complex of the internal transcribed spacer 1.

PubMed

Lalev, A I; Abeyrathne, P D; Nazar, R N

2000-09-08

The interdependency of steps in the processing of pre-rRNA in Schizosaccharomyces pombe suggests that RNA processing, at least in part, acts as a quality control mechanism which helps assure that only functional RNA is incorporated into mature ribosomes. To determine further the role of the transcribed spacer regions in rRNA processing and to detect interactions which underlie the interdependencies, the ITS1 sequence was examined for its ability to form ribonucleoprotein complexes with cellular proteins. When incubated with protein extract, the spacer formed a specific large RNP. This complex was stable to fractionation by agarose or polyacrylamide gel electrophoresis. Modification exclusion analyses indicated that the proteins interact with a helical domain which is conserved in the internal transcribed spacers. Mutagenic analyses confirmed an interaction with this sequence and indicated that this domain is critical to the efficient maturation of the precursor RNA. The protein constituents, purified by affinity chromatography using the ITS1 sequence, retained an ability to form stable RNP. Protein analyses of gel purified complex, prepared with affinity-purified proteins, indicated at least 20 protein components ranging in size from 20-200 kDa. Peptide mapping by Maldi-Toff mass spectroscopy identified eight hypothetical RNA binding proteins which included four different RNA-binding motifs. Another protein was putatively identified as a pseudouridylate synthase. Additional RNA constituents were not detected. The significance of this complex with respect to rRNA maturation and interdependence in rRNA processing is discussed. Copyright 2000 Academic Press.

Cyclin-dependent Kinase 9 Links RNA Polymerase II Transcription to Processing of Ribosomal RNA*

PubMed Central

Burger, Kaspar; Mühl, Bastian; Rohrmoser, Michaela; Coordes, Britta; Heidemann, Martin; Kellner, Markus; Gruber-Eber, Anita; Heissmeyer, Vigo; Strässer, Katja; Eick, Dirk

2013-01-01

Ribosome biogenesis is a process required for cellular growth and proliferation. Processing of ribosomal RNA (rRNA) is highly sensitive to flavopiridol, a specific inhibitor of cyclin-dependent kinase 9 (Cdk9). Cdk9 has been characterized as the catalytic subunit of the positive transcription elongation factor b (P-TEFb) of RNA polymerase II (RNAPII). Here we studied the connection between RNAPII transcription and rRNA processing. We show that inhibition of RNAPII activity by α-amanitin specifically blocks processing of rRNA. The block is characterized by accumulation of 3′ extended unprocessed 47 S rRNAs and the entire inhibition of other 47 S rRNA-specific processing steps. The transcription rate of rRNA is moderately reduced after inhibition of Cdk9, suggesting that defective 3′ processing of rRNA negatively feeds back on RNAPI transcription. Knockdown of Cdk9 caused a strong reduction of the levels of RNAPII-transcribed U8 small nucleolar RNA, which is essential for 3′ rRNA processing in mammalian cells. Our data demonstrate a pivotal role of Cdk9 activity for coupling of RNAPII transcription with small nucleolar RNA production and rRNA processing. PMID:23744076

Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing

PubMed Central

Sloan, Katherine E.; Mattijssen, Sandy; Lebaron, Simon; Tollervey, David; Pruijn, Ger J.M.

2013-01-01

Human ribosome production is up-regulated during tumorogenesis and is defective in many genetic diseases (ribosomopathies). We have undertaken a detailed analysis of human precursor ribosomal RNA (pre-rRNA) processing because surprisingly little is known about this important pathway. Processing in internal transcribed spacer 1 (ITS1) is a key step that separates the rRNA components of the large and small ribosomal subunits. We report that this was initiated by endonuclease cleavage, which required large subunit biogenesis factors. This was followed by 3′ to 5′ exonucleolytic processing by RRP6 and the exosome, an enzyme complex not previously linked to ITS1 removal. In contrast, RNA interference–mediated knockdown of the endoribonuclease MRP did not result in a clear defect in ITS1 processing. Despite the apparently high evolutionary conservation of the pre-rRNA processing pathway and ribosome synthesis factors, each of these features of human ITS1 processing is distinct from those in budding yeast. These results also provide significant insight into the links between ribosomopathies and ribosome production in human cells. PMID:23439679

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases.

PubMed

Tomecki, Rafal; Sikorski, Pawel J; Zakrzewska-Placzek, Monika

2017-07-01

Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans. © 2017 Federation of European Biochemical Societies.

Conditional Inactivation of Upstream Binding Factor Reveals Its Epigenetic Functions and the Existence of a Somatic Nucleolar Precursor Body

PubMed Central

Hamdane, Nourdine; Stefanovsky, Victor Y.; Tremblay, Michel G.; Németh, Attila; Paquet, Eric; Lessard, Frédéric; Sanij, Elaine; Hannan, Ross; Moss, Tom

2014-01-01

Upstream Binding Factor (UBF) is a unique multi-HMGB-box protein first identified as a co-factor in RNA polymerase I (RPI/PolI) transcription. However, its poor DNA sequence selectivity and its ability to generate nucleosome-like nucleoprotein complexes suggest a more generalized role in chromatin structure. We previously showed that extensive depletion of UBF reduced the number of actively transcribed ribosomal RNA (rRNA) genes, but had little effect on rRNA synthesis rates or cell proliferation, leaving open the question of its requirement for RPI transcription. Using gene deletion in mouse, we now show that UBF is essential for embryo development beyond morula. Conditional deletion in cell cultures reveals that UBF is also essential for transcription of the rRNA genes and that it defines the active chromatin conformation of both gene and enhancer sequences. Loss of UBF prevents formation of the SL1/TIF1B pre-initiation complex and recruitment of the RPI-Rrn3/TIF1A complex. It is also accompanied by recruitment of H3K9me3, canonical histone H1 and HP1α, but not by de novo DNA methylation. Further, genes retain penta-acetyl H4 and H2A.Z, suggesting that even in the absence of UBF the rRNA genes can maintain a potentially active state. In contrast to canonical histone H1, binding of H1.4 is dependent on UBF, strongly suggesting that it plays a positive role in gene activity. Unexpectedly, arrest of rRNA synthesis does not suppress transcription of the 5S, tRNA or snRNA genes, nor expression of the several hundred mRNA genes implicated in ribosome biogenesis. Thus, rRNA gene activity does not coordinate global gene expression for ribosome biogenesis. Loss of UBF also unexpectedly induced the formation in cells of a large sub-nuclear structure resembling the nucleolar precursor body (NPB) of oocytes and early embryos. These somatic NPBs contain rRNA synthesis and processing factors but do not associate with the rRNA gene loci (NORs). PMID:25121932

Poly(ADP-Ribose) Polymerase 1 (PARP-1) Regulates Ribosomal Biogenesis in Drosophila Nucleoli

PubMed Central

Boamah, Ernest K.; Kotova, Elena; Garabedian, Mikael; Jarnik, Michael; Tulin, Alexei V.

2012-01-01

Poly(ADP-ribose) polymerase 1 (PARP1), a nuclear protein, utilizes NAD to synthesize poly(AD-Pribose) (pADPr), resulting in both automodification and the modification of acceptor proteins. Substantial amounts of PARP1 and pADPr (up to 50%) are localized to the nucleolus, a subnuclear organelle known as a region for ribosome biogenesis and maturation. At present, the functional significance of PARP1 protein inside the nucleolus remains unclear. Using PARP1 mutants, we investigated the function of PARP1, pADPr, and PARP1-interacting proteins in the maintenance of nucleolus structure and functions. Our analysis shows that disruption of PARP1 enzymatic activity caused nucleolar disintegration and aberrant localization of nucleolar-specific proteins. Additionally, PARP1 mutants have increased accumulation of rRNA intermediates and a decrease in ribosome levels. Together, our data suggests that PARP1 enzymatic activity is required for targeting nucleolar proteins to the proximity of precursor rRNA; hence, PARP1 controls precursor rRNA processing, post-transcriptional modification, and pre-ribosome assembly. Based on these findings, we propose a model that explains how PARP1 activity impacts nucleolar functions and, consequently, ribosomal biogenesis. PMID:22242017

Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing

PubMed Central

Goldfarb, Katherine C.; Cech, Thomas R.

2017-01-01

MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR–Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor—analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing—implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation. PMID:28115465

Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae

PubMed Central

Schmidt, Christian; Berninghausen, Otto; Becker, Thomas

2017-01-01

Mechanistic understanding of eukaryotic ribosome formation requires a detailed structural knowledge of the numerous assembly intermediates, generated along a complex pathway. Here, we present the structure of a late pre-40S particle at 3.6 Å resolution, revealing in molecular detail how assembly factors regulate the timely folding of pre-18S rRNA. The structure shows that, rather than sterically blocking 40S translational active sites, the associated assembly factors Tsr1, Enp1, Rio2 and Pno1 collectively preclude their final maturation, thereby preventing untimely tRNA and mRNA binding and error prone translation. Moreover, the structure explains how Pno1 coordinates the 3’end cleavage of the 18S rRNA by Nob1 and how the late factor’s removal in the cytoplasm ensures the structural integrity of the maturing 40S subunit. PMID:29155690

Fluctuations and synchrony of RNA synthesis in nucleoli.

PubMed

Pliss, Artem; Kuzmin, Andrey N; Kachynski, Aliaksandr V; Baev, Alexander; Berezney, Ronald; Prasad, Paras N

2015-06-01

Ribosomal RNA (rRNA) sequences are synthesized at exceptionally high rates and, together with ribosomal proteins (r-proteins), are utilized as building blocks for the assembly of pre-ribosomal particles. Although it is widely acknowledged that tight regulation and coordination of rRNA and r-protein production are fundamentally important for the maintenance of cellular homeostasis, still little is known about the real-time kinetics of the ribosome component synthesis in individual cells. In this communication we introduce a label-free MicroRaman spectrometric approach for monitoring rRNA synthesis in live cultured cells. Remarkably high and rapid fluctuations of rRNA production rates were revealed by this technique. Strikingly, the changes in the rRNA output were synchronous for ribosomal genes located in separate nucleoli of the same cell. Our findings call for the development of new concepts to elucidate the coordination of ribosomal components production. In this regard, numerical modeling further demonstrated that the production of rRNA and r-proteins can be coordinated, regardless of the fluctuations in rRNA synthesis. Overall, our quantitative data reveal a spectacular interplay of inherently stochastic rates of RNA synthesis and the coordination of gene expression.

Impulsive Choice, Alcohol Consumption, and Pre-Exposure to Delayed Rewards: II. Potential Mechanisms

PubMed Central

Stein, Jeffrey S.; Renda, C. Renee; Hinnenkamp, Jay E.; Madden, Gregory J.

2014-01-01

In a prior study (Stein et al., 2013), we reported that rats pre-exposed to delayed rewards made fewer impulsive choices, but consumed more alcohol (12% wt/vol), than rats pre-exposed to immediate rewards. To understand the mechanisms that produced these findings, we again pre-exposed rats to either delayed (17.5 s; n = 32) or immediate (n = 30) rewards. In post-tests, delay-exposed rats made significantly fewer impulsive choices at both 15- and 30-s delays to a larger, later food reward than the immediacy-exposed comparison group. Behavior in an open-field test provided little evidence of differential stress exposure between groups. Further, consumption of either 12% alcohol or isocaloric sucrose in subsequent tests did not differ between groups. Because Stein et al. introduced alcohol concentration gradually (3–12%), we speculate that their group differences in 12% alcohol consumption were not determined by alcohol’s pharmacological effects, but by another variable (e.g., taste) that was preserved as an artifact from lower concentrations. We conclude that pre-exposure to delayed rewards generalizes beyond the pre-exposure delay; however, this same experimental variable does not robustly influence alcohol consumption. PMID:25418607

Coupled transcription and processing of mouse ribosomal RNA in a cell-free system.

PubMed Central

Mishima, Y; Mitsuma, T; Ogata, K

1985-01-01

An in vitro processing system of mouse rRNA was achieved using an RNA polymerase I-specific transcription system, (S100) and recombinant plasmids consisting of mouse rRNA gene (rDNA) segments containing the transcription initiation and 5'-terminal region of 18S (or 41S) rRNA. Pulse-chase experiments showed that a specific processing occurred with transcripts of the plasmid DNAs when the direction of transcription was the correct orientation relative to the 18S rRNA coding sequence, but not with transcripts of the DNA templates in which this coding sequence was in the opposite orientation. From the S1 nuclease protection analyses, we concluded that there are several steps of endonucleolytic cleavage including one 105 nucleotides upstream from the 5' end of 18S rRNA. Intermediates cleaved at this site were identified in in vivo processing of rRNA. This result indicates that endonucleolytic cleavage takes place 105 nucleotides upstream from the 5' terminus of 18S rRNA prior to the formation of mature 18S rRNA. Trimming or cleavage of the 105 nucleotides may be involved in the formation of the 5' terminus of mature 18S rRNA. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:3004977

Laboratory diagnosis of gestational diabetes: An in silico investigation into the effects of pre-analytical processing on the diagnostic sensitivity and specificity of the oral glucose tolerance test.

PubMed

Mansell, Erin; Lunt, Helen; Docherty, Paul

2017-06-01

Delayed separation of red cells from plasma causes pre analytical glucose loss, which in turn results in an under-diagnosis of GDM (gestational diabetes) based on the OGTT (oral glucose tolerance test). In silico investigations may help laboratory decision making, when exploring pragmatic improvements to sample processing. Late pregnancy 0, 1 and 2h 75g OGTT values were obtained from two distinct populations of pregnant women: 1. Values derived from the HAPO (Hyperglycemia and Adverse Pregnancy Outcome) Study and 2. New Zealand women identified as at higher risk of GDM by their caregivers, undergoing OGTT during routine antenatal care. In both populations studied, in silico modelling focussed on the effects of pre-analytical delays in plasma separation, when using fluoride collection tubes. Using a model that 'batched' samples from the three OGTT collection times, diagnostic sensitivity was estimated as follows: 66.1% for HAPO research population and 48.4% for the 1305 women receiving routine antenatal care. If samples were not batched, but processed shortly after each blood sample was collected, then sensitivity increased to 81%. Exploration of a range of clinical and laboratory scenarios using in silico modelling, showed that delaying the processing of pregnancy OGTT samples, using batched sample collection into fluoride tubes, causes unacceptable loss of GDM diagnostic sensitivity across two distinct population groups. This modelling approach will hopefully provide information that helps with final decision making around improved laboratory processing techniques. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

PANGEA: pipeline for analysis of next generation amplicons.

PubMed

Giongo, Adriana; Crabb, David B; Davis-Richardson, Austin G; Chauliac, Diane; Mobberley, Jennifer M; Gano, Kelsey A; Mukherjee, Nabanita; Casella, George; Roesch, Luiz F W; Walts, Brandon; Riva, Alberto; King, Gary; Triplett, Eric W

2010-07-01

High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching and classification, have been compiled into a pipeline called PANGEA. The PANGEA pipeline was written in Perl and can be run on Mac OSX, Windows or Linux. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities. Two different sets of bacterial 16S rRNA sequences were used to show the efficiency of this workflow. The first set of 16S rRNA sequences is derived from various soils from Hawaii Volcanoes National Park. The second set is derived from stool samples collected from diabetes-resistant and diabetes-prone rats. The workflow described here allows the investigator to quickly assess libraries of sequences on personal computers with customized databases. PANGEA is provided for users as individual scripts for each step in the process or as a single script where all processes, except the chi(2) step, are joined into one program called the 'backbone'.

Practical solution for control of the pre-analytical phase in decentralized clinical laboratories for meeting the requirements of the medical laboratory accreditation standard DIN EN ISO 15189.

PubMed

Vacata, Vladimir; Jahns-Streubel, Gerlinde; Baldus, Mirjana; Wood, William Graham

2007-01-01

This report was written in response to the article by Wood published recently in this journal. It describes a practical solution to the problems of controlling the pre-analytical phase in the clinical diagnostic laboratory. As an indicator of quality in the pre-analytical phase of sample processing, a target analyte was chosen which is sensitive to delay in centrifugation and/or analysis. The results of analyses of the samples sent by satellite medical practitioners were compared with those from an on-site hospital laboratory with a controllable optimized pre-analytical phase. The aim of the comparison was: (a) to identify those medical practices whose mean/median sample values significantly deviate from those of the control situation in the hospital laboratory due to the possible problems in the pre-analytical phase; (b) to aid these laboratories in the process of rectifying these problems. A Microsoft Excel-based Pre-Analytical Survey tool (PAS tool) has been developed which addresses the above mentioned problems. It has been tested on serum potassium which is known to be sensitive to delay and/or irregularities in sample treatment. The PAS tool has been shown to be one possibility for improving the quality of the analyses by identifying the sources of problems within the pre-analytical phase, thus allowing them to be rectified. Additionally, the PAS tool has an educational value and can also be adopted for use in other decentralized laboratories.

RNase MRP is required for entry of 35S precursor rRNA into the canonical processing pathway.

PubMed

Lindahl, Lasse; Bommankanti, Ananth; Li, Xing; Hayden, Lauren; Jones, Adrienne; Khan, Miriam; Oni, Tolulope; Zengel, Janice M

2009-07-01

RNase MRP is a nucleolar RNA-protein enzyme that participates in the processing of rRNA during ribosome biogenesis. Previous experiments suggested that RNase MRP makes a nonessential cleavage in the first internal transcribed spacer. Here we report experiments with new temperature-sensitive RNase MRP mutants in Saccharomyces cerevisiae that show that the abundance of all early intermediates in the processing pathway is severely reduced upon inactivation of RNase MRP. Transcription of rRNA continues unabated as determined by RNA polymerase run-on transcription, but the precursor rRNA transcript does not accumulate, and appears to be unstable. Taken together, these observations suggest that inactivation of RNase MRP blocks cleavage at sites A0, A1, A2, and A3, which in turn, prevents precursor rRNA from entering the canonical processing pathway (35S > 20S + 27S > 18S + 25S + 5.8S rRNA). Nevertheless, at least some cleavage at the processing site in the second internal transcribed spacer takes place to form an unusual 24S intermediate, suggesting that cleavage at C2 is not blocked. Furthermore, the long form of 5.8S rRNA is made in the absence of RNase MRP activity, but only in the presence of Xrn1p (exonuclease 1), an enzyme not required for the canonical pathway. We conclude that RNase MRP is a key enzyme for initiating the canonical processing of precursor rRNA transcripts, but alternative pathway(s) might provide a backup for production of small amounts of rRNA.

Improving operating room first start efficiency - value of both checklist and a pre-operative facilitator.

PubMed

Panni, M K; Shah, S J; Chavarro, C; Rawl, M; Wojnarwsky, P K; Panni, J K

2013-10-01

There are multiple components leading to improved operating room efficiency. We undertook a project focusing on first case starts; accounting for each delay component on a global basis. Our hypothesis was there would be a reduction in first start delays after we implemented strategies to address the issues identified through this accounting process. An orange sheet checklist was implemented, with specific items that needed to be clear prior to roll back to the operating room (OR), and an OR facilitator was employed to intervene whenever there were any missing items needed for a specific patient. We present the data from this quality improvement project over an 18-month period. Initially, 10.07 (± 0.73) delayed first starts occurred per day but declined steadily over time to a low of 4.95 (± 0.38) per day after 6 months (-49.2 %, P < 0.001). By the end of the project, the most common reasons for delay still included late surgical attending (19%), schedule changes (14%) as well as 'other reasons' (13%), but with an overall reduction per day of each. Total anaesthesia delay initially totalled 11% of the first start delays, but was negligible (< 1%) at the project's completion. While we have a challenging operating room environment based on our patient population, multiple trainees in both the surgery and anaesthesiology teams: an orange sheet - pre-operative checklist in addition to a dedicated pre-operative facilitator; allowed us to make a substantial improvement in our first start on time starts. © 2013 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

U14 small nucleolar RNA makes multiple contacts with the pre-ribosomal RNA.

PubMed

Morrissey, J P; Tollervey, D

1997-06-01

The small nucleolar RNA (snoRNA) U14 has two regions of extended primary sequence complementarity to the 18S rRNA. The 3' region (domain B) shows the consensus structure for the methylation guide class of snoRNAs, whereas base-pairing between the 5' region (domain A) and the 18S rRNA sequence is required for the formation of functional ribosomes. Between domains A and B lies another essential region (domain Y). Here we report that yeast U14 can be cross-linked in vivo to the pre-rRNA; cross-linking is detected exclusively with the 35S primary transcript. Many nucleotides in U14 that lie outside of domains A and B are cross-linked to the pre-rRNA; in particular the essential domain Y region is cross-linked at several sites. U14 is, therefore, in far more extensive contact with the pre-rRNA than predicted from simple base-pairing models. Moreover, U14 can be cross-linked to other small RNA species. The functional interactions made by U14 during ribosome synthesis are likely to be very complex.

The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript.

PubMed Central

Veldman, G M; Klootwijk, J; van Heerikhuizen, H; Planta, R J

1981-01-01

We have determined the nucleotide sequence of part of a cloned yeast ribosomal RNA operon extending from the 5.8S RNA gene downstream into the 5' -terminal region of the 26S RNA gene. We mapped the pertinent processing sites, viz. the 5' end of 26S rRNA and the 3'ends of 5.8S rRNA and its immediate precursor, 7S RNA. At the 3' end of 7S RNA we find the sequence UCGUUU which is very similar to the type I consensus sequence UCAUUA/U present at the 3' ends of 17S, 5.8S and 26S rRNA as well as 18S precursor rRNA in yeast. At the 5' end of the 26S RNA gene we find a sequence of thirteen nucleotides which is homologous to the type II sequence present at the 5' termini of both the 17S and the 5.8S RNA gene. These findings further support the suggestion put forward earlier (G.M. Veldman et al. (1980) Nucl. Acids Res. 8, 2907-2920) that both consensus sequences are involved in the recognition of precursor rRNA by the processing nuclease(s). We discuss a model for the processing of yeast rRNA in which a processing enzyme sequentially recognizes several combinations of a type I and a type II consensus sequence. We also describe the existence of a significant base complementarity between sequences in the 5' -terminal region of 26S rRNA and the 3' -terminal region of 5.8S rRNA. We suggest that base pairing between these sequences contributes to the binding between 5.8S and 26S rRNA. Images PMID:7312619

Automatic Generation of Cycle-Approximate TLMs with Timed RTOS Model Support

NASA Astrophysics Data System (ADS)

Hwang, Yonghyun; Schirner, Gunar; Abdi, Samar

This paper presents a technique for automatically generating cycle-approximate transaction level models (TLMs) for multi-process applications mapped to embedded platforms. It incorporates three key features: (a) basic block level timing annotation, (b) RTOS model integration, and (c) RTOS overhead delay modeling. The inputs to TLM generation are application C processes and their mapping to processors in the platform. A processor data model, including pipelined datapath, memory hierarchy and branch delay model is used to estimate basic block execution delays. The delays are annotated to the C code, which is then integrated with a generated SystemC RTOS model. Our abstract RTOS provides dynamic scheduling and inter-process communication (IPC) with processor- and RTOS-specific pre-characterized timing. Our experiments using a MP3 decoder and a JPEG encoder show that timed TLMs, with integrated RTOS models, can be automatically generated in less than a minute. Our generated TLMs simulated three times faster than real-time and showed less than 10% timing error compared to board measurements.

Building Schema through Writing: The Effects of Writing as a Pre-Reading Activity on Delayed Recall of Narrative Text.

ERIC Educational Resources Information Center

Marino, Jacqueline L.; And Others

Drawing upon research on the composing process and schema theory, a study explored the effects of a generative writing task presented prior to reading on the delayed recall of fourth grade students. The purpose of the study was to determine if a writing task that required the learner to identify with events in a text to be read later would assist…

Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing.

PubMed

Goldfarb, Katherine C; Cech, Thomas R

2017-01-01

MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR-Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor-analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing-implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation. © 2017 Goldfarb and Cech; Published by Cold Spring Harbor Laboratory Press.

An eye movement pre-training fosters the comprehension of processes and functions in technical systems.

PubMed

Skuballa, Irene T; Fortunski, Caroline; Renkl, Alexander

2015-01-01

The main research goal of the present study was to investigate in how far pre-training eye movements can facilitate knowledge acquisition in multimedia (pre-training principle). We combined considerations from research on eye movement modeling and pre-training to design and test a non-verbal eye movement-based pre-training. Participants in the experimental condition watched an animated circle moving in close spatial resemblance to a static visualization of a solar plant accompanied by a narration in a subsequently presented learning environment. This training was expected to foster top-down processes as reflected in gaze behavior during the learning process and enhance knowledge acquisition. We compared two groups (N = 45): participants in the experimental condition received pre-training in a first step and processed the learning material in a second step, whereas the control group underwent the second step without any pre-training. The pre-training group outperformed the control group in their learning outcomes, particularly in knowledge about processes and functions of the solar plant. However, the superior learning outcomes in the pre-training group could not be explained by eye-movement patterns. Furthermore, the pre-training moderated the relationship between experienced stress and learning outcomes. In the control group, high stress levels hindered learning, which was not found for the pre-training group. On a delayed posttest participants were requested to draw a picture of the learning content. Despite a non-significant effect of training on the quality of drawings, the pre-training showed associations between learning outcomes at the first testing time and process-related aspects in the quality of their drawings. Overall, non-verbal pre-training is a successful instructional intervention to promote learning processes in novices although these processes did not directly reflect in learners' eye movement behavior during learning.

Exploiting Pre-rRNA Processing in Diamond Blackfan Anemia Gene Discovery and Diagnosis

PubMed Central

Farrar, Jason E.; Quarello, Paola; Fisher, Ross; O’Brien, Kelly A.; Aspesi, Anna; Parrella, Sara; Henson, Adrianna L.; Seidel, Nancy E.; Atsidaftos, Eva; Prakash, Supraja; Bari, Shahla; Garelli, Emanuela; Arceci, Robert J.; Dianzani, Irma; Ramenghi, Ugo; Vlachos, Adrianna; Lipton, Jeffrey M.; Bodine, David M.; Ellis, Steven R.

2014-01-01

Diamond Blackfan anemia (DBA), a syndrome primarily characterized by anemia and physical abnormalities, is one among a group of related inherited bone marrow failure syndromes (IBMFS) which share overlapping clinical features. Heterozygous mutations or single-copy deletions have been identified in 12 ribosomal protein genes in approximately 60% of DBA cases, with the genetic etiology unexplained in most remaining patients. Unlike many IBMFS, for which functional screening assays complement clinical and genetic findings, suspected DBA in the absence of typical alterations of the known genes must frequently be diagnosed after exclusion of other IBMFS. We report here a novel deletion in a child that presented such a diagnostic challenge and prompted development of a novel functional assay that can assist in the diagnosis of a significant fraction of patients with DBA. The ribosomal proteins affected in DBA are required for pre-rRNA processing, a process which can be interrogated to monitor steps in the maturation of 40S and 60S ribosomal subunits. In contrast to prior methods used to assess pre-rRNA processing, the assay reported here, based on capillary electrophoresis measurement of the maturation of rRNA in pre-60S ribosomal subunits, would be readily amenable to use in diagnostic laboratories. In addition to utility as a diagnostic tool, we applied this technique to gene discovery in DBA, resulting in the identification of RPL31 as a novel DBA gene. PMID:25042156

Salinity inhibits post transcriptional processing of chloroplast 16S rRNA in shoot cultures of jojoba (Simmondsia chinesis).

PubMed

Mizrahi-Aviv, Ela; Mills, David; Benzioni, Aliza; Bar-Zvi, Dudy

2005-03-01

Chloroplast metabolism is rapidly affected by salt stress. Photosynthesis is one of the first processes known to be affected by salinity. Here, we report that salinity inhibits chloroplast post-transcriptional RNA processing. A differentially expressed 680-bp cDNA, containing the 3' sequence of 16S rRNA, transcribed intergenic spacer, exon 1 and intron of tRNA(Ile), was isolated by differential display reverse transcriptase PCR from salt-grown jojoba (Simmondsia chinesis) shoot cultures. Northern blot analysis indicated that although most rRNA appears to be fully processed, partially processed chloroplast 16S rRNA accumulates in salt-grown cultures. Thus, salinity appears to decrease the processing of the rrn transcript. The possible effect of this decreased processing on physiological processes is, as yet, unknown.

Assessing the costs attributed to project delay during project pre-construction stages

DOT National Transportation Integrated Search

2016-03-01

This project for the Texas Department of Transportation (TxDOT) developed a simple but sound : methodology for estimating the cost of delaying most types of highway projects. Researchers considered the : cost of delays during the pre-construction pha...

Assessing the costs attributed to project delay during project pre-construction stages.

DOT National Transportation Integrated Search

2016-03-01

This project for the Texas Department of Transportation (TxDOT) developed a simple but sound : methodology for estimating the cost of delaying most types of highway projects. Researchers considered the : cost of delays during the pre-construction pha...

Towards acute pediatric status epilepticus intervention teams: Do we need "Seizure Codes"?

PubMed

Stredny, Coral M; Abend, Nicholas S; Loddenkemper, Tobias

2018-05-01

To identify areas of treatment delay and barriers to care in pediatric status epilepticus, review ongoing quality improvement initiatives, and provide suggestions for further innovations to improve and standardize these patient care processes. Narrative review of current status epilepticus management algorithms, anti-seizure medication administration and outcomes associated with delays, and initiatives to improve time to treatment. Articles reviewing or reporting quality improvement initiatives were identified through a PubMed search with keywords "status epilepticus," "quality improvement," "guideline adherence," and/or "protocol;" references of included articles were also reviewed. Rapid initiation and escalation of status epilepticus treatment has been associated with shortened seizure duration and more favorable outcomes. Current evidence-based guidelines for management of status epilepticus propose medication algorithms with suggested times for each management step. However, time to antiseizure medication administration for pediatric status epilepticus remains delayed in both the pre- and in-hospital settings. Barriers to timely treatment include suboptimal preventive care, inaccurate seizure detection, infrequent or restricted use of home rescue medications by caregivers and pre-hospital emergency personnel, delayed summoning and arrival of emergency personnel, and use of inappropriately dosed medications. Ongoing quality improvement initiatives in the pre- and in-hospital settings targeting these barriers are reviewed. Improved preventive care, seizure detection, and rescue medication education may advance pre-hospital management, and we propose the use of acute status epilepticus intervention teams to initiate and incorporate in-hospital interventions as time-sensitive "Seizure Code" emergencies. Copyright © 2018 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

Improving first case start times using Lean in an academic medical center.

PubMed

Deldar, Romina; Soleimani, Tahereh; Harmon, Carol; Stevens, Larry H; Sood, Rajiv; Tholpady, Sunil S; Chu, Michael W

2017-06-01

Lean is a process improvement strategy that can improve efficiency of the perioperative process. The purpose of this study was to identify etiologies of late surgery start times, implement Lean interventions, and analyze their effects. A retrospective review of all first-start surgery cases was performed. Lean was implemented in May 2015, and cases 7 months before and after implementation were analyzed. A total of 4,492 first-start cases were included; 2,181 were pre-Lean and 2,311 were post-Lean. The post-Lean group had significantly higher on-time starts than the pre-Lean group (69.0% vs 57.0%, P < .01). The most common delay etiology was surgeon-related for both groups. Delayed post-Lean cases were significantly less likely to be due to preoperative assessment (14.9% vs 9.9%, P < .01) and more likely due to patient-related (16.5% vs 22.3%, P < .01) or chaplain (1.8% vs 4.0%, P < .01) factors. Delayed starts occurred more often on snowy and cold days, and less often on didactic days (P < .01). Modifying preoperative tasks using Lean methods can improve operating room efficiency and increase on-time starts. Copyright © 2016 Elsevier Inc. All rights reserved.

A Novel Association between Two Trypanosome-Specific Factors and the Conserved L5-5S rRNA Complex

PubMed Central

Ciganda, Martin; Prohaska, Kimberly; Hellman, Kristina; Williams, Noreen

2012-01-01

P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are involved in and essential for ribosome biogenesis. The proteins interact with the 5S rRNA with nearly identical binding characteristics. We have shown that this interaction is achieved mainly through the LoopA region of the RNA, but P34 and P37 also protect the L5 binding site located on LoopC. We now provide evidence to show that these factors form a novel pre-ribosomal particle through interactions with both 5S rRNA and the L5 ribosomal protein. Further in silico and in vitro analysis of T. brucei L5 indicates a lower affinity for 5S rRNA than expected, based on other eukaryotic L5 proteins. We hypothesize that P34 and P37 complement L5 and bridge the interaction with 5S rRNA, stabilizing it and aiding in the early steps of ribosome biogenesis. PMID:22859981

Ribosomal proteins L7 and L8 function in concert with six A3 assembly factors to propagate assembly of domains I and II of 25S rRNA in yeast 60S ribosomal subunits

PubMed Central

Jakovljevic, Jelena; Ohmayer, Uli; Gamalinda, Michael; Talkish, Jason; Alexander, Lisa; Linnemann, Jan; Milkereit, Philipp; Woolford, John L.

2012-01-01

Ribosome biogenesis is a complex multistep process that involves alternating steps of folding and processing of pre-rRNAs in concert with assembly of ribosomal proteins. Recently, there has been increased interest in the roles of ribosomal proteins in eukaryotic ribosome biogenesis in vivo, focusing primarily on their function in pre-rRNA processing. However, much less is known about participation of ribosomal proteins in the formation and rearrangement of preribosomal particles as they mature to functional subunits. We have studied ribosomal proteins L7 and L8, which are required for the same early steps in pre-rRNA processing during assembly of 60S subunits but are located in different domains within ribosomes. Depletion of either leads to defects in processing of 27SA3 to 27SB pre-rRNA and turnover of pre-rRNAs destined for large ribosomal subunits. A specific subset of proteins is diminished from these residual assembly intermediates: six assembly factors required for processing of 27SA3 pre-rRNA and four ribosomal proteins bound to domain I of 25S and 5.8S rRNAs surrounding the polypeptide exit tunnel. In addition, specific sets of ribosomal proteins are affected in each mutant: In the absence of L7, proteins bound to domain II, L6, L14, L20, and L33 are greatly diminished, while proteins L13, L15, and L36 that bind to domain I are affected in the absence of L8. Thus, L7 and L8 might establish RNP structures within assembling ribosomes necessary for the stable association and function of the A3 assembly factors and for proper assembly of the neighborhoods containing domains I and II. PMID:22893726

A cog in cognition: how the alpha 7 nicotinic acetylcholine receptor is geared towards improving cognitive deficits.

PubMed

Leiser, Steven C; Bowlby, Mark R; Comery, Thomas A; Dunlop, John

2009-06-01

Cognition, memory, and attention and arousal have been linked to nicotinic acetylcholine receptors (nAChRs). Thus it is not surprising that nAChRs have been strongly implicated as therapeutic targets for treating cognitive deficits in disorders such as schizophrenia and Alzheimer's disease (AD). In particular the alpha7 (alpha7) nAChR has been closely linked with normalization of P50 auditory evoked potential (AEP) gating deficits, and to a lesser extent improvements in pre-pulse inhibition (PPI) of the acoustic startle response. These two brain phenomena can be considered as pre-attentive, occurring while sensory information is being processed, and are important endophenotypes in schizophrenia with deficits likely contributing to the cognitive fragmentation associated with the disease. In addition alpha7 nAChRs have been implicated in attention, in particular under high attentional demand, and in more demanding working memory tasks such as long delays in delayed matching tasks. Efficacy of alpha7 nAChR agonists across a range of cognitive processes ranging from pre-attentive to attentive states and working and recognition memory provides a solid basis for their pro-cognitive effects. This review will focus on the recent work highlighting the role of alpha7 in cognition and cognitive processes.

A nuclear-encoded chloroplast protein harboring a single CRM domain plays an important role in the Arabidopsis growth and stress response.

PubMed

Lee, Kwanuk; Lee, Hwa Jung; Kim, Dong Hyun; Jeon, Young; Pai, Hyun-Sook; Kang, Hunseung

2014-04-16

Although several chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins have been characterized for intron splicing and rRNA processing during chloroplast gene expression, the functional role of a majority of CRM domain proteins in plant growth and development as well as chloroplast RNA metabolism remains largely unknown. Here, we characterized the developmental and stress response roles of a nuclear-encoded chloroplast protein harboring a single CRM domain (At4g39040), designated CFM4, in Arabidopsis thaliana. Analysis of CFM4-GFP fusion proteins revealed that CFM4 is localized to chloroplasts. The loss-of-function T-DNA insertion mutants for CFM4 (cfm4) displayed retarded growth and delayed senescence, suggesting that CFM4 plays a role in growth and development of plants under normal growth conditions. In addition, cfm4 mutants showed retarded seed germination and seedling growth under stress conditions. No alteration in the splicing patterns of intron-containing chloroplast genes was observed in the mutant plants, but the processing of 16S and 4.5S rRNAs was abnormal in the mutant plants. Importantly, CFM4 was determined to possess RNA chaperone activity. These results suggest that the chloroplast-targeted CFM4, one of two Arabidopsis genes encoding a single CRM domain-containing protein, harbors RNA chaperone activity and plays a role in the Arabidopsis growth and stress response by affecting rRNA processing in chloroplasts.

A nuclear-encoded chloroplast protein harboring a single CRM domain plays an important role in the Arabidopsis growth and stress response

PubMed Central

2014-01-01

Background Although several chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins have been characterized for intron splicing and rRNA processing during chloroplast gene expression, the functional role of a majority of CRM domain proteins in plant growth and development as well as chloroplast RNA metabolism remains largely unknown. Here, we characterized the developmental and stress response roles of a nuclear-encoded chloroplast protein harboring a single CRM domain (At4g39040), designated CFM4, in Arabidopsis thaliana. Results Analysis of CFM4-GFP fusion proteins revealed that CFM4 is localized to chloroplasts. The loss-of-function T-DNA insertion mutants for CFM4 (cfm4) displayed retarded growth and delayed senescence, suggesting that CFM4 plays a role in growth and development of plants under normal growth conditions. In addition, cfm4 mutants showed retarded seed germination and seedling growth under stress conditions. No alteration in the splicing patterns of intron-containing chloroplast genes was observed in the mutant plants, but the processing of 16S and 4.5S rRNAs was abnormal in the mutant plants. Importantly, CFM4 was determined to possess RNA chaperone activity. Conclusions These results suggest that the chloroplast-targeted CFM4, one of two Arabidopsis genes encoding a single CRM domain-containing protein, harbors RNA chaperone activity and plays a role in the Arabidopsis growth and stress response by affecting rRNA processing in chloroplasts. PMID:24739417

PreSSUB II: The prehospital stroke study at the Universitair Ziekenhuis Brussel II

PubMed Central

Espinoza, Alexis Valenzuela; Van Hooff, Robbert-Jan; De Smedt, Ann; Moens, Maarten; Yperzeele, Laetitia; Nieboer, Koenraad; Hubloue, Ives; De Keyser, Jacques; Dupont, Alain; De Wit, Liesbet; Putman, Koen; Brouns, Raf

2015-01-01

Rationale Stroke is a time-critical medical emergency requiring specialized treatment. Prehospital delay contributes significantly to delayed or missed treatment opportunities. In-ambulance telemedicine can bring stroke expertise to the prehospital arena and facilitate this complex diagnostic and therapeutic process. Aims This study evaluates the efficacy, safety, feasibility, reliability and cost-effectiveness of in-ambulance telemedicine for patients with suspicion of acute stroke. We hypothesize that this approach will reduce the delay to in-hospital treatment by streamlining the diagnostic process and that prehospital stroke care will be improved by expert stroke support via telemedicine during the ambulance transportation. Design PreSSUB II is an interventional, prospective, randomized, open-blinded, end-point, single-center trial comparing standard emergency care by the Paramedic Intervention Team of the Universitair Ziekenhuis Brussel (control) with standard emergency care complemented with in-ambulance teleconsultation service by stroke experts (PreSSUB). Study Outcomes The primary efficacy endpoint is the call-to-brain imaging time. Secondary endpoints for the efficacy analysis include the prevalence of medical events diagnosed and corrected during in-ambulance teleconsultation, the proportion of patients with ischemic stroke receiving recanalization therapy, the assessment of disability, functional status, quality of life and overall well-being. Mortality at 90 days after stroke is the primary safety endpoint. Secondary safety analysis will involve the registration of any adverse event. Other analyses include assessment of feasibility and reliability and a health economic evaluation. PMID:27847888

Interaction Between Strategic and Local Traffic Flow Controls

NASA Technical Reports Server (NTRS)

Grabbe, Son; Sridhar, Banavar; Mukherjee, Avijit; Morando, Alexander

2010-01-01

The loosely coordinated sets of traffic flow management initiatives that are operationally implemented at the national- and local-levels have the potential to under, over, and inconsistently control flights. This study is designed to explore these interactions through fast-time simulations with an emphasis on identifying inequitable situations in which flights receive multiple uncoordinated delays. Two operationally derived scenarios were considered in which flights arriving into the Dallas/Fort Worth International Airport were first controlled at the national-level, either with a Ground Delay Program or a playbook reroute. These flights were subsequently controlled at the local level. The Traffic Management Advisor assigned them arrival scheduling delays. For the Ground Delay Program scenarios, between 51% and 53% of all arrivals experience both pre-departure delays from the Ground Delay Program and arrival scheduling delays from the Traffic Management Advisor. Of the subset of flights that received multiple delays, between 5.7% and 6.4% of the internal departures were first assigned a pre-departure delay by the Ground Delay Program, followed by a second pre-departure delay as a result of the arrival scheduling. For the playbook reroute scenario, Dallas/Fort Worth International Airport arrivals were first assigned pre-departure reroutes based on the MW_2_DALLAS playbook plan, and were subsequently assigned arrival scheduling delays by the Traffic Management Advisor. Since the airport was operating well below capacity when the playbook reroute was in effect, only 7% of the arrivals were observed to receive both rerouting and arrival scheduling delays. Findings from these initial experiments confirm field observations that Ground Delay Programs operated in conjunction with arrival scheduling can result in inequitable situations in which flights receive multiple uncoordinated delays.

Effect of a comprehensive health education program on pre-hospital delay intentions in high-risk stroke population and caregivers.

PubMed

Yang, Li; Zhao, Qiuli; Zhu, Xuemei; Shen, Xiaoying; Zhu, Yulan; Yang, Liu; Gao, Wei; Li, Minghui

2017-08-01

Many factors influence pre-hospital delays in the event of stroke. This study aimed to develop and evaluate a comprehensive educational program for decreasing pre-hospital delays in high-risk stroke population. We enrolled 220 high-risk stroke population and caregivers from six urban communities in Harbin from May 2013 to May 2015, and randomly divided them into intervention and control groups. We implemented a comprehensive educational program (intervention group), comprising public lectures, instructional brochures, case videos, simulations, and role-playing from May 2013 to May 2015. We delivered conventional oral education in the control group. We compared stroke pre-hospital delay behavioral intention (SPDBI), pre-hospital stroke symptom coping test (PSSCT), and stroke pre-symptoms alert test (SPSAT) results between the groups before and 6, 12, and 18 months after health intervention. There were significant differences between before and after intervention (P < 0.01). SPDBI, PSSCT, and SPSAT scores were significantly different between the groups (P < 0.01). The interaction between time and intervention method was significant (P < 0.01). According to multivariate repeated measures analysis of variance, SPDBI, PSSCT, and SPSAT scores were significantly different at each time after intervention (P < 0.05). The comprehensive educational program was significantly effective in decreasing SPDBI, improving knowledge, enhancing stroke pre-symptoms alert, and reducing the possibility of pre-hospital delays.

Heat shock represses rRNA synthesis by inactivation of TIF-IA and lncRNA-dependent changes in nucleosome positioning.

PubMed

Zhao, Zhongliang; Dammert, Marcel A; Hoppe, Sven; Bierhoff, Holger; Grummt, Ingrid

2016-09-30

Attenuation of ribosome biogenesis in suboptimal growth environments is crucial for cellular homeostasis and genetic integrity. Here, we show that shutdown of rRNA synthesis in response to elevated temperature is brought about by mechanisms that target both the RNA polymerase I (Pol I) transcription machinery and the epigenetic signature of the rDNA promoter. Upon heat shock, the basal transcription factor TIF-IA is inactivated by inhibition of CK2-dependent phosphorylations at Ser170/172. Attenuation of pre-rRNA synthesis in response to heat stress is accompanied by upregulation of PAPAS, a long non-coding RNA (lncRNA) that is transcribed in antisense orientation to pre-rRNA. PAPAS interacts with CHD4, the adenosine triphosphatase subunit of NuRD, leading to deacetylation of histones and movement of the promoter-bound nucleosome into a position that is refractory to transcription initiation. The results exemplify how stress-induced inactivation of TIF-IA and lncRNA-dependent changes of chromatin structure ensure repression of rRNA synthesis in response to thermo-stress. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Exploring visual-graphic symbol acquisition by pre-school age children with developmental and language delays.

PubMed

Barton, Andrea; Sevcik, Rose A; Romski, Mary Ann

2006-03-01

The process of language acquisition requires an individual to organize the world through a system of symbols and referents. For children with severe intellectual disabilities and language delays, the ability to link a symbol to its referent may be a difficult task. In addition to the intervention strategy, issues such as the visual complexity and iconicity of a symbol arise when deciding what to select as a medium to teach language. This study explored the ability of four pre-school age children with developmental and language delays to acquire the meanings of Blissymbols and lexigrams using an observational experiential language intervention. In production, all four of the participants demonstrated symbol-referent relationships, while in comprehension, three of the four participants demonstrated at least emerging symbol-referent relationships. Although the number of symbols learned across participants varied, there were no differences between the learning of arbitrary and comparatively iconic symbols. The participants' comprehension skills appeared to influence their performance.

Effects of comprehensive education protocol in decreasing pre-hospital stroke delay among Chinese urban community population.

PubMed

Chen, Shengyun; Sun, Haixin; Zhao, Xingquan; Fu, Paul; Yan, Wang; Yilong, Wang; Hongyan, Jia; Yan, Zhang; Wenzhi, Wang

2013-06-01

Studies have shown that awareness of early stroke symptoms and the use of ambulances are two important factors in decreasing pre-hospital stroke delay. The purpose of this study is to evaluate a comprehensive educational stroke protocol in improving stroke response times. Two urban communities in Beijing (population ≍50 000), matched in economic status and geography, were enrolled in this study. A comprehensive educational protocol, which included public lectures and distribution of instructive material for the community and its medical staff, was implemented from August 2008 to December 2010. Surveillance of new onset stroke in both communities was carried out during the same period. Pre-hospital delay time and percentage of patients using emergency medical services (EMS) were compared between the two communities. After comprehensive educational protocol, we found that: (i) pre-hospital delay (time from stroke symptom onset to hospital arrival) decreased from 180 to 79 minutes, (ii) the proportion of patients arriving within three hours of stroke onset increased from 55·8% to 80·4%, (iii) pre-hospital delay of stroke patients with symptoms of paralysis, numbness, and speech impediments was decreased, and (iv) the proportion of stroke patients calling for EMS increased from 50·4% to 60·7%. The comprehensive educational stroke protocol was significantly effective in decreasing pre-hospital stroke delay.

Nucleolar sub-compartments in motion during rRNA synthesis inhibition: Contraction of nucleolar condensed chromatin and gathering of fibrillar centers are concomitant

PubMed Central

Tchelidze, Pavel; Benassarou, Aassif; Kaplan, Hervé; O’Donohue, Marie-Françoise; Lucas, Laurent; Terryn, Christine; Rusishvili, Levan; Mosidze, Giorgi; Lalun, Nathalie

2017-01-01

The nucleolus produces the large polycistronic transcript (47S precursor) containing the 18S, 5.8S and 28S rRNA sequences and hosts most of the nuclear steps of pre-rRNA processing. Among numerous components it contains condensed chromatin and active rRNA genes which adopt a more accessible conformation. For this reason, it is a paradigm of chromosome territory organization. Active rRNA genes are clustered within several fibrillar centers (FCs), in which they are maintained in an open configuration by Upstream Binding Factor (UBF) molecules. Here, we used the reproducible reorganization of nucleolar components induced by the inhibition of rRNA synthesis by Actinomycin D (AMD) to address the steps of the spatiotemporal reorganization of FCs and nucleolar condensed chromatin. To reach that goal, we used two complementary approaches: i) time-lapse confocal imaging of cells expressing one or several GFP-tagged proteins (fibrillarin, UBF, histone H2B) and ii) ultrastructural identification of nucleolar components involved in the reorganization. Data obtained by time lapse confocal microscopy were analyzed through detailed 3D imaging. This allowed us to demonstrate that AMD treatment induces no fusion and no change in the relative position of the different nucleoli contained in one nucleus. In contrast, for each nucleolus, we observed step by step gathering and fusion of both FCs and nucleolar condensed chromatin. To analyze the reorganization of FCs and condensed chromatin at a higher resolution, we performed correlative light and electron microscopy electron microscopy (CLEM) imaging of the same cells. We demonstrated that threads of intranucleolar condensed chromatin are localized in a complex 3D network of vacuoles. Upon AMD treatment, these structures coalesce before migrating toward the perinucleolar condensed chromatin, to which they finally fuse. During their migration, FCs, which are all linked to ICC, are pulled by the latter to gather as caps disposed at the periphery of nucleoli. PMID:29190286

A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs.

PubMed

Hammond, Ming C; Wachter, Andreas; Breaker, Ronald R

2009-05-01

Transcription factor IIIA (TFIIIA) is required for eukaryotic synthesis of 5S ribosomal RNA by RNA polymerase III. Here we report the discovery of a structured RNA element with clear resemblance to 5S rRNA that is conserved within TFIIIA precursor mRNAs from diverse plant lineages. TFIIIA protein expression is controlled by alternative splicing of the exon containing the plant 5S rRNA mimic (P5SM). P5SM triggers exon skipping upon binding of ribosomal protein L5, a natural partner of 5S rRNA, which demonstrates the functional adaptation of its structural mimicry. As the exon-skipped splice product encodes full-length TFIIIA protein, these results reveal a ribosomal protein-mRNA interaction that is involved in 5S rRNA synthesis and has implications for cross-coordination of ribosomal components. This study also provides insight into the origin and function of a newfound class of structured RNA that regulates alternative splicing.

Contamination of salmon fillets and processing plants with spoilage bacteria.

PubMed

Møretrø, Trond; Moen, Birgitte; Heir, Even; Hansen, Anlaug Å; Langsrud, Solveig

2016-11-21

The processing environment of salmon processing plants represents a potential major source of bacteria causing spoilage of fresh salmon. In this study, we have identified major contamination routes of important spoilage associated species within the genera Pseudomonas, Shewanella and Photobacterium in pre-rigor processing of salmon. Bacterial counts and culture-independent 16S rRNA gene analysis on salmon fillet from seven processing plants showed higher levels of Pseudomonas spp. and Shewanella spp. in industrially processed fillets compared to salmon processed under strict hygienic conditions. Higher levels of Pseudomonas spp. and Shewanella spp. were found on fillets produced early on the production day compared to later processed fillets. The levels of Photobacterium spp. were not dependent on the processing method or time of processing. In follow-up studies of two plants, bacterial isolates (n=2101) from the in-plant processing environments (sanitized equipment/machines and seawater) and from salmon collected at different sites in the production were identified by partial 16S rRNA gene sequencing. Pseudomonas spp. dominated in equipment/machines after sanitation with 72 and 91% of samples from the two plants being Pseudomonas-positive. The phylogenetic analyses, based on partial 16S rRNA gene sequencing, showed 48 unique sequence profiles of Pseudomonas of which two were dominant. Only six profiles were found on both machines and in fillets in both plants. Shewanella spp. were found on machines after sanitation in the slaughter department while Photobacterium spp. were not detected after sanitation in any parts of the plants. Shewanella spp. and Photobacterium spp. were found on salmon in the slaughter departments. Shewanella was frequently present in seawater tanks used for bleeding/short term storage. In conclusion, this study provides new knowledge on the processing environment as a source of contamination of salmon fillets with Pseudomonas spp. and Shewanella spp., while Photobacterium spp. most likely originate from the live fish and seawater. The study show that strict hygiene during processing is a prerequisite for optimal shelf life of salmon fillets and that about 90% reductions in the initial levels of bacteria on salmon fillets can be obtained using optimal hygienic conditions. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Breast cancer patient delay in Fukushima, Japan following the 2011 triple disaster: a long-term retrospective study.

PubMed

Ozaki, Akihiko; Nomura, Shuhei; Leppold, Claire; Tsubokura, Masaharu; Tanimoto, Tetsuya; Yokota, Takeru; Saji, Shigehira; Sawano, Toyoaki; Tsukada, Manabu; Morita, Tomohiro; Ochi, Sae; Kato, Shigeaki; Kami, Masahiro; Nemoto, Tsuyoshi; Kanazawa, Yukio; Ohira, Hiromichi

2017-06-19

Little information is available concerning how patient delay may be affected by mass disasters. The main objectives of the present study are to identify whether there was a post-disaster increase in the risk of experiencing patient delay among breast cancer patients in an area affected by the 2011 triple disaster in Fukushima, Japan, and to elucidate factors associated with post-disaster patient delay. Sociodemographic factors (age, employment status, cohabitant status and evacuation status), health characteristics, and health access- and disaster-related factors were specifically considered. Records of symptomatic breast cancer patients diagnosed from 2005 to 2016 were retrospectively reviewed to calculate risk ratios (RRs) for patient delay in every year post-disaster compared with the pre-disaster baseline. Total and excessive patient delays were respectively defined as three months or more and twelve months or more from symptom recognition to first medical consultation. Logistic regression analysis was conducted for pre- and post-disaster patient delay in order to reveal any factors potentially associated with patient delay, and changes after the disaster. Two hundred nineteen breast cancer patients (122 pre-disaster and 97 post-disaster) were included. After adjustments for age, significant post-disaster increases in RRs of experiencing both total (RR: 1.66, 95% Confidence Interval (CI): 1.02-2.70, p < 0.05) and excessive patient delay (RR: 4.49, 95% CI: 1.73-11.65, p < 0.01) were observed. The RRs for total patient delay peaked in the fourth year post-disaster, and significant increases in the risk of excessive patient delay were observed in the second, fourth, and fifth years post-disaster, with more than five times the risk observed pre-disaster. A family history of any cancer was the only factor significantly associated with total patient delay post-disaster (odds ratio: 0.38, 95% CI: 0.15-0.95, p < 0.05), while there were no variables associated with delay pre-disaster. The triple disaster in Fukushima appears to have led to an increased risk of patient delay among breast cancer patients, and this trend has continued for five years following the disaster.

Processing of intervening sequences: a new yeast mutant which fails to excise intervening sequences from precursor tRNAs.

PubMed

Hopper, A K; Schultz, L D; Shapiro, R A

1980-03-01

By using conditional loss of suppression an an assay, we have been successful in screening for a yeast mutant which is defective in tRNA processing. The los1-1 mutation causes an accumulation of a subset of precursor tRNAs at the nonpermissive temperature. These pre-tRNAs are like those which accumulate in the yeast mutant ts 136 (rna1) in that they have transcribed intervening sequences. The mutations at los1-1 and rna1 complement and segregate independently of each other. The los1-1 mutation affects the expression of all 8 tyrosine-inserting suppressor loci, but does not seem to affect rRNA or mRNA synthesis.

Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene.

PubMed

Schneider, Mary D; Bains, Anupinder K; Rajendra, T K; Dominski, Zbigniew; Matera, A Gregory; Simmonds, Andrew J

2010-11-01

MRP RNA is a noncoding RNA component of RNase mitochondrial RNA processing (MRP), a multi-protein eukaryotic endoribonuclease reported to function in multiple cellular processes, including ribosomal RNA processing, mitochondrial DNA replication, and cell cycle regulation. A recent study predicted a potential Drosophila ortholog of MRP RNA (CR33682) by computer-based genome analysis. We have confirmed the expression of this gene and characterized the phenotype associated with this locus. Flies with mutations that specifically affect MRP RNA show defects in growth and development that begin in the early larval period and end in larval death during the second instar stage. We present several lines of evidence demonstrating a role for Drosophila MRP RNA in rRNA processing. The nuclear fraction of Drosophila MRP RNA localizes to the nucleolus. Further, a mutant strain shows defects in rRNA processing that include a defect in 5.8S rRNA processing, typical of MRP RNA mutants in other species, as well as defects in early stages of rRNA processing.

An eye movement pre-training fosters the comprehension of processes and functions in technical systems

PubMed Central

Skuballa, Irene T.; Fortunski, Caroline; Renkl, Alexander

2015-01-01

The main research goal of the present study was to investigate in how far pre-training eye movements can facilitate knowledge acquisition in multimedia (pre-training principle). We combined considerations from research on eye movement modeling and pre-training to design and test a non-verbal eye movement-based pre-training. Participants in the experimental condition watched an animated circle moving in close spatial resemblance to a static visualization of a solar plant accompanied by a narration in a subsequently presented learning environment. This training was expected to foster top-down processes as reflected in gaze behavior during the learning process and enhance knowledge acquisition. We compared two groups (N = 45): participants in the experimental condition received pre-training in a first step and processed the learning material in a second step, whereas the control group underwent the second step without any pre-training. The pre-training group outperformed the control group in their learning outcomes, particularly in knowledge about processes and functions of the solar plant. However, the superior learning outcomes in the pre-training group could not be explained by eye-movement patterns. Furthermore, the pre-training moderated the relationship between experienced stress and learning outcomes. In the control group, high stress levels hindered learning, which was not found for the pre-training group. On a delayed posttest participants were requested to draw a picture of the learning content. Despite a non-significant effect of training on the quality of drawings, the pre-training showed associations between learning outcomes at the first testing time and process-related aspects in the quality of their drawings. Overall, non-verbal pre-training is a successful instructional intervention to promote learning processes in novices although these processes did not directly reflect in learners' eye movement behavior during learning. PMID:26029138

A Classroom Collaborative Strategy Designed To Improve Oral Motor Skill Deficits in Developmentally Delayed Pre-Kindergarten Students.

ERIC Educational Resources Information Center

Hoffman, Lorri J.

This practicum report describes the design and implementation of an oral motor program to increase the verbal communication skills of seven pre-kindergarten children with developmental delays, including hypotonia in oral motor development with moderate to severe articulation difficulties. Collaborative planning by the pre-kindergarten special…

Reducing door-to-needle times using Toyota's lean manufacturing principles and value stream analysis.

PubMed

Ford, Andria L; Williams, Jennifer A; Spencer, Mary; McCammon, Craig; Khoury, Naim; Sampson, Tomoko R; Panagos, Peter; Lee, Jin-Moo

2012-12-01

Earlier tissue-type plasminogen activator (tPA) treatment for acute ischemic stroke increases efficacy, prompting national efforts to reduce door-to-needle times. We used lean process improvement methodology to develop a streamlined intravenous tPA protocol. In early 2011, a multidisciplinary team analyzed the steps required to treat patients with acute ischemic stroke with intravenous tPA using value stream analysis (VSA). We directly compared the tPA-treated patients in the "pre-VSA" epoch with the "post-VSA" epoch with regard to baseline characteristics, protocol metrics, and clinical outcomes. The VSA revealed several tPA protocol inefficiencies: routing of patients to room, then to CT, then back to the room; serial processing of workflow; and delays in waiting for laboratory results. On March 1, 2011, a new protocol incorporated changes to minimize delays: routing patients directly to head CT before the patient room, using parallel process workflow, and implementing point-of-care laboratories. In the pre and post-VSA epochs, 132 and 87 patients were treated with intravenous tPA, respectively. Compared with pre-VSA, door-to-needle times and percent of patients treated ≤60 minutes from hospital arrival were improved in the post-VSA epoch: 60 minutes versus 39 minutes (P<0.0001) and 52% versus 78% (P<0.0001), respectively, with no change in symptomatic hemorrhage rate. Lean process improvement methodology can expedite time-dependent stroke care without compromising safety.

Reducing Door-to-Needle Times using Toyota’s Lean Manufacturing Principles and Value Stream Analysis

PubMed Central

Ford, Andria L.; Williams, Jennifer A.; Spencer, Mary; McCammon, Craig; Khoury, Naim; Sampson, Tomoko; Panagos, Peter; Lee, Jin-Moo

2012-01-01

Background Earlier tPA treatment for acute ischemic stroke increases efficacy, prompting national efforts to reduce door-to-needle times (DNTs). We utilized lean process improvement methodology to develop a streamlined IV tPA protocol. Methods In early 2011, a multi-disciplinary team analyzed the steps required to treat acute ischemic stroke patients with IV tPA, utilizing value stream analysis (VSA). We directly compared the tPA-treated patients in the “pre-VSA” epoch to the “post-VSA” epoch with regard to baseline characteristics, protocol metrics, and clinical outcomes. Results The VSA revealed several tPA protocol inefficiencies: routing of patients to room, then to CT, then back to room; serial processing of work flow; and delays in waiting for lab results. On 3/1/2011, a new protocol incorporated changes to minimize delays: routing patients directly to head CT prior to patient room, utilizing parallel process work-flow, and implementing point-of-care labs. In the pre-and post-VSA epochs, 132 and 87 patients were treated with IV tPA, respectively. Compared to pre-VSA, DNTs and percent of patients treated ≤60 minutes from hospital arrival were improved in the post-VSA epoch: 60 min vs. 39 min (p<0.0001) and 52% vs. 78% (p<0.0001), respectively, with no change in symptomatic hemorrhage rate. Conclusions Lean process improvement methodology can expedite time-dependent stroke care, without compromising safety. PMID:23138440

Apoptosis-like programmed cell death induces antisense ribosomal RNA (rRNA) fragmentation and rRNA degradation in Leishmania.

PubMed

Padmanabhan, P K; Samant, M; Cloutier, S; Simard, M J; Papadopoulou, B

2012-12-01

Few natural antisense (as) RNAs have been reported as yet in the unicellular protozoan Leishmania. Here, we describe that Leishmania produces natural asRNAs complementary to all ribosomal RNA (rRNA) species. Interestingly, we show that drug-induced apoptosis-like programmed cell death triggers fragmentation of asRNA complementary to the large subunit gamma (LSU-γ) rRNA, one of the six 28S rRNA processed fragments in Leishmania. Heat and oxidative stress also induce fragmentation of asrRNA, but to a lesser extent. Extensive asrRNA cleavage correlates with rRNA breakdown and translation inhibition. Indeed, overexpression of asLSU-γ rRNA accelerates rRNA degradation upon induction of apoptosis. In addition, we provide mechanistic insight into the regulation of apoptosis-induced asrRNA fragmentation by a 67 kDa ATP-dependent RNA helicase of the DEAD-box subfamily. This helicase binds both sense (s)LSU-γ and asLSU-γ rRNAs, and appears to have a key role in protecting rRNA from degradation by preventing asrRNA cleavage and thus cell death. Remarkably, the asrRNA fragmentation process operates not only in trypanosomatid protozoa but also in mammals. Our findings uncover a novel mechanism of regulation involving asrRNA fragmentation and rRNA breakdown, that is triggered by apoptosis and conditions of reduced translation under stress, and seems to be evolutionary conserved.

RlmCD-mediated U747 methylation promotes efficient G748 methylation by methyltransferase RlmAII in 23S rRNA in Streptococcus pneumoniae; interplay between two rRNA methylations responsible for telithromycin susceptibility

PubMed Central

Shoji, Tatsuma; Takaya, Akiko; Sato, Yoshiharu; Kimura, Satoshi; Suzuki, Tsutomu; Yamamoto, Tomoko

2015-01-01

Adenine at position 752 in a loop of helix 35 from positions 745 to 752 in domain II of 23S rRNA is involved in binding to the ribosome of telithromycin (TEL), a member of ketolides. Methylation of guanine at position 748 by the intrinsic methyltransferase RlmAII enhances binding of telithromycin (TEL) to A752 in Streptococcus pneumoniae. We have found that another intrinsic methylation of the adjacent uridine at position 747 enhances G748 methylation by RlmAII, rendering TEL susceptibility. U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae. Inactivation of RlmCD reduced N1-methylated level of G748 by RlmAII in vivo, leading to TEL resistance when the nucleotide A2058, located in domain V of 23S rRNA, was dimethylated by the dimethyltransferase Erm(B). In vitro methylation of rRNA showed that RlmAII activity was significantly enhanced by RlmCD-mediated pre-methylation of 23S rRNA. These results suggest that RlmCD-mediated U747 methylation promotes efficient G748 methylation by RlmAII, thereby facilitating TEL binding to the ribosome. PMID:26365244

Metabolic profiling of body fluids and multivariate data analysis.

PubMed

Trezzi, Jean-Pierre; Jäger, Christian; Galozzi, Sara; Barkovits, Katalin; Marcus, Katrin; Mollenhauer, Brit; Hiller, Karsten

2017-01-01

Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids. This protocol can be applied on blood serum/plasma, saliva and cerebrospinal fluid (CSF) samples of humans and other vertebrates. It covers sample collection, sample pre-processing, metabolite extraction, GC-MS measurement and guidelines for the subsequent data analysis. Advantages of this protocol include: •Robust and reproducible metabolomics results, taking into account pre-analytical variations that may occur during the sampling process•Small sample volume required•Rapid and cost-effective processing of biological samples•Logistic regression based determination of biomarker signatures for in-depth data analysis.

31 CFR 560.515 - 30-day delayed effective date for pre-May 7, 1995 trade contracts involving Iran.

Code of Federal Regulations, 2012 CFR

2012-07-01

...-May 7, 1995 trade contracts involving Iran. 560.515 Section 560.515 Money and Finance: Treasury....515 30-day delayed effective date for pre-May 7, 1995 trade contracts involving Iran. (a) All... involving Iran (a pre-existing trade contract), including the exportation of goods, services (including...

Mesoamerican Origin and Pre- and Post-Columbian Expansions of the Ranges of Acanthoscelides obtectus Say, a Cosmopolitan Insect Pest of the Common Bean

PubMed Central

Oliveira, Márcia Rodrigues Carvalho; Corrêa, Alberto Soares; de Souza, Giselle Anselmo; Guedes, Raul Narciso Carvalho; de Oliveira, Luiz Orlando

2013-01-01

An unprecedented global transfer of agricultural resources followed the discovery of the New World; one consequence of this process was that staple food plants of Neotropical origin, such as the common bean (Phaseolus vulgaris), soon expanded their ranges overseas. Yet many pests and diseases were also transported. Acanthoscelides obtectus is a cosmopolitan seed predator associated with P. vulgaris. Codispersal within the host seed seems to be an important determinant of the ability of A. obtectus to expand its range over long distances. We examined the phylogeographic structure of A. obtectus by (a) sampling three mitochondrial gene sequences (12s rRNA, 16s rRNA, and the gene that encodes cytochrome c oxidase subunit I (COI)) throughout most of the species’ range and (b) exploring its late evolutionary history. Our findings indicate a Mesoamerican origin for the current genealogical lineages of A. obtectus. Each of the two major centers of genetic diversity of P. vulgaris (the Andes and Mesoamerica) contains a highly differentiated lineage of the bean beetle. Brazil has two additional, closely related lineages, both of which predate the Andean lineage and have the Mesoamerican lineage as their ancestor. The cosmopolitan distribution of A. obtectus has resulted from recent expansions of the two Brazilian lineages. We present additional evidence for both pre-Columbian and post-Columbian range expansions as likely events that shaped the current distribution of A. obtectus worldwide. PMID:23936139

Chaperoning 5S RNA assembly

PubMed Central

Madru, Clément; Lebaron, Simon; Blaud, Magali; Delbos, Lila; Pipoli, Juliana; Pasmant, Eric; Réty, Stéphane; Leulliot, Nicolas

2015-01-01

In eukaryotes, three of the four ribosomal RNAs (rRNAs)—the 5.8S, 18S, and 25S/28S rRNAs—are processed from a single pre-rRNA transcript and assembled into ribosomes. The fourth rRNA, the 5S rRNA, is transcribed by RNA polymerase III and is assembled into the 5S ribonucleoprotein particle (RNP), containing ribosomal proteins Rpl5/uL18 and Rpl11/uL5, prior to its incorporation into preribosomes. In mammals, the 5S RNP is also a central regulator of the homeostasis of the tumor suppressor p53. The nucleolar localization of the 5S RNP and its assembly into preribosomes are performed by a specialized complex composed of Rpf2 and Rrs1 in yeast or Bxdc1 and hRrs1 in humans. Here we report the structural and functional characterization of the Rpf2–Rrs1 complex alone, in complex with the 5S RNA, and within pre-60S ribosomes. We show that the Rpf2–Rrs1 complex contains a specialized 5S RNA E-loop-binding module, contacts the Rpl5 protein, and also contacts the ribosome assembly factor Rsa4 and the 25S RNA. We propose that the Rpf2–Rrs1 complex establishes a network of interactions that guide the incorporation of the 5S RNP in preribosomes in the initial conformation prior to its rotation to form the central protuberance found in the mature large ribosomal subunit. PMID:26159998

Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge.

PubMed

Pervin, Hasina M; Batstone, Damien J; Bond, Philip L

2013-06-01

Thermophilic biological pre-treatment enables enhanced anaerobic digestion for treatment of wastewater sludges but, at present, there is limited understanding of the hydrolytic-acidogenic microbial composition and its contribution to this process. In this study, the process was assessed by comparing the microbiology of thermophilic (50-65 °C) and mesophilic (35 °C) pre-treatment reactors treating primary sludge. A full-cycle approach for the 16S rRNA genes was applied in order to monitor the diversity of bacteria and their abundance in a thermophilic pre-treatment reactor treating primary sludge. For the thermophilic pre-treatment (TP), over 90% of the sequences were previously undetected and these had less than 97% sequence similarity to cultured organisms. During the first 83 days, members of the Betaproteobacteria dominated the community sequences and a newly designed probe was used to monitor a previously unknown bacterium affiliated with the genus Brachymonas. Between days 85 and 183, three phylotypes that affiliated with the genera Comamonas, Clostridium and Lysobacter were persistently dominant in the TP community, as revealed by terminal-restriction fragment length polymorphism (T-RFLP). Hydrolytic and fermentative functions have been speculated for these bacteria. Mesophilic pre-treatment (MP) and TP communities were different but they were both relatively dynamic. Statistical correlation analysis and the function of closely allied reference organisms indicated that previously unclassified bacteria dominated the TP community and may have been functionally involved in the enhanced hydrolytic performance of thermophilic anaerobic pre-treatment. This study is the first to reveal the diversity and dynamics of bacteria during anaerobic digestion of primary sludge. Copyright © 2013 Elsevier GmbH. All rights reserved.

Simultaneous separation of five major ribonucleic acids by capillary electrophoresis with laser-induced fluorescence in the presence of electroosmotic flow: application to the rapid screening of 5S rRNA from ovarian cancer cells.

PubMed

Shih, Ya-Chu; Liao, Ching-Ru; Chung, I-Che; Chang, Yu-Sun; Chang, Po-Ling

2014-10-17

RNA integrity is important in RNA studies because poor RNA quality may impact downstream methodologies. This study proposes a rapid and cost-effective method for the determination of RNA integrity based on CE-LIF in the presence of electroosmotic flow. The proposed method uses poly(ethylene) oxide (Mavg=4,000,000 Da) as a sieving matrix for total RNA separation. Ethidium bromide (μg mL(-1)) was dissolved in a polymer solution as an interchelating dye for on-column fluorescent labeling. The 28S rRNA, 18S rRNA, 5.8S rRNA, 5S rRNA and tRNA from the total human RNA extracted from the cells were fully separated using the proposed method. The lowest detectable concentration of total RNA achieved was 100 pg μL(-1) with a 6 min sample injection followed by on-column concentration. In addition, the temperature-induced degradation of total RNA was observed by CE-LIF. The electropherograms revealed more fragmentation of 28S and 18S rRNAs by temperature-induced hydrolysis compared with the 5.8S rRNA, 5S rRNA and tRNA. Therefore, the results indicated that RNA degradation should be considered for long-term, high-temperature incubations in RNA-related experiments involving RNA hybridization. The proposed method is furthermore, applied to the determination of 5S rRNA overexpressed in ovarian cancer cells as compared to the cervical cancer cells. Overall, CE-LIF is highly promising for rapid screening of ovarian cancers without tedious pre-amplification steps. Copyright © 2014 Elsevier B.V. All rights reserved.

Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils.

PubMed

Webster, Gordon; Embley, T Martin; Freitag, Thomas E; Smith, Zena; Prosser, James I

2005-05-01

Molecular approaches have revealed considerable diversity and uncultured novelty in natural prokaryotic populations, but not direct links between the new genotypes detected and ecosystem processes. Here we describe the influence of the structure of communities of ammonia-oxidizing bacteria on nitrogen cycling in microcosms containing natural and managed grasslands and amended with artificial sheep urine, a major factor determining local ammonia concentrations in these environments. Nitrification kinetics were assessed by analysis of changes in urea, ammonia, nitrite and nitrate concentrations and ammonia oxidizer communities were characterized by analysis of 16S rRNA genes amplified from extracted DNA using ammonia oxidizer-specific primers. In natural soils, ammonia oxidizer community structure determined the delay preceding nitrification, which depended on the relative abundance of two Nitrosospira clusters, termed 3a and 3b. In batch cultures, pure culture and enrichment culture representatives of Nitrosospira 3a were sensitive to high ammonia concentration, while Nitrosospira cluster 3b representatives and Nitrosomonas europaea were tolerant. Delays in nitrification occurred in natural soils dominated by Nitrosospira cluster 3a and resulted from the time required for growth of low concentrations of Nitrosospira cluster 3b. In microcosms dominated by Nitrosospira cluster 3b and Nitrosomonas, no substantial delays were observed. In managed soils, no delays in nitrification were detected, regardless of initial ammonia oxidizer community structure, most probably resulting from higher ammonia oxidizer cell concentrations. The data therefore demonstrate a direct link between bacterial community structure, physiological diversity and ecosystem function.

Temporal programming of chloroplast and cytoplasmic ribosomal RNA transcription in the synchronous cell cycle of Chlamydomonas reinhardtii

PubMed Central

1977-01-01

Approximately 90% of the Chlamydomonas reinhardtii chloroplast and cytoplasmic rRNAs was transcribed in the nuclear G1 phase, which occurred during the light period under an alternating light-dark synchronization regime of 12 h each. The remaining 10% of chloroplast and cytoplasmic rRNAs was transcribed from its respective DNAs in the dark period, in the midst of an apparent turnover of a transcription appeared to be prokaryotic in sophistication. The transcription was not interrupted during chloroplast DNA synthesis which occurred during the light period. However, transcription of the nuclear DNA was repressed severely during the nuclear S phase in the dark period. The patterns of incorporation of 32P into chloroplast and cytoplasmic rRNA species in the cell cycle were similar to those of the actual rRNA synthesis as measured optically. However, the quantity of 32P incorporation per unit amount of rRNA synthesized varied considerably during the cell cycle, increasing in all rRNA's during the dark period. 32P incorporation data obtained from continuous and pulse 32P-labeling experiments also revealed a turnover of a small amount of both cytoplasmic and chloroplast rRNAs at the end of the S phase. The 32P incorporation into cytoplasmic and chloroplast rRNAs was well matched temporally with the 32P incorporation into their corresponding ribosomes, indicating that the newly synthesized rRNA molecules are utilized without delay throughout the cell cycle in the assembly of ribosomes. PMID:833204

Apoptosis-like programmed cell death induces antisense ribosomal RNA (rRNA) fragmentation and rRNA degradation in Leishmania

PubMed Central

Padmanabhan, P K; Samant, M; Cloutier, S; Simard, M J; Papadopoulou, B

2012-01-01

Few natural antisense (as) RNAs have been reported as yet in the unicellular protozoan Leishmania. Here, we describe that Leishmania produces natural asRNAs complementary to all ribosomal RNA (rRNA) species. Interestingly, we show that drug-induced apoptosis-like programmed cell death triggers fragmentation of asRNA complementary to the large subunit gamma (LSU-γ) rRNA, one of the six 28S rRNA processed fragments in Leishmania. Heat and oxidative stress also induce fragmentation of asrRNA, but to a lesser extent. Extensive asrRNA cleavage correlates with rRNA breakdown and translation inhibition. Indeed, overexpression of asLSU-γ rRNA accelerates rRNA degradation upon induction of apoptosis. In addition, we provide mechanistic insight into the regulation of apoptosis-induced asrRNA fragmentation by a 67 kDa ATP-dependent RNA helicase of the DEAD-box subfamily. This helicase binds both sense (s)LSU-γ and asLSU-γ rRNAs, and appears to have a key role in protecting rRNA from degradation by preventing asrRNA cleavage and thus cell death. Remarkably, the asrRNA fragmentation process operates not only in trypanosomatid protozoa but also in mammals. Our findings uncover a novel mechanism of regulation involving asrRNA fragmentation and rRNA breakdown, that is triggered by apoptosis and conditions of reduced translation under stress, and seems to be evolutionary conserved. PMID:22767185

FunGene: the functional gene pipeline and repository.

PubMed

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

Estimation of contrast agent bolus arrival delays for improved reproducibility of liver DCE MRI

NASA Astrophysics Data System (ADS)

Chouhan, Manil D.; Bainbridge, Alan; Atkinson, David; Punwani, Shonit; Mookerjee, Rajeshwar P.; Lythgoe, Mark F.; Taylor, Stuart A.

2016-10-01

Delays between contrast agent (CA) arrival at the site of vascular input function (VIF) sampling and the tissue of interest affect dynamic contrast enhanced (DCE) MRI pharmacokinetic modelling. We investigate effects of altering VIF CA bolus arrival delays on liver DCE MRI perfusion parameters, propose an alternative approach to estimating delays and evaluate reproducibility. Thirteen healthy volunteers (28.7  ±  1.9 years, seven males) underwent liver DCE MRI using dual-input single compartment modelling, with reproducibility (n  =  9) measured at 7 days. Effects of VIF CA bolus arrival delays were assessed for arterial and portal venous input functions. Delays were pre-estimated using linear regression, with restricted free modelling around the pre-estimated delay. Perfusion parameters and 7 days reproducibility were compared using this method, freely modelled delays and no delays using one-way ANOVA. Reproducibility was assessed using Bland-Altman analysis of agreement. Maximum percent change relative to parameters obtained using zero delays, were  -31% for portal venous (PV) perfusion, +43% for total liver blood flow (TLBF), +3247% for hepatic arterial (HA) fraction, +150% for mean transit time and  -10% for distribution volume. Differences were demonstrated between the 3 methods for PV perfusion (p  =  0.0085) and HA fraction (p  <  0.0001), but not other parameters. Improved mean differences and Bland-Altman 95% Limits-of-Agreement for reproducibility of PV perfusion (9.3 ml/min/100 g, ±506.1 ml/min/100 g) and TLBF (43.8 ml/min/100 g, ±586.7 ml/min/100 g) were demonstrated using pre-estimated delays with constrained free modelling. CA bolus arrival delays cause profound differences in liver DCE MRI quantification. Pre-estimation of delays with constrained free modelling improved 7 days reproducibility of perfusion parameters in volunteers.

Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda.

PubMed

Wu, Shu; Xiong, Jie; Yu, Yuhe

2015-01-01

Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.

Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

PubMed Central

Wu, Shu; Xiong, Jie; Yu, Yuhe

2015-01-01

Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1–9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy. PMID:26107258

Blood Substrate Collection and Handling Procedures under Pseudo-Field Conditions: Evaluation of Suitability for Inflammatory Biomarker Measurement

PubMed Central

Danese, Andrea; Shalev, Idan; Williams, Benjamin S.; Caspi, Avshalom

2015-01-01

Routine incorporation of blood-based biomarker measurements in population studies has been hampered by challenges in obtaining samples suitable for biomarker assessment outside of laboratory settings. Here, we assessed the suitability of venous blood left unprocessed for four, 24 or 48 hours post-collection at either room temperature or 4°C for quantification of two biomarkers, Interleukin-6 (IL-6) and C-Reactive Protein (CRP). Blood samples were collected in both K2EDTA tubes and a dedicated plasma-preservation tube, P100. Dried Blood Spot (DBS) samples from the same subjects were also collected in order to compare delayed-processing plasma performance against a popular alternative collection method. K2EDTA mean plasma concentrations of both IL-6 and CRP were not significantly different from concentrations in plasma processed immediately; this was observed for tubes stored up to 48 hours pre-processing at either temperature. Concentrations of IL-6 measured in P100 tubes showed significant time-dependent increases when stored at room temperature; otherwise, levels of IL-6 and CRP were similar to those processed immediately. Levels of CRP in DBS were correlated with plasma CRP levels, even when pre-processed blood was stored for up to 48 hours. These data indicate that plasma is suitable for IL-6 and CRP estimation under data-collection conditions that involve processing delays. PMID:26652682

Blood Substrate Collection and Handling Procedures under Pseudo-Field Conditions: Evaluation of Suitability for Inflammatory Biomarker Measurement.

PubMed

Sugden, Karen; Danese, Andrea; Shalev, Idan; Williams, Benjamin S; Caspi, Avshalom

2015-01-01

Routine incorporation of blood-based biomarker measurements in population studies has been hampered by challenges in obtaining samples suitable for biomarker assessment outside of laboratory settings. Here, we assessed the suitability of venous blood left unprocessed for 4, 24, or 48 hours post-collection at either room temperature or 4°C for quantification of two biomarkers, Interleukin-6 (IL-6) and C-reactive protein (CRP). Blood samples were collected in both K2EDTA tubes and a dedicated plasma-preservation tube, P100. Dried blood spot (DBS) samples from the same subjects were also collected in order to compare delayed-processing plasma performance against a popular alternative collection method. We found that K2EDTA mean plasma concentrations of both IL-6 and CRP were not significantly different from concentrations in plasma processed immediately; this was observed for tubes stored up to 48 hours pre-processing at either temperature. Concentrations of IL-6 measured in P100 tubes showed significant time-dependent increases when stored at room temperature; otherwise, levels of IL-6 and CRP were similar to those found in samples processed immediately. Levels of CRP in DBS were correlated with plasma CRP levels, even when pre-processed blood was stored for up to 48 hours. These data indicate that plasma is suitable for IL-6 and CRP estimation under data collection conditions that involve processing delays.

Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3' end formation.

PubMed

Briggs, M W; Burkard, K T; Butler, J S

1998-05-22

The eukaryotic 25 S, 18 S, and 5.8 S rRNAs are synthesized as a single transcript with two internal transcribed spacers (ITS1 and ITS2), which are removed by endo- and exoribonucleolytic steps to produce mature rRNA. Genetic selection for suppressors of a polyadenylation defect yielded two cold-sensitive alleles of a gene that we named RRP6 (ribosomal RNA processing). Molecular cloning of RRP6 revealed its homology to a 100-kDa human, nucleolar PM-Scl autoantigen and to Escherichia coli RNase D, a 3'-5' exoribonuclease. Recessive mutations in rrp6 result in the accumulation of a novel 5. 8 S rRNA processing intermediate, called 5.8 S*, which has normal 5' ends, but retains approximately 30 nucleotides of ITS2. Pulse-chase analysis of 5.8 S rRNA processing in an rrp6- strain revealed a precursor-product relationship between 5.8 S* and 5.8 S rRNAs, suggesting that Rrp6p plays a role in the removal of the last 30 nucleotides of ITS2 from 5.8 S precursors. A portion of 5.8 S* rRNA assembles into 60 S ribosomes which form polyribosomes, suggesting that they function in protein synthesis. These findings indicate that Rrp6p plays a role in 5.8 S rRNA 3' end formation, and they identify a functional intermediate in the rRNA processing pathway.

Comparative analysis of the 5S rRNA and its associated proteins reveals unique primitive rather than parasitic features in Giardia lamblia.

PubMed

Feng, Jin-Mei; Sun, Jun; Xin, De-Dong; Wen, Jian-Fan

2012-01-01

5S rRNA is a highly conserved ribosomal component. Eukaryotic 5S rRNA and its associated proteins (5S rRNA system) have become very well understood. Giardia lamblia was thought by some researchers to be the most primitive extant eukaryote while others considered it a highly evolved parasite. Previous reports have indicated that some aspects of its 5S rRNA system are simpler than that of common eukaryotes. We here explore whether this is true to its entire system, and whether this simplicity is a primitive or parasitic feature. By collecting and confirming pre-existing data and identifying new data, we obtained almost complete datasets of the system of three isolates of G. lamblia, two other parasitic excavates (Trichomonas vaginalis, Trypanosoma cruzi), and one free-living one (Naegleria gruberi). After comprehensively comparing each aspect of the system among these excavates and also with those of archaea and common eukaryotes, we found all the three Giardia isolates to harbor a same simplified 5S rRNA system, which is not only much simpler than that of common eukaryotes but also the simplest one among those of these excavates, and is surprisingly very similar to that of archaea; we also found among these excavates the system in parasitic species is not necessarily simpler than that in free-living species, conversely, the system of free-living species is even simpler in some respects than those of parasitic ones. The simplicity of Giardia 5S rRNA system should be considered a primitive rather than parasitically-degenerated feature. Therefore, Giardia 5S rRNA system might be a primitive system that is intermediate between that of archaea and the common eukaryotic model system, and it may reflect the evolutionary history of the eukaryotic 5S rRNA system from the archaeal form. Our results also imply G. lamblia might be a primitive eukaryote with secondary parasitically-degenerated features.

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

Yoshikatsu, Yuki; Ishida, Yo-ichi; Sudo, Haruka

Nuclear VCP-like 2 (NVL2) is a member of the chaperone-like AAA-ATPase family and is involved in the biosynthesis of 60S ribosomal subunits in mammalian cells. We previously showed the interaction of NVL2 with a DExD/H-box RNA helicase MTR4/DOB1, which is a known cofactor for an exoribonuclease complex, the exosome. This finding implicated NVL2 in RNA metabolic processes during ribosome biogenesis. In the present study, we found that a series of mutations within the ATPase domain of NVL2 causes a defect in pre-rRNA processing into mature 28S and 5.8S rRNAs. Co-immunoprecipitation analysis showed that NVL2 was associated with the nuclear exosomemore » complex, which includes RRP6 as a nucleus-specific catalytic subunit. This interaction was prevented by depleting either MTR4 or RRP6, indicating their essential role in mediating this interaction with NVL2. Additionally, knockdown of MPP6, another cofactor for the nuclear exosome, also prevented the interaction by causing MTR4 to dissociate from the nuclear exosome. These results suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex. - Highlights: • ATPase-deficient mutants of NVL2 have decreased pre-rRNA processing. • NVL2 associates with the nuclear exosome through interactions with MTR4 and RRP6. • MPP6 stabilizes MTR4-RRP6 interaction and allows NVL2 to interact with the complex.« less

RlmCD-mediated U747 methylation promotes efficient G748 methylation by methyltransferase RlmAII in 23S rRNA in Streptococcus pneumoniae; interplay between two rRNA methylations responsible for telithromycin susceptibility.

PubMed

Shoji, Tatsuma; Takaya, Akiko; Sato, Yoshiharu; Kimura, Satoshi; Suzuki, Tsutomu; Yamamoto, Tomoko

2015-10-15

Adenine at position 752 in a loop of helix 35 from positions 745 to 752 in domain II of 23S rRNA is involved in binding to the ribosome of telithromycin (TEL), a member of ketolides. Methylation of guanine at position 748 by the intrinsic methyltransferase RlmA(II) enhances binding of telithromycin (TEL) to A752 in Streptococcus pneumoniae. We have found that another intrinsic methylation of the adjacent uridine at position 747 enhances G748 methylation by RlmA(II), rendering TEL susceptibility. U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae. Inactivation of RlmCD reduced N1-methylated level of G748 by RlmA(II) in vivo, leading to TEL resistance when the nucleotide A2058, located in domain V of 23S rRNA, was dimethylated by the dimethyltransferase Erm(B). In vitro methylation of rRNA showed that RlmA(II) activity was significantly enhanced by RlmCD-mediated pre-methylation of 23S rRNA. These results suggest that RlmCD-mediated U747 methylation promotes efficient G748 methylation by RlmA(II), thereby facilitating TEL binding to the ribosome. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

rRNA Genes Are Not Fully Activated in Mouse Somatic Cell Nuclear Transfer Embryos*

PubMed Central

Zheng, Zhong; Jia, Jia-Lin; Bou, Gerelchimeg; Hu, Li-Li; Wang, Zhen-Dong; Shen, Xing-Hui; Shan, Zhi-Yan; Shen, Jing-Ling; Liu, Zhong-Hua; Lei, Lei

2012-01-01

The well known and most important function of nucleoli is ribosome biogenesis. However, the nucleolus showed delayed development and malfunction in somatic cell nuclear transfer (NT) embryos. Previous studies indicated that nearly half rRNA genes (rDNA) in somatic cells were inactive and not transcribed. We compared the rDNA methylation level, active nucleolar organizer region (NORs) numbers, nucleolar proteins (upstream binding factor (UBF), nucleophosmin (B23)) distribution, and nucleolar-related gene expression in three different donor cells and NT embryos. The results showed embryonic stem cells (ESCs) had the most active NORs and lowest rDNA methylation level (7.66 and 6.76%), whereas mouse embryonic fibroblasts (MEFs) were the opposite (4.70 and 22.57%). After the donor cells were injected into enucleated MII oocytes, cumulus cells and MEFs nuclei lost B23 and UBF signals in 20 min, whereas in ESC-NT embryos, B23 and UBF signals could still be detected at 60 min post-NT. The embryos derived from ESCs, cumulus cells, and MEFs showed the same trend in active NORs numbers (7.19 versus 6.68 versus 5.77, p < 0.05) and rDNA methylation levels (6.36 versus 9.67% versus 15.52%) at the 4-cell stage as that in donor cells. However, the MEF-NT embryos displayed low rRNA synthesis/processing potential at morula stage and had an obvious decrease in blastocyst developmental rate. The results presented clear evidences that the rDNA reprogramming efficiency in NT embryos was determined by the rDNA activity in donor cells from which they derived. PMID:22467869

Application of the differentiation process into the correlation-based leak detection in urban pipeline networks

NASA Astrophysics Data System (ADS)

Gao, Yan; Liu, Yuyou; Ma, Yifan; Cheng, Xiaobin; Yang, Jun

2018-11-01

One major challenge currently facing pipeline networks across the world is the improvement of leak detection technologies in urban environments. There is an imperative to locate accurately leaks in buried water pipes to avoid serious environmental, social and economic consequences. Much attention has been paid to time delay estimation (TDE) in determining the position of a leak by utilising cross-correlation, which has been proven to be effective with varying degrees of success over the past half century. Previous research in published literature has demonstrated the effectiveness of the pre-whitening process for accentuating the peak in the cross-correlation associated with the time delay. This paper is concerned with the implementation of the differentiation process for TDE, with particular focus on the problem of determining a leak in pipelines by means of pipe pressure measurements. Rather than the pre-whitening operation, the proposed cross-correlation via the differentiation process, termed here DIF, changes the characteristics of the pipe system so that the pipe effectively acts as a band-pass filter. This method has the potential to eliminate some ambiguity caused by the interference at low frequencies and to allow more high frequency information to pass. Given an appropriate differentiation order, a more pronounced and reliable peak is obtained in the cross-correlation result. The use of differentiation process may provide a viable cross-correlation method suited to water leak detection. Its performance in relation to leak detection is further compared to the basic cross-correlation and pre-whitening methods for TDE in detecting a leak from actual PVC water pipes. Experimental results are presented to show an additional property of the DIF compensating for the resonance effects that may exist in cross-spectral density measurements, and hence better performance for TDE.

Rrp12 and the Exportin Crm1 participate in late assembly events in the nucleolus during 40S ribosomal subunit biogenesis.

PubMed

Moriggi, Giulia; Nieto, Blanca; Dosil, Mercedes

2014-12-01

During the biogenesis of small ribosomal subunits in eukaryotes, the pre-40S particles formed in the nucleolus are rapidly transported to the cytoplasm. The mechanisms underlying the nuclear export of these particles and its coordination with other biogenesis steps are mostly unknown. Here we show that yeast Rrp12 is required for the exit of pre-40S particles to the cytoplasm and for proper maturation dynamics of upstream 90S pre-ribosomes. Due to this, in vivo elimination of Rrp12 leads to an accumulation of nucleoplasmic 90S to pre-40S transitional particles, abnormal 35S pre-rRNA processing, delayed elimination of processing byproducts, and no export of intermediate pre-40S complexes. The exportin Crm1 is also required for the same pre-ribosome maturation events that involve Rrp12. Thus, in addition to their implication in nuclear export, Rrp12 and Crm1 participate in earlier biosynthetic steps that take place in the nucleolus. Our results indicate that, in the 40S subunit synthesis pathway, the completion of early pre-40S particle assembly, the initiation of byproduct degradation and the priming for nuclear export occur in an integrated manner in late 90S pre-ribosomes.

Choice between delayed food and immediate oxycodone in rats.

PubMed

Secci, Maria E; Factor, Julie A; Schindler, Charles W; Panlilio, Leigh V

2016-12-01

The choice to seek immediate drug effects instead of more meaningful but delayed rewards is a defining feature of addiction. To develop a rodent model of this behavior, we allowed rats to choose between immediate intravenous delivery of the prescription opioid oxycodone (50 μg/kg) and delayed delivery of palatable food pellets. Rats preferred food at delays up to 30 s, but they chose oxycodone and food equally at 60-s delay and preferred oxycodone over food at 120-s delay. Comparison of food-drug choice, food-only, and drug-only conditions indicated that food availability decreased drug intake, but drug availability increased food intake. In the food-only condition, food was effective as a reinforcer even when delayed by 120 s. Pre-session feeding with chow slowed acquisition of food and drug self-administration, but did not affect choice. To establish procedures for testing potential anti-addiction medications, noncontingent pre-treatment with oxycodone or naltrexone (analogous to substitution and antagonist therapies, respectively) were tested on a baseline in which oxycodone was preferred over delayed food. Naltrexone pre-treatment decreased drug intake and increased food intake. Oxycodone pre-treatment decreased drug intake, but also produced extended periods with no food or drug responding. These findings show that the contingencies that induce preference for drugs over more meaningful but less immediate rewards in humans can be modeled in rodents, and they suggest that the model could be useful for assessing the therapeutic potential of treatments and exploring the underlying behavioral and neural mechanisms involved in addiction.

Comparison of in-situ delay monitors for use in Adaptive Voltage Scaling

NASA Astrophysics Data System (ADS)

Pour Aryan, N.; Heiß, L.; Schmitt-Landsiedel, D.; Georgakos, G.; Wirnshofer, M.

2012-09-01

In Adaptive Voltage Scaling (AVS) the supply voltage of digital circuits is tuned according to the circuit's actual operating condition, which enables dynamic compensation to PVTA variations. By exploiting the excessive safety margins added in state-of-the-art worst-case designs considerable power saving is achieved. In our approach, the operating condition of the circuit is monitored by in-situ delay monitors. This paper presents different designs to implement the in-situ delay monitors capable of detecting late but still non-erroneous transitions, called Pre-Errors. The developed Pre-Error monitors are integrated in a 16 bit multiplier test circuit and the resulting Pre-Error AVS system is modeled by a Markov chain in order to determine the power saving potential of each Pre-Error detection approach.

Nucleolar DEAD-Box RNA Helicase TOGR1 Regulates Thermotolerant Growth as a Pre-rRNA Chaperone in Rice

PubMed Central

Tang, Ding; Zhang, Yu’e; Cheng, Zhukuan; Xue, Yongbiao

2016-01-01

Plants have evolved a considerable number of intrinsic tolerance strategies to acclimate to ambient temperature increase. However, their molecular mechanisms remain largely obscure. Here we report a DEAD-box RNA helicase, TOGR1 (Thermotolerant Growth Required1), prerequisite for rice growth themotolerance. Regulated by both temperature and the circadian clock, its expression is tightly coupled to daily temperature fluctuations and its helicase activities directly promoted by temperature increase. Located in the nucleolus and associated with the small subunit (SSU) pre-rRNA processome, TOGR1 maintains a normal rRNA homeostasis at high temperature. Natural variation in its transcript level is positively correlated with plant height and its overexpression significantly improves rice growth under hot conditions. Our findings reveal a novel molecular mechanism of RNA helicase as a key chaperone for rRNA homeostasis required for rice thermotolerant growth and provide a potential strategy to breed heat-tolerant crops by modulating the expression of TOGR1 and its orthologs. PMID:26848586

Chaperoning 5S RNA assembly.

PubMed

Madru, Clément; Lebaron, Simon; Blaud, Magali; Delbos, Lila; Pipoli, Juliana; Pasmant, Eric; Réty, Stéphane; Leulliot, Nicolas

2015-07-01

In eukaryotes, three of the four ribosomal RNAs (rRNAs)—the 5.8S, 18S, and 25S/28S rRNAs—are processed from a single pre-rRNA transcript and assembled into ribosomes. The fourth rRNA, the 5S rRNA, is transcribed by RNA polymerase III and is assembled into the 5S ribonucleoprotein particle (RNP), containing ribosomal proteins Rpl5/uL18 and Rpl11/uL5, prior to its incorporation into preribosomes. In mammals, the 5S RNP is also a central regulator of the homeostasis of the tumor suppressor p53. The nucleolar localization of the 5S RNP and its assembly into preribosomes are performed by a specialized complex composed of Rpf2 and Rrs1 in yeast or Bxdc1 and hRrs1 in humans. Here we report the structural and functional characterization of the Rpf2-Rrs1 complex alone, in complex with the 5S RNA, and within pre-60S ribosomes. We show that the Rpf2-Rrs1 complex contains a specialized 5S RNA E-loop-binding module, contacts the Rpl5 protein, and also contacts the ribosome assembly factor Rsa4 and the 25S RNA. We propose that the Rpf2-Rrs1 complex establishes a network of interactions that guide the incorporation of the 5S RNP in preribosomes in the initial conformation prior to its rotation to form the central protuberance found in the mature large ribosomal subunit. © 2015 Madru et al.; Published by Cold Spring Harbor Laboratory Press.

SSB-1 of the yeast Saccharomyces cerevisiae is a nucleolar-specific, silver-binding protein that is associated with the snR10 and snR11 small nuclear RNAs

PubMed Central

1990-01-01

SSB-1, the yeast single-strand RNA-binding protein, is demonstrated to be a yeast nucleolar-specific, silver-binding protein. In double-label immunofluorescence microscopy experiments antibodies to two other nucleolar proteins, RNA Pol I 190-kD and fibrillarin, were used to reveal the site of rRNA transcription; i.e., the fibrillar region of the nucleolus. SSB-1 colocalized with fibrillarin in a double-label immunofluorescence mapping experiment to the yeast nucleolus. SSB-1 is located, though, over a wider region of the nucleolus than the transcription site marker. Immunoprecipitations of yeast cell extracts with the SSB-1 antibody reveal that in 150 mM NaCl SSB-1 is bound to two small nuclear RNAs (snRNAs). These yeast snRNAs are snR10 and snR11, with snR10 being predominant. Since snR10 has been implicated in pre-rRNA processing, the association of SSB-1 and snR10 into a nucleolar snRNP particle indicates SSB-1 involvement in rRNA processing as well. Also, another yeast protein, SSB-36-kD, isolated by single- strand DNA chromatography, is shown to bind silver under the conditions used for nucleolar-specific staining. It is, most likely, another yeast nucleolar protein. PMID:2121740

Study of the quality characteristics in cold-smoked salmon (Salmo salar) originating from pre- or post-rigor raw material.

PubMed

Birkeland, S; Akse, L

2010-01-01

Improved slaughtering procedures in the salmon industry have caused a delayed onset of rigor mortis and, thus, a potential for pre-rigor secondary processing. The aim of this study was to investigate the effect of rigor status at time of processing on quality traits color, texture, sensory, microbiological, in injection salted, and cold-smoked Atlantic salmon (Salmo salar). Injection of pre-rigor fillets caused a significant (P<0.001) contraction (-7.9%± 0.9%) on the caudal-cranial axis. No significant differences in instrumental color (a*, b*, C*, or h*), texture (hardness), or sensory traits (aroma, color, taste, and texture) were observed between pre- or post-rigor processed fillets; however, post-rigor (1477 ± 38 g) fillets had a significant (P>0.05) higher fracturability than pre-rigor fillets (1369 ± 71 g). Pre-rigor fillets were significantly (P<0.01) lighter, L*, (39.7 ± 1.0) than post-rigor fillets (37.8 ± 0.8) and had significantly lower (P<0.05) aerobic plate count (APC), 1.4 ± 0.4 log CFU/g against 2.6 ± 0.6 log CFU/g, and psychrotrophic count (PC), 2.1 ± 0.2 log CFU/g against 3.0 ± 0.5 log CFU/g, than post-rigor processed fillets. This study showed that similar quality characteristics can be obtained in cold-smoked products processed either pre- or post-rigor when using suitable injection salting protocols and smoking techniques. © 2010 Institute of Food Technologists®

Engineering fluidic delays in paper-based devices using laser direct-writing.

PubMed

He, P J W; Katis, I N; Eason, R W; Sones, C L

2015-10-21

We report the use of a new laser-based direct-write technique that allows programmable and timed fluid delivery in channels within a paper substrate which enables implementation of multi-step analytical assays. The technique is based on laser-induced photo-polymerisation, and through adjustment of the laser writing parameters such as the laser power and scan speed we can control the depth and/or the porosity of hydrophobic barriers which, when fabricated in the fluid path, produce controllable fluid delay. We have patterned these flow delaying barriers at pre-defined locations in the fluidic channels using either a continuous wave laser at 405 nm, or a pulsed laser operating at 266 nm. Using this delay patterning protocol we generated flow delays spanning from a few minutes to over half an hour. Since the channels and flow delay barriers can be written via a common laser-writing process, this is a distinct improvement over other methods that require specialist operating environments, or custom-designed equipment. This technique can therefore be used for rapid fabrication of paper-based microfluidic devices that can perform single or multistep analytical assays.

The Human RNA Polymerase I Transcription Terminator Complex Acts as a Replication Fork Barrier That Coordinates the Progress of Replication with rRNA Transcription Activity.

PubMed

Akamatsu, Yufuko; Kobayashi, Takehiko

2015-05-01

In S phase, the replication and transcription of genomic DNA need to accommodate each other, otherwise their machineries collide, with chromosomal instability as a possible consequence. Here, we characterized the human replication fork barrier (RFB) that is present downstream from the 47S pre-rRNA gene (ribosomal DNA [rDNA]). We found that the most proximal transcription terminator, Sal box T1, acts as a polar RFB, while the other, Sal box T4/T5, arrests replication forks bidirectionally. The fork-arresting activity at these sites depends on polymerase I (Pol I) transcription termination factor 1 (TTF-1) and a replisome component, TIMELESS (TIM). We also found that the RFB activity was linked to rDNA copies with hypomethylated CpG and coincided with the time that actively transcribed rRNA genes are replicated. Failed fork arrest at RFB sites led to a slowdown of fork progression moving in the opposite direction to rRNA transcription. Chemical inhibition of transcription counteracted this deceleration of forks, indicating that rRNA transcription impedes replication in the absence of RFB activity. Thus, our results reveal a role of RFB for coordinating the progression of replication and transcription activity in highly transcribed rRNA genes. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Visual stimuli in intervention approaches for pre-schoolers diagnosed with phonological delay.

PubMed

Pedro, Cassandra Ferreira; Lousada, Marisa; Hall, Andreia; Jesus, Luis M T

2018-04-01

The aim of this study was to develop and content validate specific speech and language intervention picture cards: The Letter-Sound (L&S) cards. The present study was also focused on assessing the influence of these cards on letter-sound correspondences and speech sound production. An expert panel of six speech and language therapists analysed and discussed the L&S cards based on several criteria previously established. A Speech and Language Therapist carried out a 6-week therapeutic intervention with a group of seven Portuguese phonologically delayed pre-schoolers aged 5;3 to 6;5. The modified Bland-Altman method revealed good agreement among evaluators, that is the majority of the values was between the agreement limits. Additional outcome measures were collected before and after the therapeutic intervention process. Results indicate that the L&S cards facilitate the acquisition of letter-sound correspondences. Regarding speech sound production, some improvements were also observed at word level. The L&S cards are therefore likely to give phonetic cues, which are crucial for the correct production of therapeutic targets. These visual cues seemed to have helped children with phonological delay develop the above-mentioned skills.

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils.

PubMed

Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

2016-01-01

Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability.

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils

PubMed Central

Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

2016-01-01

Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability. PMID:27486444

[Analysis of the Localization of Fibrillarin and Sites of Pre-rRNA Synthesis in the Nucleolus-Like Bodies of Mouse GV Oocytes after Mild Treatment with Proteinase K].

PubMed

Shishova, K V; Khodarovich, Yu M; Lavrentyeva, E A; Zatsepina, O V

2015-01-01

Postnatal development of mammalian oocytes is accompanied by functional and structural remodeling of the nucleolar apparatus: the final stage of this process is the formation of large objects (up to 10 μm in diameter) termed nucleolus-like bodies (NLBs) in preovulatory GV oocytes. N LB material was shown to be essential for early embryonic development, but its composition is still uncharacterized. In the present study, the protein-binding dye fluorescein-5-isothiocyanate (FITC) was used to show that proteins characterized by a high local concentration are essential NLB components in mouse GV oocytes. One of these proteins was able to be identified for the first time using a mild treatment of oocytes with proteinase K; the protein identified was fibrillarin, a factor of early pre-rRNA processing. Fibrillarin is present in the inner NLB mass of all oocytes capable of synthesizing rRNA; however, it is not colocalized with BrUTP microinjected into oocytes in order to identify transcribed ribosomal genes, in contrast to the "surface" fibrillarin. These observations imply the accumulation of nucleolar proteins not involved in ribosome biogenesis inside the NLB. All NLBs present in an individual nucleus of an NSN-type GV oocyte contain fibrillarin and are associated with active ribosomal genes. The results obtained in the present work demonstrate that proteinase K treatment of GV mouse oocytes allows for: (1) identification of "cryptic" proteins inside the densely packed NLB material and (2) the enhancement of oocyte image quality during BrUTP-based identification of rRNA synthesis sites but (3) not for the detection of active ribosomal genes in the inner mass of the NLB. The fluorescent dye FITC can be recommended for assessment of intracellular protein localization in the oocytes of all mammalian species.

Comparative Analysis of the 5S rRNA and Its Associated Proteins Reveals Unique Primitive Rather Than Parasitic Features in Giardia lamblia

PubMed Central

Xin, De-Dong; Wen, Jian-Fan

2012-01-01

Background 5S rRNA is a highly conserved ribosomal component. Eukaryotic 5S rRNA and its associated proteins (5S rRNA system) have become very well understood. Giardia lamblia was thought by some researchers to be the most primitive extant eukaryote while others considered it a highly evolved parasite. Previous reports have indicated that some aspects of its 5S rRNA system are simpler than that of common eukaryotes. We here explore whether this is true to its entire system, and whether this simplicity is a primitive or parasitic feature. Methodology/Principal Findings By collecting and confirming pre-existing data and identifying new data, we obtained almost complete datasets of the system of three isolates of G. lamblia, two other parasitic excavates (Trichomonas vaginalis, Trypanosoma cruzi), and one free-living one (Naegleria gruberi). After comprehensively comparing each aspect of the system among these excavates and also with those of archaea and common eukaryotes, we found all the three Giardia isolates to harbor a same simplified 5S rRNA system, which is not only much simpler than that of common eukaryotes but also the simplest one among those of these excavates, and is surprisingly very similar to that of archaea; we also found among these excavates the system in parasitic species is not necessarily simpler than that in free-living species, conversely, the system of free-living species is even simpler in some respects than those of parasitic ones. Conclusion/Significance The simplicity of Giardia 5S rRNA system should be considered a primitive rather than parasitically-degenerated feature. Therefore, Giardia 5S rRNA system might be a primitive system that is intermediate between that of archaea and the common eukaryotic model system, and it may reflect the evolutionary history of the eukaryotic 5S rRNA system from the archaeal form. Our results also imply G. lamblia might be a primitive eukaryote with secondary parasitically-degenerated features. PMID:22685540

The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs.

PubMed

Root-Bernstein, Robert; Root-Bernstein, Meredith

2016-05-21

We have proposed that the ribosome may represent a missing link between prebiotic chemistries and the first cells. One of the predictions that follows from this hypothesis, which we test here, is that ribosomal RNA (rRNA) must have encoded the proteins necessary for ribosomal function. In other words, the rRNA also functioned pre-biotically as mRNA. Since these ribosome-binding proteins (rb-proteins) must bind to the rRNA, but the rRNA also functioned as mRNA, it follows that rb-proteins should bind to their own mRNA as well. This hypothesis can be contrasted to a "null" hypothesis in which rb-proteins evolved independently of the rRNA sequences and therefore there should be no necessary similarity between the rRNA to which rb-proteins bind and the mRNA that encodes the rb-protein. Five types of evidence reported here support the plausibility of the hypothesis that the mRNA encoding rb-proteins evolved from rRNA: (1) the ubiquity of rb-protein binding to their own mRNAs and autogenous control of their own translation; (2) the higher-than-expected incidence of Arginine-rich modules associated with RNA binding that occurs in rRNA-encoded proteins; (3) the fact that rRNA-binding regions of rb-proteins are homologous to their mRNA binding regions; (4) the higher than expected incidence of rb-protein sequences encoded in rRNA that are of a high degree of homology to their mRNA as compared with a random selection of other proteins; and (5) rRNA in modern prokaryotes and eukaryotes encodes functional proteins. None of these results can be explained by the null hypothesis that assumes independent evolution of rRNA and the mRNAs encoding ribosomal proteins. Also noteworthy is that very few proteins bind their own mRNAs that are not associated with ribosome function. Further tests of the hypothesis are suggested: (1) experimental testing of whether rRNA-encoded proteins bind to rRNA at their coding sites; (2) whether tRNA synthetases, which are also known to bind to their own mRNAs, are encoded by the tRNA sequences themselves; (3) and the prediction that archaeal and prokaryotic (DNA-based) genomes were built around rRNA "genes" so that rRNA-related sequences will be found to make up an unexpectedly high proportion of these genomes. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

The rRNA methyltransferase Bud23 shows functional interaction with components of the SSU processome and RNase MRP.

PubMed

Sardana, Richa; White, Joshua P; Johnson, Arlen W

2013-06-01

Bud23 is responsible for the conserved methylation of G1575 of 18S rRNA, in the P-site of the small subunit of the ribosome. bud23Δ mutants have severely reduced small subunit levels and show a general failure in cleavage at site A2 during rRNA processing. Site A2 is the primary cleavage site for separating the precursors of 18S and 25S rRNAs. Here, we have taken a genetic approach to identify the functional environment of BUD23. We found mutations in UTP2 and UTP14, encoding components of the SSU processome, as spontaneous suppressors of a bud23Δ mutant. The suppressors improved growth and subunit balance and restored cleavage at site A2. In a directed screen of 50 ribosomal trans-acting factors, we identified strong positive and negative genetic interactions with components of the SSU processome and strong negative interactions with components of RNase MRP. RNase MRP is responsible for cleavage at site A3 in pre-rRNA, an alternative cleavage site for separating the precursor rRNAs. The strong negative genetic interaction between RNase MRP mutants and bud23Δ is likely due to the combined defects in cleavage at A2 and A3. Our results suggest that Bud23 plays a role at the time of A2 cleavage, earlier than previously thought. The genetic interaction with the SSU processome suggests that Bud23 could be involved in triggering disassembly of the SSU processome, or of particular subcomplexes of the processome.

Identification of educational and infrastructural barriers to prompt antibiotic delivery in febrile neutropenia: a quality improvement initiative.

PubMed

Burry, Erica; Punnett, Angela; Mehta, Ashley; Thull-Freedman, Jennifer; Robinson, Lisa; Gupta, Sumit

2012-09-01

Antibiotic administration within 60 minutes of presentation for medical care may be used as a treatment target for febrile neutropenia (FN); however, anecdotal evidence suggests this target is often missed. Few studies have examined the prevalence or causes of delay. We describe the median time to antibiotic administration at our institution, predictors of delay, and barriers to prompt administration to inform quality improvement strategies. A random sample of 50 episodes of FN presenting to the emergency department (ED) between 2008 and 2009 were reviewed. Times between triage, MD assessment, lab results, and antibiotic administration were recorded. Patient and ED variables were examined as possible predictors of delay. In parallel, lean methodology was used to identify system inefficiencies. A trained moderator conducted group interviews with interdisciplinary representatives involved in the emergency care of neutropenic patients to identify process barriers to prompt antibiotics. The median time from triage to antibiotics was 216 minutes (interquartile range [IQR] = 151-274 minutes). The greatest delay occurred following the reporting of lab results (152 minutes, IQR = 84-210 minutes). Only fall season predicted a longer time to antibiotics (P = 0.03). The lean process identified unnecessary areas of delay between departments. Time to antibiotic administration exceeded 1 hour. The chart review and lean process suggested targets for educational and infrastructural interventions, including an ED pre-printed order sheet, targeted combined subspecialty education between emergency and hematology/oncology staff, and family education. A mixed methodology approach represents a model for improving process efficiency and meeting "best-practice" targets in medicine. Copyright © 2011 Wiley Periodicals, Inc.

Study of Relationship Between Illness Perception and Delay in Seeking Help for Breast Cancer Patients Based on Leventhal's Self-Regulation Model.

PubMed

Attari, Seyedeh Maryam; Ozgoli, Giti; Solhi, Mahnaz; Alavi Majd, Hamid

2016-01-01

One of the major causes of morbidity and mortality in breast cancer patients is delay in seeking help. Leventhal's self-regulation model provides an appropriate framework to assess delay in seeking help. The aim of this study was to investigate the relationship between "illness perception" and "help seeking delay" in breast cancer patients based on Leventhal's self-regulation model. In this correlational descriptive study with convenience sampling conducted in 2013, participants were 120 women with breast cancer who were diagnosed in the last year and referred to chemotherapy and radiotherapy centers in Rasht, Iran. Data collection scales included demographic data, Revised Illness Perception Questionnaire (IPQ-R)and a researcher made questionnaire to measure the delay in seeking help. Pre-hospital delay (help seeking delay) was evaluated in 3 phases (assessment, disease, behavior). The data were analyzed using SPSS-19. The mean (SD) age calculated for the patients was 47.3±10.2. Some 43% of the patients had a high school or higher education level and 82% were married. The "pre-hospital delay" was reported ≥3 months. Logistic regression analysis showed that none of the illness perception components were correlated with appraisal and behavioral delay phases. In the illness delay phase, "time line" (p-value =0.04) and "risk factors"(p-value=0.03) had significant effects on reducing and "psychological attributions" had significant effects on increasing the delay (p-value =0.01). "Illness coherence" was correlated with decreased pre-hospital patient delay (p-value<0.01). Women's perceptions of breast cancer influences delay in seeking help. In addition to verifying the validity of Leventhal's self-regulation model in explaining delay in seeking help, the results signify the importance of the "illness delay phase" (decision to seek help) and educational interventions-counseling for women in the community.

Modulation of a Fronto-Parietal Network in Event-Based Prospective Memory: An rTMS Study

ERIC Educational Resources Information Center

Bisiacchi, P. S.; Cona, G.; Schiff, S.; Basso, D.

2011-01-01

Event-based prospective memory (PM) is a multi-component process that requires remembering the delayed execution of an intended action in response to a pre-specified PM cue, while being actively engaged in an ongoing task. Some neuroimaging studies have suggested that both prefrontal and parietal areas are involved in the maintenance and…

FREQUENCY DEPENDENCE OF POLARIZATION OF ZEBRA PATTERN IN TYPE-IV SOLAR RADIO BURSTS

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

Kaneda, Kazutaka; Misawa, H.; Tsuchiya, F.

2015-08-01

We investigated the polarization characteristics of a zebra pattern (ZP) in a type-IV solar radio burst observed with AMATERAS on 2011 June 21 for the purpose of evaluating the generation processes of ZPs. Analyzing highly resolved spectral and polarization data revealed the frequency dependence of the degree of circular polarization and the delay between two polarized components for the first time. The degree of circular polarization was 50%–70% right-handed and it varied little as a function of frequency. Cross-correlation analysis determined that the left-handed circularly polarized component was delayed by 50–70 ms relative to the right-handed component over the entiremore » frequency range of the ZP and this delay increased with the frequency. We examined the obtained polarization characteristics by using pre-existing ZP models and concluded that the ZP was generated by the double-plasma-resonance process. Our results suggest that the ZP emission was originally generated in a completely polarized state in the O-mode and was partly converted into the X-mode near the source. Subsequently, the difference between the group velocities of the O-mode and X-mode caused the temporal delay.« less

A novel comparator featured with input data characteristic

NASA Astrophysics Data System (ADS)

Jiang, Xiaobo; Ye, Desheng; Xu, Xiangmin; Zheng, Shuai

2016-03-01

Two types of low-power asynchronous comparators featured with input data statistical characteristic are proposed in this article. The asynchronous ripple comparator stops comparing at the first unequal bit but delivers the result to the least significant bit. The pre-stop asynchronous comparator can completely stop comparing and obtain results immediately. The proposed and contrastive comparators were implemented in SMIC 0.18 μm process with different bit widths. Simulation shows that the proposed pre-stop asynchronous comparator features the lowest power consumption, shortest average propagation delay and highest area efficiency among the comparators. Data path of low-density parity check decoder using the proposed pre-stop asynchronous comparators are most power efficient compared with other data paths with synthesised, clock gating and bitwise competition logic comparators.

LKB1 promotes cell survival by modulating TIF-IA-mediated pre-ribosomal RNA synthesis under uridine downregulated conditions

PubMed Central

Liu, Xiuju; Huang, Henry; Wilkinson, Scott C.; Zhong, Diansheng; Khuri, Fadlo R.; Fu, Haian; Marcus, Adam; He, Yulong; Zhou, Wei

2016-01-01

We analyzed the mechanism underlying 5-aminoimidazole-4-carboxamide riboside (AICAR) mediated apoptosis in LKB1-null non-small cell lung cancer (NSCLC) cells. Metabolic profile analysis revealed depletion of the intracellular pyrimidine pool after AICAR treatment, but uridine was the only nucleotide precursor capable of rescuing this apoptosis, suggesting the involvement of RNA metabolism. Because half of RNA transcription in cancer is for pre-ribosomal RNA (rRNA) synthesis, which is suppressed by over 90% after AICAR treatment, we evaluated the role of TIF-IA-mediated rRNA synthesis. While the depletion of TIF-IA by RNAi alone promoted apoptosis in LKB1-null cells, the overexpression of a wild-type or a S636A TIF-IA mutant, but not a S636D mutant, attenuated AICAR-induced apoptosis. In LKB1-null H157 cells, pre-rRNA synthesis was not suppressed by AICAR when wild-type LKB1 was present, and cellular fractionation analysis indicated that TIF-IA quickly accumulated in the nucleus in the presence of a wild-type LKB1 but not a kinase-dead mutant. Furthermore, ectopic expression of LKB1 was capable of attenuating AICAR-induced death in AMPK-null cells. Because LKB1 promotes cell survival by modulating TIF-IA-mediated pre-rRNA synthesis, this discovery suggested that targeted depletion of uridine related metabolites may be exploited in the clinic to eliminate LKB1-null cancer cells. PMID:26506235

LKB1 promotes cell survival by modulating TIF-IA-mediated pre-ribosomal RNA synthesis under uridine downregulated conditions.

PubMed

Liu, Fakeng; Jin, Rui; Liu, Xiuju; Huang, Henry; Wilkinson, Scott C; Zhong, Diansheng; Khuri, Fadlo R; Fu, Haian; Marcus, Adam; He, Yulong; Zhou, Wei

2016-01-19

We analyzed the mechanism underlying 5-aminoimidazole-4-carboxamide riboside (AICAR) mediated apoptosis in LKB1-null non-small cell lung cancer (NSCLC) cells. Metabolic profile analysis revealed depletion of the intracellular pyrimidine pool after AICAR treatment, but uridine was the only nucleotide precursor capable of rescuing this apoptosis, suggesting the involvement of RNA metabolism. Because half of RNA transcription in cancer is for pre-ribosomal RNA (rRNA) synthesis, which is suppressed by over 90% after AICAR treatment, we evaluated the role of TIF-IA-mediated rRNA synthesis. While the depletion of TIF-IA by RNAi alone promoted apoptosis in LKB1-null cells, the overexpression of a wild-type or a S636A TIF-IA mutant, but not a S636D mutant, attenuated AICAR-induced apoptosis. In LKB1-null H157 cells, pre-rRNA synthesis was not suppressed by AICAR when wild-type LKB1 was present, and cellular fractionation analysis indicated that TIF-IA quickly accumulated in the nucleus in the presence of a wild-type LKB1 but not a kinase-dead mutant. Furthermore, ectopic expression of LKB1 was capable of attenuating AICAR-induced death in AMPK-null cells. Because LKB1 promotes cell survival by modulating TIF-IA-mediated pre-rRNA synthesis, this discovery suggested that targeted depletion of uridine related metabolites may be exploited in the clinic to eliminate LKB1-null cancer cells.

RNA Processing Factor 5 is required for efficient 5' cleavage at a processing site conserved in RNAs of three different mitochondrial genes in Arabidopsis thaliana.

PubMed

Hauler, Aron; Jonietz, Christian; Stoll, Birgit; Stoll, Katrin; Braun, Hans-Peter; Binder, Stefan

2013-05-01

The 5' ends of many mitochondrial transcripts are generated post-transcriptionally. Recently, we identified three RNA PROCESSING FACTORs required for 5' end maturation of different mitochondrial mRNAs in Arabidopsis thaliana. All of these factors are pentatricopeptide repeat proteins (PPRPs), highly similar to RESTORERs OF FERTILTY (RF), that rescue male fertility in cytoplasmic male-sterile lines from different species. Therefore, we suggested a general role of these RF-like PPRPs in mitochondrial 5' processing. We now identified RNA PROCESSING FACTOR 5, a PPRP not classified as an RF-like protein, required for the efficient 5' maturation of the nad6 and atp9 mRNAs as well as 26S rRNA. The precursor molecules of these RNAs share conserved sequence elements, approximately ranging from positions -50 to +9 relative to mature 5' mRNA termini, suggesting these sequences to be at least part of the cis elements required for processing. The knockout of RPF5 has only a moderate influence on 5' processing of atp9 mRNA, whereas the generation of the mature nad6 mRNA and 26S rRNA is almost completely abolished in the mutant. The latter leads to a 50% decrease of total 26S rRNA species, resulting in an imbalance between the large rRNA and 18S rRNA. Despite these severe changes in RNA levels and in the proportion between the 26S and 18S rRNAs, mitochondrial protein levels appear to be unaltered in the mutant, whereas seed germination capacity is markedly reduced. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Impact of magnetic resonance imaging on ventricular tachyarrhythmia sensing: Results of the Evera MRI Study.

PubMed

Gold, Michael R; Sommer, Torsten; Schwitter, Juerg; Kanal, Emanuel; Bernabei, Matthew A; Love, Charles J; Surber, Ralf; Ramza, Brian; Cerkvenik, Jeffrey; Merkely, Béla

2016-08-01

Studies have shown that magnetic resonance imaging (MRI) conditional pacemakers experience no significant effect from MRI on device function, sensing, or pacing. More recently, similar safety outcomes were demonstrated with MRI conditional defibrillators (implantable cardioverter-defibrillator [ICD]), but the impact on ventricular arrhythmias has not been assessed. The purpose of this study was to assess the effect of MRI on ICD sensing and treatment of ventricular tachyarrhythmias. The Evera MRI Study was a worldwide trial of 156 patients implanted with an ICD designed to be MRI conditional. Device-detected spontaneous and induced ventricular tachycardia/ventricular fibrillation (VT/VF) episodes occurring before and after whole body MRI were evaluated by a blinded episode review committee. Detection delay was computed as the sum of RR intervals of undersensed beats. A ≥5-second delay in detection due to undersensing was prospectively defined as clinically significant. Post-MRI, there were 22 polymorphic VT/VF episodes in 21 patients, with 16 of these patients having 17 VT/VF episodes pre-MRI. Therapy was successful for all episodes, with no failures to treat or terminate arrhythmias. The mean detection delay due to undersensing pre- and post-MRI was 0.60 ± 0.59 and 0.33 ± 0.63 seconds, respectively (P = .17). The maximum detection delay was 2.19 seconds pre-MRI and 2.87 seconds post-MRI. Of the 17 pre-MRI episodes, 14 (82%) had some detection delay as compared with 11 of 22 (50%) post-MRI episodes (P = .03); no detection delay was clinically significant. Detection and treatment of VT/VF was excellent, with no detection delays or significant impact of MRI observed. Copyright © 2016 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Methods for understanding microbial community structures and functions in microbial fuel cells: a review.

PubMed

Zhi, Wei; Ge, Zheng; He, Zhen; Zhang, Husen

2014-11-01

Microbial fuel cells (MFCs) employ microorganisms to recover electric energy from organic matter. However, fundamental knowledge of electrochemically active bacteria is still required to maximize MFCs power output for practical applications. This review presents microbiological and electrochemical techniques to help researchers choose the appropriate methods for the MFCs study. Pre-genomic and genomic techniques such as 16S rRNA based phylogeny and metagenomics have provided important information in the structure and genetic potential of electrode-colonizing microbial communities. Post-genomic techniques such as metatranscriptomics allow functional characterizations of electrode biofilm communities by quantifying gene expression levels. Isotope-assisted phylogenetic analysis can further link taxonomic information to microbial metabolisms. A combination of electrochemical, phylogenetic, metagenomic, and post-metagenomic techniques offers opportunities to a better understanding of the extracellular electron transfer process, which in turn can lead to process optimization for power output. Copyright © 2014 Elsevier Ltd. All rights reserved.

Neural Processing of Target Distance by Echolocating Bats: Functional Roles of the Auditory Midbrain

PubMed Central

Wenstrup, Jeffrey J.; Portfors, Christine V.

2011-01-01

Using their biological sonar, bats estimate distance to avoid obstacles and capture moving prey. The primary distance cue is the delay between the bat's emitted echolocation pulse and the return of an echo. The mustached bat's auditory midbrain (inferior colliculus, IC) is crucial to the analysis of pulse-echo delay. IC neurons are selective for certain delays between frequency modulated (FM) elements of the pulse and echo. One role of the IC is to create these “delay-tuned”, “FM-FM” response properties through a series of spectro-temporal integrative interactions. A second major role of the midbrain is to project target distance information to many parts of the brain. Pathways through auditory thalamus undergo radical reorganization to create highly ordered maps of pulse-echo delay in auditory cortex, likely contributing to perceptual features of target distance analysis. FM-FM neurons in IC also project strongly to pre-motor centers including the pretectum and the pontine nuclei. These pathways may contribute to rapid adjustments in flight, body position, and sonar vocalizations that occur as a bat closes in on a target. PMID:21238485

Pre-school children with and without developmental delay: behaviour problems and parenting stress over time.

PubMed

Baker, B L; McIntyre, L L; Blacher, J; Crnic, K; Edelbrock, C; Low, C

2003-01-01

Children with intellectual disability are at heightened risk for behaviour problems and diagnosed mental disorder. The present authors studied the early manifestation and continuity of problem behaviours in 205 pre-school children with and without developmental delays. Behaviour problems were quite stable over the year from age 36-48 months. Children with developmental delays were rated higher on behaviour problems than their non-delayed peers, and were three times as likely to score in the clinical range. Mothers and fathers showed high agreement in their rating of child problems, especially in the delayed group. Parenting stress was also higher in the delayed group, but was related to the extent of behaviour problems rather than to the child's developmental delay. Over time, a transactional model fit the relationship between parenting stress and behaviour problems: high parenting stress contributed to a worsening in child behaviour problems over time, and high child behaviour problems contributed to a worsening in parenting stress. Findings for mothers and fathers were quite similar.

Comparison of two poultry litter qPCR assays targeting the 16S rRNA gene of Brevibacterium sp

EPA Science Inventory

Chicken feces are vectors of human pathogens and are also important sources of fecal pollution in environmental waters. Consequently, methods that can detect chicken fecal pollution are needed in public health and environmental monitoring studies. In this study, we compared a pre...

Role of Assessment Tests in the Stability of Intelligence Scoring of Pre-School Children with Uneven/Delayed Cognitive Profile

ERIC Educational Resources Information Center

Yang, P.; Jong, Y-J.; Hsu, H-Y.; Lung, F-W.

2011-01-01

Background: As part of an ongoing clinical service programme for pre-school children with developmental delay in an Asian developing country, we analysed the effect of three assessment tests, that is, Bayley Scale of Infant Development-II, Leiter International Performance Scale-Revised and Wechsler Preschool and Primary Scale of…

Determination of Bifidobacterium and Lactobacillus in breast milk of healthy women by digital PCR.

PubMed

Qian, L; Song, H; Cai, W

2016-09-01

Breast milk is one of the most important sources of postnatal microbes. Quantitative real-time polymerase chain reaction (qRT-PCR) is currently used for the quantitative analysis of bacterial 16S rRNA genes in breast milk. However, this method relies on the use of standard curves and is imprecise when quantitating target DNA of low abundance. In contrast, droplet digital PCR (DD-PCR) provides an absolute quantitation without the need for calibration curves. A comparison between DD-PCR and qRT-PCR was conducted for the quantitation of Bifidobacterium and Lactobacillus 16S RNA genes in human breast milk, and the impacts of selected maternal factors were studied on the composition of these two bacteria in breast milk. From this study, DD-PCR reported between 0-34,460 16S rRNA gene copies of Bifidobacterium genera and between 1,108-634,000 16S rRNA gene copies of Lactobacillus genera in 1 ml breast milk. The 16S rRNA gene copy number of Lactobacillus genera was much greater than that of Bifidobacterium genera in breast milk. DD-PCR showed a 10-fold lower limit of quantitation as compared to qRT-PCR. A higher correlation and agreement was observed between qRT-PCR and DD-PCR in Lactobacillus quantitation as compared to Bifidobacterium quantitation. Based on our DD-PCR quantitation, a low abundance of Bifidobacterium bacteria in breast milk was correlated to higher pre-pregnancy body mass index (BMI). However, no significant difference was observed for these two bacteria in breast milk between mothers who had vaginal deliveries and caesarean deliveries. This study suggests that DD-PCR is a better tool to quantitate the bacterial load of breast milk compared to the conventional qRT-PCR method. The number of breast milk Bifidobacterium bacteria is influenced by maternal pre-pregnancy BMI.

An analysis of the impact of pre-analytical factors on the urine proteome: Sample processing time, temperature, and proteolysis.

PubMed

Hepburn, Sophie; Cairns, David A; Jackson, David; Craven, Rachel A; Riley, Beverley; Hutchinson, Michelle; Wood, Steven; Smith, Matthew Welberry; Thompson, Douglas; Banks, Rosamonde E

2015-06-01

We have examined the impact of sample processing time delay, temperature, and the addition of protease inhibitors (PIs) on the urinary proteome and peptidome, an important aspect of biomarker studies. Ten urine samples from patients with varying pathologies were each divided and PIs added to one-half, with aliquots of each then processed and frozen immediately, or after a delay of 6 h at 4°C or room temperature (20-22°C), effectively yielding 60 samples in total. Samples were then analyzed by 2D-PAGE, SELDI-TOF-MS, and immunoassay. Interindividual variability in profiles was the dominant feature in all analyses. Minimal changes were observed by 2D-PAGE as a result of delay in processing, temperature, or PIs and no changes were seen in IgG, albumin, β2 -microglobulin, or α1 -microglobulin measured by immunoassay. Analysis of peptides showed clustering of some samples by presence/absence of PIs but the extent was very patient-dependent with most samples showing minimal effects. The extent of processing-induced changes and the benefit of PI addition are patient- and sample-dependent. A consistent processing methodology is essential within a study to avoid any confounding of the results. © 2014 The Authors PROTEOMICS Clinical Applications Published by Wiley-VCH Verlag GmbH & Co. KGaA.

[Delays in seeking and getting care, in seriously ill women of childbearing age in Kinshasa].

PubMed

Mambu Nyangi Mondo, T; Malengreau, M; Kayembe Kalambayi, P; Lapika Dimomfu, B

2010-06-01

Mortality of adult females is very high in Democratic Republic of Congo and often caused by diseases that could have been controlled if treated in time. This is a qualitative study on delays and their causes in the care-seeking process of 60 women who died prematurely in Kinshasa from non-immediately fatal causes. This study concerned 60 women identified in two Kinshasa mortuaries in March and April 2004 who had died at the age of 18 to 49 years. Deaths considered to be unavoidable were excluded. The history of their disease and death was collected from family members and community leaders, and from the available medical records. The analysis focused on delays occurring at the different stages of the women's care seeking process, from the first signs of danger until death. The analysis identified different delays: the delay in danger awareness, the delay in taking the care-seeking decision and the delay due to alternative care linked to cultural perceptions of the disease, the delay in reaching a medical facility related to lack of money or vehicles, the delay in patient care related to an absent or incompetent health staff or by inappropriate choice of structure, and finally the delay in administration of the prescribed treatment. In Kinshasa, emergency care may be delayed by slow awareness of danger, but most of all by the poor quality and poor organisation of the health services. On the other hand, the use of non-medical alternatives and a poor perception of the medical services do rarely interfere in the decision to seek medical care. In Kinshasa, to guarantee the patients rights to quality health care, one must first strengthen and control medical services. One should also teach people to identify services appropriate to medical emergencies. Transportation and pre-financing of emergency care should be organised by local authorities. 2010 Elsevier Masson SAS. All rights reserved.

Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA.

PubMed

Hughes, J M

1996-06-21

The U3 nucleolar RNA has a remarkably wide phyletic distribution extending from the Eukarya to the Archaea. It functions in maturation of the small subunit (SSU) rRNA through a mechanism which is as yet unknown but which involves base-pairing with pre-rRNA. The most conserved part of U3 is within 30 nucleotides of the 5' end, but as yet no function for this domain has been proposed. Elements within this domain are complementary to highly conserved sequences in the SSU rRNA which, in the mature form, fold into a universally conserved pseudoknot. The nature of the complementarity suggests a novel mechanism for U3 function whereby U3 facilitates correct folding of the pseudoknot. Wide phylogenetic comparison provides compelling evidence in support of the interaction in that significant complementary changes have taken place, particularly in the archaeon Sulfolobus, which maintain the base-pairing. Base-substitution mutations in yeast U3 designed to disrupt the base-pairing indicate that the interaction is probably essential. These include cold-sensitivity mutations which exhibit phenotypes similar to U3-depletion, but without impairment of the AO processing step, which occurs within the 5' ETS. These phenotypes are consistent with the destabilization of SSU precursors and partial impairment of the processing steps A1, at the 5' ETS/18 S boundary, and A2, within the ITS1.

Paleosols in central Illinois as potential sources of ammonium in groundwater

USGS Publications Warehouse

Glessner, Justin J. G.; Roy, W.R.

2009-01-01

Glacially buried paleosols of pre-Holocene age were evaluated as potential sources for anomalously large concentrations of ammonium in groundwater in East Central Illinois. Ammonium has been detected at concentrations that are problematic to water treatment facilities (greater than 2.0 mg/L) in this region. Paleosols characterized for this study were of Quaternary age, specifically Robein Silt samples. Paleosol samples displayed significant capacity to both store and release ammonium through experiments measuring processes of sorption, ion exchange, and weathering. Bacteria and fungi within paleosols may significantly facilitate the leaching of ammonium into groundwater by the processes of assimilation and mineralization. Bacterial genetic material (DNA) was successfully extracted from the Robein Silt, purified, and amplified by polymerase chain reaction to produce 16S rRNA terminal restriction fragment length polymorphism (TRFLP) community analyses. The Robein Silt was found to have established diverse and viable bacterial communities. 16S rRNA TRFLP comparisons to well-known bacterial species yielded possible matches with facultative chemolithotrophs, cellulose consumers, nitrate reducers, and actinomycetes. It was concluded that the Robein Silt is both a source and reservoir for groundwater ammonium. Therefore, the occurrence of relatively large concentrations of ammonium in groundwater monitoring data may not necessarily be an indication of only anthropogenic contamination. The results of this study, however, need to be placed in a hydrological context to better understand whether paleosols can be a significant source of ammonium to drinking water supplies. ?? 2009 National Ground Water Association.

Can the attention training technique turn one marshmallow into two? Improving children's ability to delay gratification.

PubMed

Murray, Joanne; Theakston, Anna; Wells, Adrian

2016-02-01

The seminal Marshmallow Test (Mischel & Ebbesen, 1970) has reliably demonstrated that children who can delay gratification are more likely to be emotionally stable and successful later in life. However, this is not good news for those children who can't delay. Therefore, this study aimed to explore whether a metacognitive therapy technique, Attention Training (ATT: Wells, 1990) can improve young children's ability to delay gratification. One hundred children participated. Classes of 5-6 year olds were randomly allocated to either the ATT or a no-intervention condition and were tested pre and post-intervention on ability to delay gratification, verbal inhibition (executive control), and measures of mood. The ATT intervention significantly increased (2.64 times) delay of gratification compared to the no-intervention condition. After controlling for age and months in school, the ATT intervention and verbal inhibition task performance were significant independent predictors of delay of gratification. These results provide evidence that ATT can improve children's self-regulatory abilities with the implication that this might reduce psychological vulnerability later in life. The findings highlight the potential contribution that the Self-Regulatory Executive Function (S-REF) model could make to designing techniques to enhance children's self-regulatory processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Neural correlates of cigarette health warning avoidance among smokers.

PubMed

Stothart, George; Maynard, Olivia; Lavis, Rosie; Munafò, Marcus

2016-04-01

Eye-tracking technology has indicated that daily smokers actively avoid pictorial cigarette package health warnings. Avoidance may be due to a pre-cognitive perceptual bias or a higher order cognitive bias, such as reduced emotional processing. Using electroencephalography (EEG), this study aimed to identify the temporal point at which smokers' responses to health warnings begin to differ. Non-smokers (n=20) and daily smokers (n=20) viewed pictorial cigarette package health warnings and neutral control stimuli. These elicited Event Related Potentials reflecting early perceptual processing (visual P1), pre-attentive change detection (visual Mismatch Negativity), selective attentional orientation (P3) and a measure of emotional processing, the Late Positive Potential (LPP). There was no evidence for a difference in P1 responses between smokers and non-smokers. There was no difference in vMMN and P3 amplitude but some evidence for a delay in vMMN latency amongst smokers. There was strong evidence for delayed and reduced LPP to health warning stimuli amongst smokers compared to non-smokers. We find no evidence for an early perceptual bias in smokers' visual perception of health warnings but strong evidence that smokers are less sensitive to the emotional content of cigarette health warnings. Future health warning development should focus on increasing the emotional salience of pictorial health warning content amongst smokers. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

31 CFR 560.515 - 30-day delayed effective date for pre-May 7, 1995 trade contracts involving Iran.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false 30-day delayed effective date for pre-May 7, 1995 trade contracts involving Iran. 560.515 Section 560.515 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY IRANIAN TRANSACTIONS REGULATIONS...

31 CFR 538.506 - 30-day delayed effective date for pre-November 4, 1997 trade contracts involving Sudan.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false 30-day delayed effective date for pre-November 4, 1997 trade contracts involving Sudan. 538.506 Section 538.506 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY SUDANESE SANCTIONS REGULATIONS...

31 CFR 538.506 - 30-day delayed effective date for pre-November 4, 1997 trade contracts involving Sudan.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false 30-day delayed effective date for pre-November 4, 1997 trade contracts involving Sudan. 538.506 Section 538.506 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY SUDANESE SANCTIONS REGULATIONS...

31 CFR 538.506 - 30-day delayed effective date for pre-November 4, 1997 trade contracts involving Sudan.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false 30-day delayed effective date for pre-November 4, 1997 trade contracts involving Sudan. 538.506 Section 538.506 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY SUDANESE SANCTIONS REGULATIONS...

31 CFR 560.515 - 30-day delayed effective date for pre-May 7, 1995 trade contracts involving Iran.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false 30-day delayed effective date for pre-May 7, 1995 trade contracts involving Iran. 560.515 Section 560.515 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY IRANIAN TRANSACTIONS REGULATIONS...

Toward an Understanding of Changes in Diversity Associated with Fecal Microbiome Transplantation Based on 16S rRNA Gene Deep Sequencing

PubMed Central

Shahinas, Dea; Silverman, Michael; Sittler, Taylor; Chiu, Charles; Kim, Peter; Allen-Vercoe, Emma; Weese, Scott; Wong, Andrew; Low, Donald E.; Pillai, Dylan R.

2012-01-01

ABSTRACT Fecal microbiome transplantation by low-volume enema is an effective, safe, and inexpensive alternative to antibiotic therapy for patients with chronic relapsing Clostridium difficile infection (CDI). We explored the microbial diversity of pre- and posttransplant stool specimens from CDI patients (n = 6) using deep sequencing of the 16S rRNA gene. While interindividual variability in microbiota change occurs with fecal transplantation and vancomycin exposure, in this pilot study we note that clinical cure of CDI is associated with an increase in diversity and richness. Genus- and species-level analysis may reveal a cocktail of microorganisms or products thereof that will ultimately be used as a probiotic to treat CDI. PMID:23093385

Speech and language delay in two children: an unusual presentation of hyperthyroidism.

PubMed

Sohal, Aman P S; Dasarathi, Madhuri; Lodh, Rajib; Cheetham, Tim; Devlin, Anita M

2013-01-01

Hyperthyroidism is rare in pre-school children. Untreated, it can have a profound effect on normal growth and development, particularly in the first 2 years of life. Although neurological manifestations of dysthyroid states are well known, specific expressive speech and language disorder as a presentation of hyperthyroidism is rarely documented. Case reports of two children with hyperthyroidism presenting with speech and language delay. We report two pre-school children with hyperthyroidism, who presented with expressive speech and language delay, and demonstrated a significant improvement in their language skills following treatment with anti-thyroid medication. Hyperthyroidism must be considered in all children presenting with speech and language difficulties, particularly expressive speech delay. Prompt recognition and early treatment are likely to improve outcome.

Pre- and post-diagnosis costs of tuberculosis to patients on Directly Observed Treatment Short course in districts of southwestern Ethiopia: a longitudinal study.

PubMed

Asres, Abyot; Jerene, Degu; Deressa, Wakgari

2018-05-21

Financial burden on tuberculosis (TB) patients results in delayed treatment and poor compliance. We assessed pre- and post-diagnosis costs to TB patients. A longitudinal study among 735 new TB cases was conducted from January 2015 through June 2016 in 10 woredas (districts) of southwestern Ethiopia. Direct out-of-pocket, payments, and lost income (indirect cost) were solicited from patients during the first 2 months and at the end of treatment. Thus, we ascertained direct medical, nonmedical, and indirect costs incurred by patients during pre- and post-diagnosis periods. We categorized costs incurred from onset of illness until TB diagnosis as pre-diagnosis and that incurred after diagnosis through treatment completion as post-diagnosis. Pre- and post-diagnosis costs constitute total cost incurred by the patients. We fitted linear regression model to identify predictors of cost. Between onset of illness and anti-TB treatment course, patients incurred a median (inter-quartile range (IQR)) of US$201.48 (136.7-318.94). Of the total cost, the indirect and direct costs respectively constituted 70.6 and 29.4%. TB patients incurred a median (IQR) of US$97.62 (6.43-184.22) and US$93.75 (56.91-141.54) during the pre- and post-diagnosis periods, respectively. Thus, patients incurred 53.6% of the total cost during the pre-diagnosis period. Direct out-of-pocket expenses during the pre- and post-diagnosis periods respectively amount to median (IQR) of US$21.64 (10.23-48.31) and US$35.02 (0-70.04). Patient delay days (p < 0.001), provider delay days (p < 0.001), number of healthcare facilities visited until TB diagnosis (p < 0.001), and TB diagnosis at private facilities (p = 0.02) independently predicted increased pre-diagnosis cost. Similarly, rural residence (p < 0.001), hospitalization during anti-TB treatment (p < 0.001), patient delay days (p < 0.001), and provider delay days (p < 0.001) predicted increased post-diagnosis costs. TB patients incur substantial cost for care seeking and treatment despite "free service" for TB. Therefore, promoting early care seeking, decentralizing efficient diagnosis, and treatment services within reach of peoples, and introducing reimbursement system for direct costs can help minimize financial burden to the patient.

Dyskeratosis congenita mutations in the H/ACA domain of human telomerase RNA affect its assembly into a pre-RNP

PubMed Central

Trahan, Christian; Dragon, François

2009-01-01

Dyskeratosis congenita (DC) is an inherited disorder that implicates defects in the biology of telomeres, which are maintained by telomerase, a ribonucleoprotein with reverse transcriptase activity. Like all H/ACA RNAs, the H/ACA domain of nascent human telomerase RNA (hTR) forms a pre-RNP with H/ACA proteins NAF1, dyskerin, NOP10, and NHP2 in vivo. To assess the pre-RNP assembly of hTR mutants that poorly accumulate in vivo, we developed an in vitro system that uses components of human origin. Pre-RNPs were reconstituted with synthetic 32P-labeled RNAs and 35S-labeled proteins produced in rabbit reticulocyte lysate, and immunoprecipitations were carried out to analyze RNP formation. We show that human NAF1 cannot bind directly to the H/ACA domain of hTR, and requires the core trimer dyskerin-NOP10-NHP2 to be efficiently incorporated into the pre-RNP. This order of assembly seems common to H/ACA RNAs since it was observed with snoRNA ACA36 and scaRNA U92, which are predicted to guide pseudouridylation of 18S rRNA and U2 snRNA, respectively. However, the processing H/ACA snoRNA U17 did not conform to this rule, as NAF1 alone was able to bind it. We also provide the first evidence that DC-related mutations of hTR C408G and Δ378-451 severely impair pre-RNP assembly. Integrity of boxes H and ACA of hTR are also crucial for pre-RNP assembly, while the CAB box is dispensable. Our results offer new insights into the defects caused by some mutations located in the H/ACA domain of hTR. PMID:19095616

Impulsive choice and pre-exposure to delays: iv. effects of delay- and immediacy-exposure training relative to maturational changes in impulsivity.

PubMed

Renee Renda, C; Rung, Jillian M; Hinnenkamp, Jay E; Lenzini, Stephanie N; Madden, Gregory J

2018-04-23

Impulsive choice describes preference for smaller, sooner rewards over larger, later rewards. Excessive delay discounting (i.e., rapid devaluation of delayed rewards) underlies some impulsive choices, and is observed in many maladaptive behaviors (e.g., substance abuse, gambling). Interventions designed to reduce delay discounting may provide therapeutic gains. One such intervention provides rats with extended training with delayed reinforcers. When compared to a group given extended training with immediate reinforcers, delay-exposed rats make significantly fewer impulsive choices. To what extent is this difference due to delay-exposure training shifting preference toward self-control or immediacy-exposure training (the putative control group) shifting preference toward impulsivity? The current study compared the effects of delay- and immediacy-exposure training to a no-training control group and evaluated within-subject changes in impulsive choice across 51 male Wistar rats. Delay-exposed rats made significantly fewer impulsive choices than immediacy-exposed and control rats. Between-group differences in impulsive choice were not observed in the latter two groups. While delay-exposed rats showed large, significant pre- to posttraining reductions in impulsive choice, immediacy-exposed and control rats showed small reductions in impulsive choice. These results suggest that extended training with delayed reinforcers reduces impulsive choice, and that extended training with immediate reinforcers does not increase impulsive choice. © 2018 Society for the Experimental Analysis of Behavior.

Anchorage Arrival Scheduling Under Off-Nominal Weather Conditions

NASA Technical Reports Server (NTRS)

Grabbe, Shon; Chan, William N.; Mukherjee, Avijit

2012-01-01

Weather can cause flight diversions, passenger delays, additional fuel consumption and schedule disruptions at any high volume airport. The impacts are particularly acute at the Ted Stevens Anchorage International Airport in Anchorage, Alaska due to its importance as a major international portal. To minimize the impacts due to weather, a multi-stage scheduling process is employed that is iteratively executed, as updated aircraft demand and/or airport capacity data become available. The strategic scheduling algorithm assigns speed adjustments for flights that originate outside of Anchorage Center to achieve the proper demand and capacity balance. Similarly, an internal departure-scheduling algorithm assigns ground holds for pre-departure flights that originate from within Anchorage Center. Tactical flight controls in the form of airborne holding are employed to reactively account for system uncertainties. Real-world scenarios that were derived from the January 16, 2012 Anchorage visibility observations and the January 12, 2012 Anchorage arrival schedule were used to test the initial implementation of the scheduling algorithm in fast-time simulation experiments. Although over 90% of the flights in the scenarios arrived at Anchorage without requiring any delay, pre-departure scheduling was the dominant form of control for Anchorage arrivals. Additionally, tactical scheduling was used extensively in conjunction with the pre-departure scheduling to reactively compensate for uncertainties in the arrival demand. For long-haul flights, the strategic scheduling algorithm performed best when the scheduling horizon was greater than 1,000 nmi. With these long scheduling horizons, it was possible to absorb between ten and 12 minutes of delay through speed control alone. Unfortunately, the use of tactical scheduling, which resulted in airborne holding, was found to increase as the strategic scheduling horizon increased because of the additional uncertainty in the arrival times of the aircraft. Findings from these initial experiments indicate that it is possible to schedule arrivals into Anchorage with minimal delays under low-visibility conditions with less disruption to high-cost, international flights.

Folate deficiency facilitates recruitment of upstream binding factor to hot spots of DNA double-strand breaks of rRNA genes and promotes its transcription.

PubMed

Xie, Qiu; Li, Caihua; Song, Xiaozhen; Wu, Lihua; Jiang, Qian; Qiu, Zhiyong; Cao, Haiyan; Yu, Kaihui; Wan, Chunlei; Li, Jianting; Yang, Feng; Huang, Zebing; Niu, Bo; Jiang, Zhengwen; Zhang, Ting

2017-03-17

The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) landscape in mouse embryonic stem cells. A significant DSB enhancement was detected in the genome of these cells and a large majority of these DSBs were found in rRNA genes. Furthermore, spontaneous DSBs in cells under folate deficiency conditions were located exclusively within the rRNA gene units, representing a H3K4me1 hallmark. Enrichment H3K4me1 at the hot spots of DSB regions enhanced the recruitment of upstream binding factor (UBF) to rRNA genes, resulting in the increment of rRNA genes transcription. Supplement of folate resulted in a restored UBF binding across DNA breakage sites of rRNA genes, and normal rRNA gene transcription. In samples from neural tube defects (NTDs) with low folate level, up-regulation of rRNA gene transcription was observed, along with aberrant UBF level. Our results present a new view by which alterations in folate levels affects DNA breakage through epigenetic control leading to the regulation of rRNA gene transcription during the early stage of development. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Interference Cognizant Network Scheduling

NASA Technical Reports Server (NTRS)

Hall, Brendan (Inventor); Bonk, Ted (Inventor); DeLay, Benjamin F. (Inventor); Varadarajan, Srivatsan (Inventor); Smithgall, William Todd (Inventor)

2017-01-01

Systems and methods for interference cognizant network scheduling are provided. In certain embodiments, a method of scheduling communications in a network comprises identifying a bin of a global timeline for scheduling an unscheduled virtual link, wherein a bin is a segment of the timeline; identifying a pre-scheduled virtual link in the bin; and determining if the pre-scheduled and unscheduled virtual links share a port. In certain embodiments, if the unscheduled and pre-scheduled virtual links don't share a port, scheduling transmission of the unscheduled virtual link to overlap with the scheduled transmission of the pre-scheduled virtual link; and if the unscheduled and pre-scheduled virtual links share a port: determining a start time delay for the unscheduled virtual link based on the port; and scheduling transmission of the unscheduled virtual link in the bin based on the start time delay to overlap part of the scheduled transmission of the pre-scheduled virtual link.

Effects of altered gravity on a distribution of rDNA and nucleolar proteins and the expression of nucleolar proteins in plants

NASA Astrophysics Data System (ADS)

Sobol, Margaryta; Kordyum, Elizabeth; Medina, Francisco Javier

The nucleolus is an inner nuclear organelle originated from the activity of hundreds of rRNA genes, typically spanning several megabases. It morphologically reflects the functional events leading to ribosome biogenesis, from the transcription of rDNA through the processing of nascent pre-rRNA to the assembly of pre-ribosomes. A typical nucleolus consists of three major elements, namely fibrillar centers (FCs), the dense fibrillar component (DFC), and granular component (GC). The rate of ribosome biosynthesis and the subnucleolar structure are reliable monitors of the general level of cell metabolism and, consequently, of the rate of cellular growth, being influenced with many external factors, among which altered gravity could be included. Thus, we can hypothesize that the structural organization of the nucleolar subcomponents and the level, distribution and quantitative/qualitative characteristics of the nucleolar proteins would be changed under conditions of altered gravity. To confirm our hypothesis, we applied parallel procedures, such as cytochemistry, immunofluorescence, confocal laser microscopy, immunogold electron microscopy, monoand bi-dimensional electrophoresis and immunoblotting in root meristematic cells from two-day cress seedlings grown under slow horizontal clinorotation (2 rpm) and in stationary control. The complex model of the ultrastructural organization and functions of the nucleolus was created based on the location of rDNA and the nucleolar proteins fibrillarin, NhL90 and NhL68, these latter being cress nucleolin homologues. The principal stages of ribosome biogenesis, namely ribosomal gene activation, rDNA transcription and pre-rRNA processing were reflected in this model. Compared to the pattern shown in control ground gravity conditions, we found firstly a redistribution of both rDNA and nucleolar proteins in nucleolar subcomponents, induced by clinorotation. Under the conditions of altered gravity, nucleolar DNA concentrated predominantly in FCs in the form of condensed chromatin inclusions and internal non condensed fibrils, redistributing from the DFC and the transition zone between FCs and the DFC, recognized as the site of rDNA transcription. Regarding nucleolar proteins, a general decrease in the levels of fibrillarin and the nucleolin homologues, evaluated by estimating the density of immunogold labeling on the nucleolus, was recorded firstly in clinorotated samples, compared to controls. Furthermore, the intranucleolar location of the investigated proteins was also observed to change in response to the growth in altered gravity conditions. In particular, a decrease in the quantity of these proteins in the transition zone FCs-DFC as well as in the bulk of the DFC was observed in the experimental samples, compared to controls, whereas the content of the proteins was much higher in the inner space of FCs. Concerning the two-dimensional nuclear proteome, we revealed a decrease in the isoelectric point (pI) range of soluble proteins, which are known to be actively engaged in RNA (including rRNA) metabolism, and a shortening in the molecular weight range of them under clinorotation. Besides, minor and major protein spots in clinorotated samples showed decreased optical densities in comparison to control ones. Moreover, we showed the shortening of both the pI and the molecular weight ranges of the spots corresponding to the major nucleolin homologue NhL90 (detected by cross-reaction with anti-onion NopA100) in the fraction of soluble proteins in altered gravity. Based on these data, an effect of altered gravity in lowering the level of rDNA transcription as well as rRNA processing, that could be the evidence of a decrease in the level of nucleolar functional activity, is suggested.

Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy

PubMed Central

Santiago-Rodriguez, Tasha M.; Fornaciari, Gino; Luciani, Stefania; Dowd, Scot E.; Toranzos, Gary A.; Marota, Isolina; Cano, Raul J.

2015-01-01

The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput sequencing and metagenomics. Firmicutes were the most abundant bacterial group, with Clostridium spp. comprising up to 96.2% of the mummified gut, while Turicibacter spp. represented 89.2% of the bacteria identified in the paleofeces. Microbiome profile of the paleofeces was unique when compared to previously characterized coprolites that did not undergo natural mummification. We identified DNA sequences homologous to Clostridium botulinum, Trypanosoma cruzi and human papillomaviruses (HPVs). Unexpectedly, putative antibiotic-resistance genes including beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters, were also identified. The presence of putative antibiotic-resistance genes suggests that resistance may not necessarily be associated with a selective pressure of antibiotics or contact with European cultures. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses. PMID:26422376

Structure of the initiation-competent RNA polymerase I and its implication for transcription

NASA Astrophysics Data System (ADS)

Pilsl, Michael; Crucifix, Corinne; Papai, Gabor; Krupp, Ferdinand; Steinbauer, Robert; Griesenbeck, Joachim; Milkereit, Philipp; Tschochner, Herbert; Schultz, Patrick

2016-07-01

Eukaryotic RNA polymerase I (Pol I) is specialized in rRNA gene transcription synthesizing up to 60% of cellular RNA. High level rRNA production relies on efficient binding of initiation factors to the rRNA gene promoter and recruitment of Pol I complexes containing initiation factor Rrn3. Here, we determine the cryo-EM structure of the Pol I-Rrn3 complex at 7.5 Å resolution, and compare it with Rrn3-free monomeric and dimeric Pol I. We observe that Rrn3 contacts the Pol I A43/A14 stalk and subunits A190 and AC40, that association re-organizes the Rrn3 interaction interface, thereby preventing Pol I dimerization; and Rrn3-bound and monomeric Pol I differ from the dimeric enzyme in cleft opening, and localization of the A12.2 C-terminus in the active centre. Our findings thus support a dual role for Rrn3 in transcription initiation to stabilize a monomeric initiation competent Pol I and to drive pre-initiation complex formation.

SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana.

PubMed

Wu, Wenjuan; Liu, Sheng; Ruwe, Hannes; Zhang, Delin; Melonek, Joanna; Zhu, Yajuan; Hu, Xupeng; Gusewski, Sandra; Yin, Ping; Small, Ian D; Howell, Katharine A; Huang, Jirong

2016-03-01

Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5' end of the 23S-4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA 'footprint' associated with this site in sot1 mutants. We found that more than half of the 23S-4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5' and 3' ends, and that the endonucleolytic cleavage product normally released from the 5' end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5' extremity of the 23S-4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5' and 3' ends. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Effects of delayed mating on the reproductive biology of the vine mealybug, Planococcus ficus (Hemiptera: Pseudococcidae).

PubMed

Lentini, A; Mura, A; Muscas, E; Nuvoli, M T; Cocco, A

2018-04-01

The effect of increasing mating delay on the reproductive performance and population growth rates of the vine mealybug, Planococcus ficus (Signoret) (Hemiptera: Pseudococcidae), was investigated under laboratory conditions. Virgin females were mated at 1, 3, 5, 7, 14, 21 and 28 days after emergence and reproductive and life table parameters were estimated. The pre-oviposition period (number of days between mating and the onset of oviposition) significantly decreased in females mated within 7 days, whereas females mated at older ages showed equivalent pre-oviposition periods (7 days, as shorter delays in mating did not reduce the population growth rates.

Data-Gathering Scheme Using AUVs in Large-Scale Underwater Sensor Networks: A Multihop Approach

PubMed Central

Khan, Jawaad Ullah; Cho, Ho-Shin

2016-01-01

In this paper, we propose a data-gathering scheme for hierarchical underwater sensor networks, where multiple Autonomous Underwater Vehicles (AUVs) are deployed over large-scale coverage areas. The deployed AUVs constitute an intermittently connected multihop network through inter-AUV synchronization (in this paper, synchronization means an interconnection between nodes for communication) for forwarding data to the designated sink. In such a scenario, the performance of the multihop communication depends upon the synchronization among the vehicles. The mobility parameters of the vehicles vary continuously because of the constantly changing underwater currents. The variations in the AUV mobility parameters reduce the inter-AUV synchronization frequency contributing to delays in the multihop communication. The proposed scheme improves the AUV synchronization frequency by permitting neighboring AUVs to share their status information via a pre-selected node called an agent-node at the static layer of the network. We evaluate the proposed scheme in terms of the AUV synchronization frequency, vertical delay (node→AUV), horizontal delay (AUV→AUV), end-to-end delay, and the packet loss ratio. Simulation results show that the proposed scheme significantly reduces the aforementioned delays without the synchronization time-out process employed in conventional works. PMID:27706042

Data-Gathering Scheme Using AUVs in Large-Scale Underwater Sensor Networks: A Multihop Approach.

PubMed

Khan, Jawaad Ullah; Cho, Ho-Shin

2016-09-30

In this paper, we propose a data-gathering scheme for hierarchical underwater sensor networks, where multiple Autonomous Underwater Vehicles (AUVs) are deployed over large-scale coverage areas. The deployed AUVs constitute an intermittently connected multihop network through inter-AUV synchronization (in this paper, synchronization means an interconnection between nodes for communication) for forwarding data to the designated sink. In such a scenario, the performance of the multihop communication depends upon the synchronization among the vehicles. The mobility parameters of the vehicles vary continuously because of the constantly changing underwater currents. The variations in the AUV mobility parameters reduce the inter-AUV synchronization frequency contributing to delays in the multihop communication. The proposed scheme improves the AUV synchronization frequency by permitting neighboring AUVs to share their status information via a pre-selected node called an agent-node at the static layer of the network. We evaluate the proposed scheme in terms of the AUV synchronization frequency, vertical delay (node→AUV), horizontal delay (AUV→AUV), end-to-end delay, and the packet loss ratio. Simulation results show that the proposed scheme significantly reduces the aforementioned delays without the synchronization time-out process employed in conventional works.

Prp43p Is a DEAH-Box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis

PubMed Central

Combs, D. Joshua; Nagel, Roland J.; Ares, Manuel; Stevens, Scott W.

2006-01-01

The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified Prp43p-associated material includes the expected spliceosomal components; however, we also identify several preribosomal complexes that are specifically purified with Prp43p. Conditional prp43 mutant alleles confer a 35S pre-rRNA processing defect, with subsequent depletion of 27S and 20S precursors. Upon a shift to a nonpermissive temperature, both large and small-ribosomal-subunit proteins accumulate in the nucleolus of prp43 mutants. Pulse-chase analysis demonstrates delayed kinetics of 35S, 27S, and 20S pre-rRNA processing with turnover of these intermediates. Microarray analysis of pre-mRNA splicing defects in prp43 mutants shows a very mild effect, similar to that of nonessential pre-mRNA splicing factors. Prp43p is the first DEXH/D-box protein shown to function in both RNA polymerase I and polymerase II transcript metabolism. Its essential function is in its newly characterized role in ribosome biogenesis of both ribosomal subunits, positioning Prp43p to regulate both pre-mRNA splicing and ribosome biogenesis. PMID:16382144

Creation of a data base for sequences of ribosomal nucleic acids and detection of conserved restriction endonucleases sites through computerized processing.

PubMed Central

Patarca, R; Dorta, B; Ramirez, J L

1982-01-01

As part of a project pertaining the organization of ribosomal genes in Kinetoplastidae, we have created a data base for published sequences of ribosomal nucleic acids, with information in Spanish. As a first step in their processing, we have written a computer program which introduces the new feature of determining the length of the fragments produced after single or multiple digestion with any of the known restriction enzymes. With this information we have detected conserved SAU 3A sites: (i) at the 5' end of the 5.8S rRNA and at the 3' end of the small subunit rRNA, both included in similar larger sequences; (ii) in the 5.8S rRNA of vertebrates (a second one), which is not present in lower eukaryotes, showing a clear evolutive divergence; and, (iii) at the 5' terminal of the small subunit rRNA, included in a larger conserved sequence. The possible biological importance of these sequences is discussed. PMID:6278402

Time-lapse processing of 2D seismic profiles with testing of static correction methods at the CO2 injection site Ketzin (Germany)

NASA Astrophysics Data System (ADS)

Bergmann, Peter; Yang, Can; Lüth, Stefan; Juhlin, Christopher; Cosma, Calin

2011-09-01

The Ketzin project provides an experimental pilot test site for the geological storage of CO2. Seismic monitoring of the Ketzin site comprises 2D and 3D time-lapse experiments with baseline experiments in 2005. The first repeat 2D survey was acquired in 2009 after 22 kt of CO2 had been injected into the Stuttgart Formation at approximately 630 m depth. Main objectives of the 2D seismic surveys were the imaging of geological structures, detection of injected CO2, and comparison with the 3D surveys. Time-lapse processing highlighted the importance of detailed static corrections to account for travel time delays, which are attributed to different near-surface velocities during the survey periods. Compensation for these delays has been performed using both pre-stack static corrections and post-stack static corrections. The pre-stack method decomposes the travel time delays of baseline and repeat datasets in a surface consistent manner, while the latter cross-aligns baseline and repeat stacked sections along a reference horizon. Application of the static corrections improves the S/N ratio of the time-lapse sections significantly. Based on our results, it is recommended to apply a combination of both corrections when time-lapse processing faces considerable near-surface velocity changes. Processing of the datasets demonstrates that the decomposed solution of the pre-stack static corrections can be used for interpretation of changes in near-surface velocities. In particular, the long-wavelength part of the solution indicates an increase in soil moisture or a shallower groundwater table in the repeat survey. Comparison with the processing results of 2D and 3D surveys shows that both image the subsurface, but with local variations which are mainly associated to differences in the acquisition geometry and source types used. Interpretation of baseline and repeat stacks shows that no CO2 related time-lapse signature is observable where the 2D lines allow monitoring of the reservoir. This finding is consistent with the time-lapse results of the 3D surveys, which show an increase in reflection amplitude centered around the injection well. To further investigate any potential CO2 signature, an amplitude versus offset (AVO) analysis was performed. The time-lapse analysis of the AVO does not indicate the presence of CO2, as expected, but shows signs of a pressure response in the repeat data.

Nucleolar evolution and coiled bodies during meiotic prophase in Olea europaea: differential localization of nucleic acids.

PubMed

Olmedilla, A; de Dios Alché, J; Rodríguez-García, M I

1997-10-01

We studied the ultrastructural evolution of the nucleolus during meiotic prophase in olive microsporocytes. During prophase, nuclear bodies morphologically similar to coiled bodies were observed. The nucleic acid composition of these bodies was examined in microsporocytes using electron microscopic techniques with EDTA preferential ribonucleoprotein staining, anti-DNA immunolabeling, the in situ terminal deoxynucleotidyl transferase-immunogold technique, and in situ hybridization with 18S rRNA and U3 snoRNA digoxigenin-labeled probes. The ultrastructural appearance of the meiocyte nucleolus indicated a low level of activity from the early prophase stage: the granular component was practically absent and nucleoli were constituted almost exclusively by dense fibrillar component containing large fibrillar centers that lacked chromatin inclusions. However, the appearance of reactivation vacuoles in the nucleolus during zygotene and high levels of rRNA in the nucleoplasm during pachytene support the presence of a peak in rRNA synthesis. Our results also show that the nuclear bodies that appear during prophase I are ribonucleoproteinaceous in nature; neither DNA nor ribosomal RNA were detected. The presence of U3 snoRNA, as shown by in situ hybridization in nuclear bodies from plant material, is also evidence that these structures are coiled bodies. We suggest that coiled bodies are involved not only in pre- and post-splicing events but also in the storage, transport or recycling of rRNA maturation elements.

False context fear memory in rats.

PubMed

Bae, Sarah E; Holmes, Nathan M; Westbrook, R Frederick

2015-10-01

Four experiments used rats to study false context fear memories. In Experiment 1, rats were pre-exposed to a distinctive chamber (context A) or to a control environment (context C), shocked after a delay in a second chamber (context B) and tested either in B or A. Rats pre-exposed to A froze just as much as control rats in B but more than control rats in A. In Experiment 2, rats were pre-exposed to A or C, subjected to an immediate shock in B and tested in B or A. Rats pre-exposed to A froze when tested in A but did not freeze when tested in B and control rats did not freeze in either A or B. The false fear memory to the pre-exposed A was contingent on its similarity with the shocked B. In Experiment 3, rats pre-exposed to A and subjected to immediate shock in B froze when tested in A but did not freeze when tested in C and rats pre-exposed to C did not freeze when tested either in A or C. In Experiment 4, rats pre-exposed to A and subjected to immediate shock in B froze more when tested in A than rats whose pre-exposure to A began with an immediate shock. The results were discussed in terms of a dual systems explanation of context fear conditioning: a hippocampal-dependent process that forms a unitary representation of context and an amygdala-based process which associates this representation with shock. © 2015 Bae et al.; Published by Cold Spring Harbor Laboratory Press.

[Creation and Evaluation of Educational Programs for Additional Delayed Scan of FDG-PET/CT].

PubMed

Wada, Ryota; Kamiya, Takashi; Fujino, Kouichi; Ueda, Junpei; Isohashi, Kayako; Tatsumi, Mitsuaki; Hatazawa, Jun

Generally, FDG-PET/CT image is acquired at the 60th minute after tracer administration. Depending on the clinical case, additional delayed scans may be useful. However, it is difficult to judge whether additional delayed scan is useful or not. The purposes of this study were creation and evaluation of educational programs to help radiological technologists to decide the usefulness of additional delayed scan of FDG-PET/CT. Educational programs consisted of the instructional materials and the judgment test of clinical cases. The instructional materials provided the valuable findings for differentiation between uptake in the wall of the colon and colon content, distinction between uptake in the lymph node and urinary tract, and evaluation of malignancy. The judgment test of clinical cases consisted of 10 cases selected by a nuclear medicine physician (for 5 of that cases additional delayed scan was decided to be useful). Five experienced technologists and five inexperienced technologists scored the volubility of additional delayed scan pre- and post-training using the instructional materials (the full marks of score is 5). After the educational programs using the instructional materials, the score was improved with the significant difference in both experienced (pre: 3.6±1.4, post: 4.0±1.2) and inexperienced (pre: 2.8±1.5, post: 3.7±1.5) groups (p<0.05). According to the educational programs, technologist might be able to decide whether the additional delayed scan is useful or not. The successful results of this study may improve the interpretation or reduce the total exposure dose of the PET/CT scan.

The Delayed Fracture of Aluminum Alloys.

DTIC Science & Technology

1981-01-01

Cracking of a Maraging Steel ," Corrosion NACE, 1971, vol. 27, no. 10, pp. 429-433. 42. H.R. Smith and D.E. Piper: "Stress- Corrosion Testing with Pre...Sivaramakrishman, and R. Kumar: "Influence of Processing Variables on the Stress Corrosion Characteristics of Weldable Al-Zn-Mg Alloys," Light Met. Age , 1979...if necessary and Identify by block number) aluminum alloys, stress- corrosion cracking, oxide film, Auger electron spectroscopy, Auger depth profiling

Root Cause Analysis and Subsequent Intervention to Improve First Dose Antibiotic Turnaround Time for Hospitalized Pediatric Patients

PubMed Central

Dee, Abigail A.; Kelly, Brian; Hampp, Christian

2010-01-01

OBJECTIVE Antibiotic timing is used as a quality standard for hospital accreditation and is an important quality measure. The study aim was to identify barriers in the process of first dose antibiotic administration on the pediatric floors at a tertiary healthcare center and carry out and test an intervention to improve turnaround time to less than one hour. METHODS We conducted a quasi-experimental pre-post study of hospitalized pediatric patients up to 18 years of age initiated on intravenous antibiotics. Every order for a first dose intravenous antibiotic was assessed on all pediatric floors (10/2008). Orders that did not meet the overall turnaround time goal of ≤ 1 hour were identified. A root cause analysis (RCA) was performed to identify reasons for delayed antibiotic administration. Barriers identified in the RCA were used to develop interventions (03/2009) to improve compliance, and the proportion of orders that met the goal was compared pre- (10/2008–02/2009) and post-intervention (04/2009–05/2009). RESULTS During the pre-intervention assessment period, 32 out of 46 total physician orders for a first dose intravenous antibiotic did not meet the one-hour overall turnaround goal. A main reason for delay was failure to label antibiotic orders as first dose. We designed an intervention that included antibiotic audits and individualized feedback to prescribers. The mean ± SD time from the written physician order to drug administration was 228 ± 58 minutes; timing improved to 55 ± 4 minutes after the intervention. The proportion of antibiotics administered within one hour improved from 42.2% to 63% (p=0.0015). CONCLUSIONS We identified system barriers associated with delayed antibiotic administration. Antibiotic timing was improved after continued surveillance and individualized feedback to providers. PMID:22477810

Altering impulsive decision making with an acceptance-based procedure.

PubMed

Morrison, Kate L; Madden, Gregory J; Odum, Amy L; Friedel, Jonathan E; Twohig, Michael P

2014-09-01

Delay discounting is one facet of impulsive decision making and involves subjectively devaluing a delayed outcome. Steeply discounting delayed rewards is correlated with substance abuse and other problematic behaviors. To the extent that steep delay discounting underlies these clinical disorders, it would be advantageous to find psychosocial avenues for reducing delay discounting. Acceptance-based interventions may prove useful as they may help to decrease the distress that arises while waiting for a delayed outcome. The current study was conducted to determine if a 60-90 minute acceptance-based training would change delay discounting rates among 30 undergraduate university students in comparison to a waitlist control. Measures given at pre- and posttraining included a hypothetical monetary delay discounting task, the Acceptance and Action Questionnaire-II (AAQ-II), and the Distress Tolerance Scale. Those assigned to the treatment group decreased their discounting of delayed money, but not distress intolerance or psychological inflexibility when compared to the waitlist control group. After the waiting period, the control group received the intervention. Combining all participants' pre- to posttreatment data, the acceptance-based treatment significantly decreased discounting of monetary rewards and increased distress tolerance. The difference in AAQ-II approached significance. Acceptance-based treatments may be a worthwhile option for decreasing delay discounting rates and, consequently, affecting the choices that underlie addiction and other problematic behaviors. Copyright © 2014. Published by Elsevier Ltd.

The constructive role of gender asymmetry in social interaction: further evidence.

PubMed

Psaltis, Charis

2011-06-01

Two hundred and sixty-four children aged 6.5-7.5 years (first graders) took part in a pre-test, interaction, and post-test experiment working on a spatial transformation task known as the 'village task'. Cognitive progress was assessed by pre- to post-test gains in both an immediate and delayed post-test in dyads and individual participants as a control. The results indicate clear links between particular pair types with both communication processes and with learning and cognitive developmental outcomes. The present study demonstrates that gender can act as a source of status asymmetry in peer interaction to influence communication, learning, and cognitive development in same- and mixed-sex dyads.

The Effect of Pre-Analytical Variability on the Measurement of MRM-MS-Based Mid- to High-Abundance Plasma Protein Biomarkers and a Panel of Cytokines

PubMed Central

Aguilar-Mahecha, Adriana; Kuzyk, Michael A.; Domanski, Dominik; Borchers, Christoph H.; Basik, Mark

2012-01-01

Blood sample processing and handling can have a significant impact on the stability and levels of proteins measured in biomarker studies. Such pre-analytical variability needs to be well understood in the context of the different proteomics platforms available for biomarker discovery and validation. In the present study we evaluated different types of blood collection tubes including the BD P100 tube containing protease inhibitors as well as CTAD tubes, which prevent platelet activation. We studied the effect of different processing protocols as well as delays in tube processing on the levels of 55 mid and high abundance plasma proteins using novel multiple-reaction monitoring-mass spectrometry (MRM-MS) assays as well as 27 low abundance cytokines using a commercially available multiplexed bead-based immunoassay. The use of P100 tubes containing protease inhibitors only conferred proteolytic protection for 4 cytokines and only one MRM-MS-measured peptide. Mid and high abundance proteins measured by MRM are highly stable in plasma left unprocessed for up to six hours although platelet activation can also impact the levels of these proteins. The levels of cytokines were elevated when tubes were centrifuged at cold temperature, while low levels were detected when samples were collected in CTAD tubes. Delays in centrifugation also had an impact on the levels of cytokines measured depending on the type of collection tube used. Our findings can help in the development of guidelines for blood collection and processing for proteomic biomarker studies. PMID:22701622

The effect of pre-analytical variability on the measurement of MRM-MS-based mid- to high-abundance plasma protein biomarkers and a panel of cytokines.

PubMed

Aguilar-Mahecha, Adriana; Kuzyk, Michael A; Domanski, Dominik; Borchers, Christoph H; Basik, Mark

2012-01-01

Blood sample processing and handling can have a significant impact on the stability and levels of proteins measured in biomarker studies. Such pre-analytical variability needs to be well understood in the context of the different proteomics platforms available for biomarker discovery and validation. In the present study we evaluated different types of blood collection tubes including the BD P100 tube containing protease inhibitors as well as CTAD tubes, which prevent platelet activation. We studied the effect of different processing protocols as well as delays in tube processing on the levels of 55 mid and high abundance plasma proteins using novel multiple-reaction monitoring-mass spectrometry (MRM-MS) assays as well as 27 low abundance cytokines using a commercially available multiplexed bead-based immunoassay. The use of P100 tubes containing protease inhibitors only conferred proteolytic protection for 4 cytokines and only one MRM-MS-measured peptide. Mid and high abundance proteins measured by MRM are highly stable in plasma left unprocessed for up to six hours although platelet activation can also impact the levels of these proteins. The levels of cytokines were elevated when tubes were centrifuged at cold temperature, while low levels were detected when samples were collected in CTAD tubes. Delays in centrifugation also had an impact on the levels of cytokines measured depending on the type of collection tube used. Our findings can help in the development of guidelines for blood collection and processing for proteomic biomarker studies.

Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors.

PubMed

Pervin, Hasina M; Dennis, Paul G; Lim, Hui J; Tyson, Gene W; Batstone, Damien J; Bond, Philip L

2013-12-01

Temperature-phased anaerobic digestion (TPAD) is an emerging technology that facilitates improved performance and pathogen destruction in anaerobic sewage sludge digestion by optimising conditions for 1) hydrolytic and acidogenic organisms in a first-stage/pre-treatment reactor and then 2) methogenic populations in a second stage reactor. Pre-treatment reactors are typically operated at 55-65 °C and as such select for thermophilic bacterial communities. However, details of key microbial populations in hydrolytic communities and links to functionality are very limited. In this study, experimental thermophilic pre-treatment (TP) and control mesophilic pre-treatment (MP) reactors were operated as first-stages of TPAD systems treating activated sludge for 340 days. The TP system was operated sequentially at 50, 60 and 65 °C, while the MP rector was held at 35 °C for the entire period. The composition of microbial communities associated with the MP and TP pre-treatment reactors was characterised weekly using terminal-restriction fragment length polymorphism (T-RFLP) supported by clone library sequencing of 16S rRNA gene amplicons. The outcomes of this approach were confirmed using 454 pyrosequencing of gene amplicons and fluorescence in-situ hybridisation (FISH). TP associated bacterial communities were dominated by populations affiliated to the Firmicutes, Thermotogae, Proteobacteria and Chloroflexi. In particular there was a progression from Thermotogae to Lutispora and Coprothermobacter and diversity decreased as temperature and hydrolysis performance increased. While change in the composition of TP associated bacterial communities was attributable to temperature, that of MP associated bacterial communities was related to the composition of the incoming feed. This study determined processes driving the dynamics of key microbial populations that are correlated with an enhanced hydrolytic functionality of the TPAD system. Copyright © 2013 Elsevier Ltd. All rights reserved.

An Archaea 5S rRNA analog is stably expressed in Escherichia coli

NASA Technical Reports Server (NTRS)

Yang, Y.; Fox, G. E.

1996-01-01

Mini-genes for 5S-like rRNA were constructed. These genes had a sequence which largely resembles that of the naturally occurring 5S rRNA of a bacterium, Halococcus morrhuae, which phylogenetically belongs to the Archaea. Plasmids carrying the mini-genes were transformed into Escherichia coli (Ec). Ribosomal incorporation was not a prerequisite for stable accumulation of the RNA product. However, only those constructs with a well-base-paired helix I accumulated RNA product. This result strongly implies that this aspect of the structure is likely to be an important condition for stabilizing 5S rRNA-like products. The results are consistent with our current understanding of 5S rRNA processing in Ec. When used in conjunction with rRNA probe technology, the resulting chimeric RNA may be useful as a monitoring tool for genetically engineered microorganisms or naturally occurring organisms that are released into the environment.

Yeast diversity during the fermentation of Andean chicha: A comparison of high-throughput sequencing and culture-dependent approaches.

PubMed

Mendoza, Lucía M; Neef, Alexander; Vignolo, Graciela; Belloch, Carmela

2017-10-01

Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Five hundred and ninety six yeasts were isolated by classical microbiological methods and 16 species identified by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns. High-throughput sequencing (HTS) of D1/D2 26S rRNA gene amplicons from chicha samples detected more than one hundred yeast species and almost fifty filamentous fungi taxa. Analysis of the data revealed that yeasts dominated the fermentation, although, a significant percentage of filamentous fungi appeared in the first step of the process. Statistical analysis of results showed that very few taxa were represented by more than 1% of the reads per sample at any step of the process. S. cerevisiae represented more than 90% of the reads in the fermentative samples. Other yeast species dominated the pre-fermentative steps and abounded in fermented samples when S. cerevisiae was in percentages below 90%. Most yeasts species detected by pyrosequencing were not recovered by cultivation. In contrast, the cultivation-based methodology detected very few yeast taxa, and most of them corresponded with very few reads in the pyrosequencing analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Enhanced shock wave generation via pre-breakdown acceleration using water electrolysis in negative streamer pulsed spark discharges

NASA Astrophysics Data System (ADS)

Lee, Kern; Chung, Kyoung-Jae; Hwang, Y. S.

2018-03-01

This paper presents a method for enhancement of shock waves generated from underwater pulsed spark discharges with negative (anode-directed) subsonic streamers, for which the pre-breakdown process is accelerated by preconditioning a gap with water electrolysis. Hydrogen microbubbles are produced at the cathode by the electrolysis and move towards the anode during the preconditioning phase. The numbers and spatial distributions of the microbubbles vary with the amplitude and duration of each preconditioning pulse. Under our experimental conditions, the optimum pulse duration is determined to be ˜250 ms at a pulse voltage of 400 V, where the buoyancy force overwhelms the electric force and causes the microbubbles to be swept out from the water gap. When a high-voltage pulse is applied to the gap just after the preconditioning pulse, the pre-breakdown process is significantly accelerated in the presence of the microbubbles. At the optimum preconditioning pulse duration, the average breakdown delay is reduced by 87% and, more importantly, the energy consumed during the pre-breakdown period decreases by 83%. This reduced energy consumption during the pre-breakdown period, when combined with the morphological advantages of negative streamers, such as thicker and longer stalks, leads to a significant improvement in the measured peak pressure (˜40%) generated by the underwater pulsed spark discharge. This acceleration of pre-breakdown using electrolysis overcomes the biggest drawback of negative subsonic discharges, which is slow vapor bubble formation due to screening effects, and thus enhances the efficiency of the shock wave generation process using pulsed spark discharges in water.

Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus.

PubMed

Poelchau, Monica F; Reynolds, Julie A; Elsik, Christine G; Denlinger, David L; Armbruster, Peter A

2013-05-22

Seasonal environments present fundamental physiological challenges to a wide range of insects. Many temperate insects surmount the exigencies of winter by undergoing photoperiodic diapause, in which photoperiod provides a token cue that initiates an alternative developmental programme leading to dormancy. Pre-diapause is a crucial preparatory phase of this process, preceding developmental arrest. However, the regulatory and physiological mechanisms of diapause preparation are largely unknown. Using high-throughput gene expression profiling in the Asian tiger mosquito, Aedes albopictus, we reveal major shifts in endocrine signalling, cell proliferation, metabolism, energy production and cellular structure across pre-diapause development. While some hallmarks of diapause, such as insulin signalling and stress response, were not important at the transcriptional level, two genes, Pepck and PCNA, appear to show diapause-induced transcriptional changes across insect taxa. These processes demonstrate physiological commonalities between Ae. albopictus pre-diapause and diapause strategies across insects, and support the idea of a genetic 'toolkit' for diapause. Observations of gene expression trends from a comparative developmental perspective suggest that individual physiological processes are delayed against a background of a fixed morphological ontogeny. Our results demonstrate how deep sequencing can provide new insights into elusive molecular bases of complex ecological adaptations.

EARLINET Single Calculus Chain - technical - Part 1: Pre-processing of raw lidar data

NASA Astrophysics Data System (ADS)

D'Amico, Giuseppe; Amodeo, Aldo; Mattis, Ina; Freudenthaler, Volker; Pappalardo, Gelsomina

2016-02-01

In this paper we describe an automatic tool for the pre-processing of aerosol lidar data called ELPP (EARLINET Lidar Pre-Processor). It is one of two calculus modules of the EARLINET Single Calculus Chain (SCC), the automatic tool for the analysis of EARLINET data. ELPP is an open source module that executes instrumental corrections and data handling of the raw lidar signals, making the lidar data ready to be processed by the optical retrieval algorithms. According to the specific lidar configuration, ELPP automatically performs dead-time correction, atmospheric and electronic background subtraction, gluing of lidar signals, and trigger-delay correction. Moreover, the signal-to-noise ratio of the pre-processed signals can be improved by means of configurable time integration of the raw signals and/or spatial smoothing. ELPP delivers the statistical uncertainties of the final products by means of error propagation or Monte Carlo simulations. During the development of ELPP, particular attention has been payed to make the tool flexible enough to handle all lidar configurations currently used within the EARLINET community. Moreover, it has been designed in a modular way to allow an easy extension to lidar configurations not yet implemented. The primary goal of ELPP is to enable the application of quality-assured procedures in the lidar data analysis starting from the raw lidar data. This provides the added value of full traceability of each delivered lidar product. Several tests have been performed to check the proper functioning of ELPP. The whole SCC has been tested with the same synthetic data sets, which were used for the EARLINET algorithm inter-comparison exercise. ELPP has been successfully employed for the automatic near-real-time pre-processing of the raw lidar data measured during several EARLINET inter-comparison campaigns as well as during intense field campaigns.

Effect of work intensity on time delay in mediation of ventilation by arterial carbon dioxide during recovery from impulse exercise.

PubMed

Afroundeh, R; Arimitsu, T; Yamanaka, R; Lian, C S; Shirakawa, K; Yunoki, T; Yano, T

2014-01-01

Time delay in the mediation of ventilation (V(.)E) by arterial CO(2) pressure (PaCO(2)) was studied during recovery from short impulse-like exercises with different work loads of recovery. Subjects performed two tests including 10-s impulse like exercise with work load of 200 watts and 15-min recovery with 25 watts in test one and 50 watts in test two. V(.)E, end tidal CO(2) pressure (PETCO(2)) and heart rate (HR) were measured continuously during rest, warming up, exercise and recovery. PaCO(2) was estimated from PETCO(2) and tidal volume (V(T)). Results showed that predicted arterial CO(2) pressure (PaCO(2 pre)) increased during recovery in both tests. In both tests, V(.)E increased and peaked at the end of exercise. V(.)E decreased in the first few seconds of recovery but started to increase again. The highest correlation coefficient between PaCO(2 pre) and V(.)E was obtained in the time delay of 7 s (r=0.854) in test one and in time delays of 6 s (r=0.451) and 31 s (r=0.567) in test two. HR was significantly higher in test two than in test one. These results indicate that PaCO(2 pre) drives V(.)E with a time delay and that higher work intensity induces a shorter time delay.

RNase MRP and the RNA processing cascade in the eukaryotic ancestor.

PubMed

Woodhams, Michael D; Stadler, Peter F; Penny, David; Collins, Lesley J

2007-02-08

Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.

The impact of place of enrollment and delay to reperfusion on 90-day post-infarction mortality in the ASSENT-4 PCI trial: assessment of the safety and efficacy of a new treatment strategy with percutaneous coronary intervention.

PubMed

Ross, Allan M; Huber, Kurt; Zeymer, Uwe; Armstrong, Paul W; Granger, Christopher B; Goldstein, Patrick; Bogaerts, Kris; Van de Werf, Frans

2009-10-01

We have performed a retrospective analysis of the data stratified by time to treatment and by enrollment site: percutaneous coronary intervention hospitals (PCIH), nonpercutaneous coronary intervention hospitals (NoPCIH), or in a pre-hospital setting (PreH). The ASSENT-4 PCI (Assessment of the Safety and Efficacy of a New Treatment Strategy with Percutaneous Coronary Intervention) trial intended to test the hypothesis that in ST-segment elevation myocardial infarction (STEMI) patients an upfront fibrinolytic bolus before PCI ("facilitated PCI") compared with primary PCI would benefit STEMI patients facing a long pre-PCI delay. Seven hundred forty-nine patients (45%) presented directly to PCIH, 578 (34%) presented to NoPCIH, and 334 (20%) were randomized and initially treated in the PreH setting. Patients in the PreH-facilitated group had the shortest delays (pain-to-fibrinolytic treatment 125 min) and the lowest 90-day mortality (3.1%). Among patients randomized to primary PCI, the shortest time from pain to first balloon was similarly in the PreH group (223 min). They had the lowest mortality of the primary PCI patient groups (4.1%). The highest mortality (8.4%) was in patients presenting to a PCIH and assigned to the facilitated strategy. Their pain-to-lysis time was 174 min and pain-to-PCI time 266 min (or 92 min after lysis). Few patients fit the target population, long delays to PCI for whom facilitated PCI was designed. Patients treated early after pain onset in the PreH setting do well after a facilitated approach. Despite limitations of post hoc subgroup analysis, these observations suggest caution in extrapolating the results of the ASSENT-4 trial to the "real world" where many patients might have potentially short pain-to-fibrinolysis time but are facing a long transport time to primary PCI.

Elevated levels of Era GTPase improve growth, 16S rRNA processing, and 70S ribosome assembly of Escherichia coli lacking highly conserved multifunctional YbeY endoribonuclease.

PubMed

Ghosal, Anubrata; Babu, Vignesh M P; Walker, Graham C

2018-06-18

YbeY is a highly conserved, multifunctional endoribonuclease that plays a significant role in ribosome biogenesis and has several additional roles. Here, we show in Escherichia coli that overexpressing the conserved GTPase, Era, partially suppresses the growth defect of a ΔybeY strain while improving 16S rRNA processing and 70S ribosome assembly. This suppression requires both Era's ability to hydrolyze GTP and the function of three exoribonucleases, RNase II, RNase R and RNase PH, suggesting a model for Era's action. Overexpressing Vibrio cholerae Era similarly partially suppresses the defects of an E. coli ΔybeY strain indicating this property of Era is conserved in bacteria other than E. coli Importance This work provides additional insights into the critical, but still incompletely understood, mechanism of the processing of the E. coli 16S rRNA 3'-terminus. The highly conserved GTPase, Era, is known to bind to the precursor of the 16S rRNA near its 3-end. Both the endoribonuclease YbeY, which binds to Era, and four exoribonucleases have been implicated in this 3'-end processing. Results reported here offer additional insights into the role of Era in 16S rRNA 3'-maturation and into the relationship between the action of the endoribonuclease YbeY and the four exoribonucleases. This study also hints at why YbeY is only essential in some bacteria and suggests that the YbeY could be a target for a new class of antibiotic in these bacteria. Copyright © 2018 American Society for Microbiology.

Oxidative damage of 18S and 5S ribosomal RNA in digestive gland of mussels exposed to trace metals.

PubMed

Kournoutou, Georgia G; Giannopoulou, Panagiota C; Sazakli, Eleni; Leotsinidis, Michel; Kalpaxis, Dimitrios L

2017-11-01

Numerous studies have shown the ability of trace metals to accumulate in marine organisms and cause oxidative stress that leads to perturbations in many important intracellular processes, including protein synthesis. This study is mainly focused on the exploration of structural changes, like base modifications, scissions, and conformational changes, caused in 18S and 5S ribosomal RNA (rRNA) isolated from the mussel Mytilus galloprovincialis exposed to 40μg/L Cu, 30μg/L Hg, or 100μg/L Cd, for 5 or 15days. 18S rRNA and 5S rRNA are components of the small and large ribosomal subunit, respectively, found in complex with ribosomal proteins, translation factors and other auxiliary components (metal ions, toxins etc). 18S rRNA plays crucial roles in all stages of protein synthesis, while 5S rRNA serves as a master signal transducer between several functional regions of 28S rRNA. Therefore, structural changes in these ribosomal constituents could affect the basic functions of ribosomes and hence the normal metabolism of cells. Especially, 18S rRNA along with ribosomal proteins forms the decoding centre that ensures the correct codon-anticodon pairing. As exemplified by ELISA, primer extension analysis and DMS footprinting analysis, each metal caused oxidative damage to rRNA, depending on the nature of metal ion and the duration of exposure. Interestingly, exposure of mussels to Cu or Hg caused structural alterations in 5S rRNA, localized in paired regions and within loops A, B, C, and E, leading to a continuous progressive loss of the 5S RNA structural integrity. In contrast, structural impairments of 5S rRNA in mussels exposed to Cd were accumulating for the initial 5days, and then progressively decreased to almost the normal level by day 15, probably due to the parallel elevation of metallothionein content that depletes the pools of free Cd. Regions of interest in 18S rRNA, such as the decoding centre, sites implicated in the binding of tRNAs (A- and P-sites) or translation factors, and areas related to translation fidelity, were found to undergo significant metal-induced conformational alterations, leading either to loosening of their structure or to more compact folding. These modifications were associated with parallel alterations in the translation process at multiple levels, a fact suggesting that structural perturbations in ribosomes, caused by metals, pose significant hurdles in translational efficiency and fidelity. Copyright © 2017 Elsevier B.V. All rights reserved.

Differences in symptoms, first medical contact and pre-hospital delay times between patients with ST- and non-ST-elevation myocardial infarction.

PubMed

Ängerud, Karin H; Sederholm Lawesson, Sofia; Isaksson, Rose-Marie; Thylén, Ingela; Swahn, Eva

2017-11-01

In ST-elevation myocardial infarction, time to reperfusion is crucial for the prognosis. Symptom presentation in myocardial infarction influences pre-hospital delay times but studies about differences in symptoms between patients with ST-elevation myocardial infarction and non-ST-elevation myocardial infarction are sparse and inconclusive. The aim was to compare symptoms, first medical contact and pre-hospital delay times in patients with ST-elevation myocardial infarction and non-ST-elevation myocardial infarction. This multicentre, observational study included 694 myocardial infarction patients from five hospitals. The patients filled in a questionnaire about their pre-hospital experiences within 24 h of hospital admittance. Chest pain was the most common symptom in ST-elevation myocardial infarction and non-ST-elevation myocardial infarction (88.7 vs 87.0%, p=0.56). Patients with cold sweat (odds ratio 3.61, 95% confidence interval 2.29-5.70), jaw pain (odds ratio 2.41, 95% confidence interval 1.04-5.58), and nausea (odds ratio 1.70, 95% confidence interval 1.01-2.87) were more likely to present with ST-elevation myocardial infarction, whereas the opposite was true for symptoms that come and go (odds ratio 0.58, 95% confidence interval 0.38-0.90) or anxiety (odds ratio 0.52, 95% confidence interval 0.29-0.92). Use of emergency medical services was higher among patients admitted with ST-elevation myocardial infarction. The pre-hospital delay time from symptom onset to first medical contact was significantly longer in non-ST-elevation myocardial infarction (2:05 h vs 1:10 h, p=0.001). Patients with ST-elevation myocardial infarction differed from those with non-ST-elevation myocardial infarction regarding symptom presentation, ambulance utilisation and pre-hospital delay times. This knowledge is important to be aware of for all healthcare personnel and the general public especially in order to recognise symptoms suggestive of ST-elevation myocardial infarction and when to decide if there is a need for an ambulance.

The biology of deception: emotion and morphine.

PubMed

Stefano, G B; Fricchione, G L

1995-01-01

The biology of deception suggests that denial-like processes are at the core of the cognitive coping. In this regard, with cognitive ability, one associates or assumes that this process occurs by way of a 'rational' mind. Such a detailed cognitive process as being rational would also lead, counter intuitively, to inactivity and or major delays in conclusion reaching. Thus, our perceived rationality may also be a deceptive behavioral response. Of equal noteworthyness, man is also 'emotional'. We surmise that emotion represents the pre-cognitive short-cut to overcome this potential for excessive rationality. In this light, we may explain certain psychiatric disorders such as obsessive-compulsive behavior as emotional extremes dealing with cognitive habits used to bind anxiety operating most probably at the pre-cognitive level. Given recent discoveries in neuroimmunology and an understanding of naturally occurring morphine as both an immune and neurological down-regulatory substance we hypothesize that abnormalities associated with emotional extremes may be due, in part, to morphinergic imbalances.

Application of preprocessing filtering on Decision Tree C4.5 and rough set theory

NASA Astrophysics Data System (ADS)

Chan, Joseph C. C.; Lin, Tsau Y.

2001-03-01

This paper compares two artificial intelligence methods: the Decision Tree C4.5 and Rough Set Theory on the stock market data. The Decision Tree C4.5 is reviewed with the Rough Set Theory. An enhanced window application is developed to facilitate the pre-processing filtering by introducing the feature (attribute) transformations, which allows users to input formulas and create new attributes. Also, the application produces three varieties of data set with delaying, averaging, and summation. The results prove the improvement of pre-processing by applying feature (attribute) transformations on Decision Tree C4.5. Moreover, the comparison between Decision Tree C4.5 and Rough Set Theory is based on the clarity, automation, accuracy, dimensionality, raw data, and speed, which is supported by the rules sets generated by both algorithms on three different sets of data.

Ontogenetic characterization of the intestinal microbiota of channel catfish through 16S rRNA gene sequencing reveals insights on temporal shifts and the influence of environmental microbes

USDA-ARS?s Scientific Manuscript database

Aquaculture recently overtook capture fisheries as the largest producer of food fish; however, to continue increasing fish production the industry is looking for ways of improving fish health and growth. Pre- and probiotic supplementation has gained attention as a means of solving these issues, howe...

Neuroprotective effects of silymarin on ischemia-induced delayed neuronal cell death in rat hippocampus.

PubMed

Hirayama, Koki; Oshima, Hideki; Yamashita, Akiko; Sakatani, Kaoru; Yoshino, Atsuo; Katayama, Yoichi

2016-09-01

We examined the effects of silymarin, which was extracted from Silybum marianum, on delayed neuronal cell death in the rat hippocampus. Rats were divided into four groups: sham-operated rats (sham group), rats which underwent ischemic surgery (control group), rats which were treated with silymarin before and after ischemic surgery (pre group), and rats which were treated with silymarin after ischemic surgery only (post group). We performed the ischemic surgery by occluding the bilateral carotid arteries for 20min and sacrificed the rats one week after the surgery. Silymarin was administered orally at 200mg/kg body weight. Smaller numbers of delayed cell deaths were noted in the rat CA1 region of the pre- and post-groups, and no significant difference was observed between these groups. There were few apoptotic cell deaths in all groups. Compared to the control group, significantly fewer cell deaths by autophagy were found in the pre- and post-group. We concluded that silymarin exerts a preservation effect on delayed neuronal cell death in the rat hippocampus and this effect has nothing to do with the timing of administering of silymarin. Copyright © 2016 Elsevier B.V. All rights reserved.

Optical Diagnostics of Multi-Gap Gas Switches for Linear Transformer Drivers

NASA Astrophysics Data System (ADS)

Sheng, Liang; Li, Yang; Sun, Tieping; Cong, Peitian; Zhang, Mei; Peng, Bodong; Zhao, Jizhen; Yue, Zhiqin; Wei, Fuli; Yuan, Yuan

2014-07-01

The trigger characteristics of a multi-gap gas switch with double insulating layers, a square-groove electrode supporter and a UV pre-ionizing structure are investigated aided by a high sensitivity fiber-bundle array detector, a UV fiber detector, and a framing camera, in addition to standard electrical diagnostics. The fiber-bundle-array detector is used to track the turn-on sequence of each electrode gap at a timing precision of 0.6 ns. Each fiber bundle, including five fibers with different azimuth angles, aims at the whole emitting area of each electrode gap and is fed to a photomultiplier tube. The UV fiber detector with a spectrum response of 260-320 nm, including a fused-quartz fiber of 200 μm in diameter and a solar-blinded photomultiplier tube, is adopted to study the effect of UV pre-ionizing on trigger characteristics. The framing camera, with a capacity of 4 frames per shot and an exposure time of 5 ns, is employed to capture the evolution of channel arcs. Based on the turn-on light signal of each electrode gap, the breakdown delay is divided into statistical delay and formative delay. A decrease in both of them, a smaller switch jitter and more channel arcs are observed with lower gas pressure. An increase in trigger voltage can reduce the statistical delay and its jitter, while higher trigger voltage has a relatively small influence on the formative delay and the number of channel arcs. With the UV pre-ionizing structure at 0.24 MPa gas pressure and 60 kV trigger voltage, the statistical delay and its jitter can be reduced by 1.8 ns and 0.67 ns, while the formative delay and its jitter can only be reduced by 0.5 ns and 0.25 ns.

Role of assessment tests in the stability of intelligence scoring of pre-school children with uneven/delayed cognitive profile.

PubMed

Yang, P; Jong, Y-J; Hsu, H-Y; Lung, F-W

2011-05-01

As part of an ongoing clinical service programme for pre-school children with developmental delay in an Asian developing country, we analysed the effect of three assessment tests, that is, Bayley Scale of Infant Development-II, Leiter International Performance Scale - Revised and Wechsler Preschool and Primary Scale of Intelligence - Revised - Chinese, on the stability of intelligence quotient (IQ) of children from pre-school through early childhood. The participants were 313 Taiwanese pre-school children with uneven or delayed cognitive profile and they were followed through early childhood. IQ stability was explored by different tests and among children of different clinical diagnosis: 168 children with non-autistic intellectual disability, 73 children with autism spectrum disorder, 58 children with mixed receptive-expressive language disorder and 14 children of other heterogeneous diagnoses. Stability of scores was evaluated using the r-squared for Pearson's coefficients to see the correlation between initial IQ (IQ1) and follow-up IQ (IQ2). Multiple linear regressions were also applied to see whether IQ1 had predictive ability for IQ2 and test-test difference in the total 313 children and each diagnostic subgroup. Results revealed that mean IQ1 was 65.8 ± 15.4 while mean IQ2 was 73.2 ± 17.9 for the total 313 children. The IQs were stable across an average follow-up duration of 38.6 ± 22.1 month from pre-school into early childhood. Patterns of positive correlations between IQ1 and IQ2 were noted by all the tests (r-squared = 0.43-0.5, all P < 0.001) and in the majority of diagnostic subgroups. Multiple regressions analysis also revealed that IQ1 could predict IQ2 significantly in all the tests (all P < 0.001). After careful choice of appropriate initial test, stability of IQ in children with developmental delay was noted from pre-school through early childhood. In addition, the translated version of cognitive assessment was valid for the required context of an Asian developing country. With the current emphasis on early identification and intervention for pre-school children with developmental delay, this information bears merit in clinical practice. © 2011 The Authors. Journal of Intellectual Disability Research © 2011 Blackwell Publishing Ltd.

Effect of amino acid starvation on UV sensitivity of Lactobacillus acidophilus cells

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

Soška, J.; Nečasová, J.

1973-11-01

In Lactobacillus acidophilus cultures uv irradiated in the exponential phase of growth, the dose-survival curve was of the simple exponential type, without any shoulder. If the bacteria were subjected to amino acid starvation prior to irradiation, a shoulder corresponding to a quasi-threshold dose (D) of about 780 ergs/mm/sup 2/ appeared in the curve. The administration of protein- or RNA-synthesis inhibitors prior to irradiation had the same effect. The effect of pre-irradiation amino acid starvation was abolished by simuitaneous thymidine starvation. It was likewise abolished if amino acid starvation was followed by incubation in the presence of amino acids (without thymidine)more » and then by irradiation of the cells. Post-irradiation amino acid starvation did not lead to the formation of a shoulder but if combined with thymidine starvation it did. It can be concluded from the results that post-irradiation repair processes are facilitated or promoted if, during the post-irradiation interval DNA synthesis is delayed. This delay represents a compensation of the pre-irradiation increase of cellular DNA-content, taking place during inhibition of proteosynthesis. The post-irradiation administration of caffeine did not abolish the formation of the shoulder induced by pre-irradiation amino acid starvation; on the contrary, it induced its formation even in exponentially growing, irradiated control bacteria. (auth)« less

Parents' and Speech and Language Therapists' Explanatory Models of Language Development, Language Delay and Intervention

ERIC Educational Resources Information Center

Marshall, Julie; Goldbart, Juliet; Phillips, Julie

2007-01-01

Background: Parental and speech and language therapist (SLT) explanatory models may affect engagement with speech and language therapy, but there has been dearth of research in this area. This study investigated parents' and SLTs' views about language development, delay and intervention in pre-school children with language delay. Aims: The aims…

Improving on-time surgical starts: the impact of implementing pre-OR timeouts and performance pay.

PubMed

Martin, Luke; Langell, John

2017-11-01

Operating room (OR) time is expensive. Underutilized OR time negatively impacts efficiency and is an unnecessary cost for hospitals. The purpose of this study was to evaluate the impact of a pre-OR timeout and performance pay incentive on the frequency of on-time, first surgical starts. At a single Veterans Affairs Medical Center, we implemented a pre-OR timeout in the form of a safety-briefing checklist and a modest performance pay incentive for on-time starts (>90% compliance) for attending surgeons. Data were collected on all first-start cases beginning before implementation in 2008 and continued through 2015. Each year, an average of 960 first starts occurred across nine surgical divisions. Before implementation of either the timeout or pay incentive, only 15% of cases started on time, and by 2015, greater than 72% were on time (P < 0.001). Over the study period, there were significant improvements in on-time starts (P = 0.01), of delays <15 min (P = 0.01), and of delays 16 to 30 min (P = 0.04). The trends for delays of 31 to 60 min or >60 min were not significant (P = 0.31; P = 0.81). Assuming a loss of 7 min per case for delays <15 min and 20 min per case for delays of 16 to 30 min, the total OR time saved from implementing these measures was 37,556 min. At an estimated cost of $20/min, gross savings from this project were $751,120. Implementation of a pre-OR timeout and performance pay for on-time starts significantly improves OR utilization and reduces unnecessary costs. Published by Elsevier Inc.

A Molecular Titration System Coordinates Ribosomal Protein Gene Transcription with Ribosomal RNA Synthesis.

PubMed

Albert, Benjamin; Knight, Britta; Merwin, Jason; Martin, Victoria; Ottoz, Diana; Gloor, Yvonne; Bruzzone, Maria Jessica; Rudner, Adam; Shore, David

2016-11-17

Cell growth potential is determined by the rate of ribosome biogenesis, a complex process that requires massive and coordinated transcriptional output. In the yeast Saccharomyces cerevisiae, ribosome biogenesis is highly regulated at the transcriptional level. Although evidence for a system that coordinates ribosomal RNA (rRNA) and ribosomal protein gene (RPG) transcription has been described, the molecular mechanisms remain poorly understood. Here we show that an interaction between the RPG transcriptional activator Ifh1 and the rRNA processing factor Utp22 serves to coordinate RPG transcription with that of rRNA. We demonstrate that Ifh1 is rapidly released from RPG promoters by a Utp22-independent mechanism following growth inhibition, but that its long-term dissociation requires Utp22. We present evidence that RNA polymerase I activity inhibits the ability of Utp22 to titrate Ifh1 from RPG promoters and propose that a dynamic Ifh1-Utp22 interaction fine-tunes RPG expression to coordinate RPG and rRNA transcription. Copyright © 2016 Elsevier Inc. All rights reserved.

Studies on transcription termination and splicing of the rRNA precursor in vivo in the presence of proflavine.

PubMed Central

Nielsen, O F; Carin, M; Westergaard, O

1984-01-01

In isolated nucleoli from Tetrahymena thermophila, low concentrations of the intercalating agent proflavine inhibit both transcription termination and splicing of the rRNA precursor. Proflavine also exerts an in vivo effect on the process of transcription termination under conditions, where the growth rate is only slightly reduced. Thus, approximately 40% of the rRNA precursor molecules, accumulated in nucleoli during 60 min of treatment with the drug, are longer than the normal 35S rRNA precursor. R-Loop mapping of these longer precursor molecules isolated after 30 and 60 min of incubation demonstrates that the RNA polymerases have a 50 fold lower elongation rate in the spacer region than in the coding region. Proflavine in the given concentration is found to have no significant effect on the splicing of properly terminated precursor molecules. In contrast, none of the longer non-terminated molecules are found to be spliced. These results indicate that proflavine primarily affects the process of transcription termination and that the splicing event is inhibited due to the improper termination of the precursor molecule. Images PMID:6694912

Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling

PubMed Central

Hotto, Amber M.; Castandet, Benoît; Gilet, Laetitia; Higdon, Andrea; Condon, Ciarán; Stern, David B.

2015-01-01

RNase III proteins recognize double-stranded RNA structures and catalyze endoribonucleolytic cleavages that often regulate gene expression. Here, we characterize the functions of RNC3 and RNC4, two Arabidopsis thaliana chloroplast Mini-RNase III-like enzymes sharing 75% amino acid sequence identity. Whereas rnc3 and rnc4 null mutants have no visible phenotype, rnc3/rnc4 (rnc3/4) double mutants are slightly smaller and chlorotic compared with the wild type. In Bacillus subtilis, the RNase Mini-III is integral to 23S rRNA maturation. In Arabidopsis, we observed imprecise maturation of 23S rRNA in the rnc3/4 double mutant, suggesting that exoribonucleases generated staggered ends in the absence of specific Mini-III-catalyzed cleavages. A similar phenotype was found at the 3′ end of the 16S rRNA, and the primary 4.5S rRNA transcript contained 3′ extensions, suggesting that Mini-III catalyzes several processing events of the polycistronic rRNA precursor. The rnc3/4 mutant showed overaccumulation of a noncoding RNA complementary to the 4.5S-5S rRNA intergenic region, and its presence correlated with that of the extended 4.5S rRNA precursor. Finally, we found rnc3/4-specific intron degradation intermediates that are probable substrates for Mini-III and show that B. subtilis Mini-III is also involved in intron regulation. Overall, this study extends our knowledge of the key role of Mini-III in intron and noncoding RNA regulation and provides important insight into plastid rRNA maturation. PMID:25724636

The effect of thermal pre-treatment of titanium hydride (TiH2) powder in argon condition

NASA Astrophysics Data System (ADS)

Franciska P., L.; Erryani, Aprilia; Annur, Dhyah; Kartika, Ika

2018-04-01

Titanium hydride (TiH2) powders are used to enhance the foaming process in the formation of a highly porous metallic material with a cellular structure. But, the low temperature of hydrogen release is one of its problems. The present study, different thermal pre-treatment temperatures were employed to investigate the decomposition behavior of TiH2 to retard or delay a hydrogen gas release process during foaming. As a foaming agent, TiH2 was subjected to various heat treatments prior at 450 and 500°C during 2 hours in argon condition. To study the formation mechanism, the thermal behavior of titanium hydride and hydrogen release are investigated by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The morphology of pre-treated titanium hydride powders were examined using Scanning Electron Microscope (SEM) while unsure mapping and elemental composition of the pre-treated powders processed by Energy Dispersive Spectroscopy (EDS). To study the phase formation was characterized by X-ray diffraction analysis (XRD). In accordance with the results, an increase in pre-treatment temperature of TiH2 to higher degrees are changing the process of releasing hydrogen from titanium hydride powder. DTA/TGA results showed that thermal pre-treatment TiH2 at 450°C, released the hydrogen gas at 560°C in heat treatment when foaming process. Meanwhile, thermal pre-treatment in TiH2 at 500°C, released the hydrogen gas at 670°C when foaming process. There is plenty of direct evidence for the existence of oxide layers that showed by EDS analysis obtained in SEM. As oxygen is a light element and qualitative proof shows that the higher pre-treatment temperature produces more and thicker oxygen layers on the surface of the TiH2 powder particles. It might the thickness of oxide layer are different from different pre-treatment temperatures, which leading to the differences in the decomposition temperature. But from SEM result that oxidation of the powder does not change the powder morphology. The oxidation process also confirmed by XRD result, which showed higher thermal pre-treatment TiH2, more oxide higher peak is formed. The oxide layer of TiH2 particles is responsible for the observed shift in decomposition temperature and can prepare the stable foam that stabilizes forming of cell walls and avoid their collapse at higher temperatures.

Overaccumulation of the chloroplast antisense RNA AS5 is correlated with decreased abundance of 5S rRNA in vivo and inefficient 5S rRNA maturation in vitro

PubMed Central

Sharwood, Robert E.; Hotto, Amber M.; Bollenbach, Thomas J.; Stern, David B.

2011-01-01

Post-transcriptional regulation in the chloroplast is exerted by nucleus-encoded ribonucleases and RNA-binding proteins. One of these ribonucleases is RNR1, a 3′-to-5′ exoribonuclease of the RNase II family. We have previously shown that Arabidopsis rnr1-null mutants exhibit specific abnormalities in the expression of the rRNA operon, including the accumulation of precursor 23S, 16S, and 4.5S species and a concomitant decrease in the mature species. 5S rRNA transcripts, however, accumulate to a very low level in both precursor and mature forms, suggesting that they are unstable in the rnr1 background. Here we demonstrate that rnr1 plants overaccumulate an antisense RNA, AS5, that is complementary to the 5S rRNA, its intergenic spacer, and the downstream trnR gene, which encodes tRNAArg, raising the possibility that AS5 destabilizes 5S rRNA or its precursor and/or blocks rRNA maturation. To investigate this, we used an in vitro system that supports 5S rRNA and trnR processing. We show that AS5 inhibits 5S rRNA maturation from a 5S-trnR precursor, and shorter versions of AS5 demonstrate that inhibition requires intergenic sequences. To test whether the sense and antisense RNAs form double-stranded regions in vitro, treatment with the single-strand-specific mung bean nuclease was used. These results suggest that 5S–AS5 duplexes interfere with a sense-strand secondary structure near the endonucleolytic cleavage site downstream from the 5S rRNA coding region. We hypothesize that these duplexes are degraded by a dsRNA-specific ribonuclease in vivo, contributing to the 5S rRNA deficiency observed in rnr1. PMID:21148395

Pre-pregnancy BMI, gestational weight gain and breast-feeding: a cohort study in China.

PubMed

Tao, Xing-Yong; Huang, Kun; Yan, Shuang-Qin; Zuo, A-Zhu; Tao, Rui-Wen; Cao, Hui; Gu, Chun-Li; Tao, Fang-Biao

2017-04-01

The purpose of the present study was to examine the influence of maternal pre-pregnancy BMI and gestational weight gain (GWG) on initiation and duration of infant breast-feeding in a prospective birth cohort study. Breast-feeding information was collected at 1, 3, 6 and 12 months postpartum. The association of pre-pregnancy BMI and GWG with delayed lactogenesis II and termination of exclusive breast-feeding was assessed with logistic regression analysis. The risk of early termination of any breast-feeding during the first year postpartum was assessed with Cox proportional hazards models. Urban city in China. Women with infants from the Ma'anshan Birth Cohort Study (n 3196). The median duration of any breast-feeding in this cohort was 7·0 months. Pre-pregnancy obese women had higher risks of delayed lactogenesis II (risk ratio=1·89; 95 % CI 1·04, 3·43) and early termination of any breast-feeding (hazard ratio=1·38; 95 % CI 1·09, 1·75) adjusted for potential maternal and infant confounders, when compared with normal-weight women. No differences in breast-feeding initiation or duration of exclusive breast-feeding according to pre-pregnancy BMI were found. Moreover, GWG was not associated with any poor breast-feeding outcomes. The present study indicated that pre-pregnancy obesity increases the risks of delayed lactogenesis II and early termination of any breast-feeding in Chinese women.

Are cognitive "insomnia" processes involved in the development and maintenance of delayed sleep wake phase disorder?

PubMed

Richardson, Cele E; Gradisar, Michael; Barbero, Sebastian C

2016-04-01

Although individuals with delayed sleep wake phase disorder (DSWPD) and chronic insomnia disorder (CID) share many of the same phenomenological experiences, theories relating to the development and maintenance of these disorders are distinct in focus. Unlike CID, theory relating to DSWPD is primarily physiologically based and assumes almost no cognitive pathway. However, recent research findings suggest that individuals with DSWPD also display many of the sleep-disordered cognitive processes that were previously assumed to be unique to the insomnia experience. As such, this review aims to summarise current research findings to address the question "Could cognitive processes be involved in the development and maintenance of DSWPD?" In particular, the presence of cognitive and physiological pre-sleep arousal, sleep-related attentional bias, distorted perception of sleep and daytime functioning, dysfunctional beliefs and safety behaviours will be investigated. As this emerging area of research requires a stronger evidence base, we highlight suggestions for future investigation and provide preliminary practice points for clinicians assessing and treating "insomnia" in patients with DSWPD. Copyright © 2015 Elsevier Ltd. All rights reserved.

RRP1B Targets PP1 to Mammalian Cell Nucleoli and Is Associated with Pre-60S Ribosomal Subunits

PubMed Central

Chamousset, Delphine; De Wever, Veerle; Moorhead, Greg B.; Chen, Yan; Boisvert, Francois-Michel; Lamond, Angus I.

2010-01-01

A pool of protein phosphatase 1 (PP1) accumulates within nucleoli and accounts for a large fraction of the serine/threonine protein phosphatase activity in this subnuclear structure. Using a combination of fluorescence imaging with quantitative proteomics, we mapped the subnuclear localization of the three mammalian PP1 isoforms stably expressed as GFP-fusions in live cells and identified RRP1B as a novel nucleolar targeting subunit that shows a specificity for PP1β and PP1γ. RRP1B, one of two mammalian orthologues of the yeast Rrp1p protein, shows an RNAse-dependent localization to the granular component of the nucleolus and distributes in a similar manner throughout the cell cycle to proteins involved in later steps of rRNA processing. Quantitative proteomic analysis of complexes containing both RRP1B and PP1γ revealed enrichment of an overlapping subset of large (60S) ribosomal subunit proteins and pre-60S nonribosomal proteins involved in mid-late processing. Targeting of PP1 to this complex by RRP1B in mammalian cells is likely to contribute to modulation of ribosome biogenesis by mechanisms involving reversible phosphorylation events, thus playing a role in the rapid transduction of cellular signals that call for regulation of ribosome production in response to cellular stress and/or changes in growth conditions. PMID:20926688

Transformation of Chloroplast Ribosomal RNA Genes in Chlamydomonas: Molecular and Genetic Characterization of Integration Events

PubMed Central

Newman, S. M.; Boynton, J. E.; Gillham, N. W.; Randolph-Anderson, B. L.; Johnson, A. M.; Harris, E. H.

1990-01-01

Transformation of chloroplast ribosomal RNA (rRNA) genes in Chlamydomonas has been achieved by the biolistic process using cloned chloroplast DNA fragments carrying mutations that confer antibiotic resistance. The sites of exchange employed during the integration of the donor DNA into the recipient genome have been localized using a combination of antibiotic resistance mutations in the 16S and 23S rRNA genes and restriction fragment length polymorphisms that flank these genes. Complete or nearly complete replacement of a region of the chloroplast genome in the recipient cell by the corresponding sequence from the donor plasmid was the most common integration event. Exchange events between the homologous donor and recipient sequences occurred preferentially near the vector:insert junctions. Insertion of the donor rRNA genes and flanking sequences into one inverted repeat of the recipient genome was followed by intramolecular copy correction so that both copies of the inverted repeat acquired identical sequences. Increased frequencies of rRNA gene transformants were achieved by reducing the copy number of the chloroplast genome in the recipient cells and by decreasing the heterology between donor and recipient DNA sequences flanking the selectable markers. In addition to producing bona fide chloroplast rRNA transformants, the biolistic process induced mutants resistant to low levels of streptomycin, typical of nuclear mutations in Chlamydomonas. PMID:1981764

Emotions delay care-seeking in patients with an acute myocardial infarction.

PubMed

Nymark, Carolin; Mattiasson, Anne-Cathrine; Henriksson, Peter; Kiessling, Anna

2014-02-01

In acute myocardial infarction the risk of death and loss of myocardial tissue is at its highest during the first few hours. However, the process from symptom onset to the decision to seek medical care can take time. To comprehend patients' pre-hospital delay, attention must be focused on the circumstances preceding the decision to seek medical care. To add a deeper understanding of patients' thoughts, feelings and actions that preceded the decision to seek medical care when afflicted by an acute myocardial infarction. Fourteen men and women with a first or second acute myocardial infarction were interviewed individually in semi-structured interviews. Data were analysed by qualitative content analysis. Four themes were conceptualized: 'being incapacitated by fear, anguish and powerlessness', 'being ashamed of oneself', 'fear of losing a healthy identity' and 'striving to avoid fear by not interacting with others'. Patients were torn between feelings such as anguish, fear, shame and powerlessness. They made an effort to uphold their self-image as being a healthy person thus affected by an unrecognized discomfort. This combined with a struggle to protect others from involvement, strengthened the barriers to seeking care. The present study indicates that emotional reactions are important and influence patients' pre-hospital behaviour. Being ashamed of oneself stood out as a novel finding. Emotions might be an important explanation of undesired and persisting patient delays. However, our findings have to and should be evaluated quantitatively. Such a study is in progress.

Tcf4 transgenic female mice display delayed adaptation in an auditory latent inhibition paradigm.

PubMed

Brzózka, M M; Rossner, M J; de Hoz, L

2016-09-01

Schizophrenia (SZ) is a severe mental disorder affecting about 1 % of the human population. Patients show severe deficits in cognitive processing often characterized by an improper filtering of environmental stimuli. Independent genome-wide association studies confirmed a number of risk variants for SZ including several associated with the gene encoding the transcription factor 4 (TCF4). TCF4 is widely expressed in the central nervous system of mice and humans and seems to be important for brain development. Transgenic mice overexpressing murine Tcf4 (Tcf4tg) in the adult brain display cognitive impairments and sensorimotor gating disturbances. To address the question of whether increased Tcf4 gene dosage may affect cognitive flexibility in an auditory associative task, we tested latent inhibition (LI) in female Tcf4tg mice. LI is a widely accepted translational endophenotype of SZ and results from a maladaptive delay in switching a response to a previously unconditioned stimulus when this becomes conditioned. Using an Audiobox, we pre-exposed Tcf4tg mice and their wild-type littermates to either a 3- or a 12-kHz tone before conditioning them to a 12-kHz tone. Tcf4tg animals pre-exposed to a 12-kHz tone showed significantly delayed conditioning when the previously unconditioned tone became associated with an air puff. These results support findings that associate TCF4 dysfunction with cognitive inflexibility and improper filtering of sensory stimuli observed in SZ patients.

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

PubMed Central

Hua, Xing; Zeller, Georg; Sunagawa, Shinichi; Voigt, Anita Y.; Hercog, Rajna; Goedert, James J.; Shi, Jianxin; Bork, Peer; Sinha, Rashmi

2016-01-01

Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population. In addition, metagenome-predicted genes, modules, and pathways in the Washington, DC cases and controls were compared to cases and controls recruited in France whose specimens were processed using the same platform. Associations between the presence of fecal Fusobacteria, Fusobacterium, and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by metagenomics, whereas higher relative abundance of Clostridia in cancer cases based on 16S rRNA was merely borderline based on metagenomics. This demonstrated that within the same sample set, most, but not all taxonomic associations were seen with both methods. Considering significant cancer associations with the relative abundance of genes, modules, and pathways in a recently published French metagenomics dataset, statistically significant associations in the Washington, DC population were detected for four out of 10 genes, three out of nine modules, and seven out of 17 pathways. In total, colorectal cancer status in the Washington, DC study was associated with 39% of the metagenome-predicted genes, modules, and pathways identified in the French study. More within and between population comparisons are needed to identify sources of variation and disease associations that can be reproduced despite these variations. Future studies should have larger sample sizes or pool data across studies to have sufficient power to detect associations that are reproducible and significant after correction for multiple testing. PMID:27171425

Hot Jet Ignition Delay Characterization of Methane and Hydrogen at Elevated Temperatures

NASA Astrophysics Data System (ADS)

Tarraf Kojok, Ali

This study contributes to a better understanding of ignition by hot combustion gases which finds application in internal combustion chambers with pre-chamber ignition as well as in wave rotor engine applications. The experimental apparatus consists of two combustion chambers: a pre chamber that generates the transient hot jet of gas and a main chamber which contains the main fuel air blend under study. Variables considered are three fuel mixtures (Hydrogen, Methane, 50% Hydrogen-Methane), initial pressure in the pre-chamber ranging from 1 to 2 atm, equivalence ratio of the fuel air mixture in the main combustion chamber ranging from 0.4 to 1.5, and initial temperature of the main combustion chamber mixture ranging from 297 K to 500 K. Experimental data makes use of 4 pressure sensors with a recorded sampling rate up to 300 kHz, as well as high speed Schlieren imaging with a recorded frame rate up to 20,833 frame per seconds. Results shows an overall increase in ignition delay with increasing equivalence ratio. High temperature of the main chamber blend was found not to affect hot jet ignition delay considerably. Physical mixing effects, and density of the main chamber mixture have a greater effect on hot jet ignition delay.

Stuttering adults' lack of pre-speech auditory modulation normalizes when speaking with delayed auditory feedback.

PubMed

Daliri, Ayoub; Max, Ludo

2018-02-01

Auditory modulation during speech movement planning is limited in adults who stutter (AWS), but the functional relevance of the phenomenon itself remains unknown. We investigated for AWS and adults who do not stutter (AWNS) (a) a potential relationship between pre-speech auditory modulation and auditory feedback contributions to speech motor learning and (b) the effect on pre-speech auditory modulation of real-time versus delayed auditory feedback. Experiment I used a sensorimotor adaptation paradigm to estimate auditory-motor speech learning. Using acoustic speech recordings, we quantified subjects' formant frequency adjustments across trials when continually exposed to formant-shifted auditory feedback. In Experiment II, we used electroencephalography to determine the same subjects' extent of pre-speech auditory modulation (reductions in auditory evoked potential N1 amplitude) when probe tones were delivered prior to speaking versus not speaking. To manipulate subjects' ability to monitor real-time feedback, we included speaking conditions with non-altered auditory feedback (NAF) and delayed auditory feedback (DAF). Experiment I showed that auditory-motor learning was limited for AWS versus AWNS, and the extent of learning was negatively correlated with stuttering frequency. Experiment II yielded several key findings: (a) our prior finding of limited pre-speech auditory modulation in AWS was replicated; (b) DAF caused a decrease in auditory modulation for most AWNS but an increase for most AWS; and (c) for AWS, the amount of auditory modulation when speaking with DAF was positively correlated with stuttering frequency. Lastly, AWNS showed no correlation between pre-speech auditory modulation (Experiment II) and extent of auditory-motor learning (Experiment I) whereas AWS showed a negative correlation between these measures. Thus, findings suggest that AWS show deficits in both pre-speech auditory modulation and auditory-motor learning; however, limited pre-speech modulation is not directly related to limited auditory-motor adaptation; and in AWS, DAF paradoxically tends to normalize their otherwise limited pre-speech auditory modulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies.

PubMed

Lagkouvardos, Ilias; Joseph, Divya; Kapfhammer, Martin; Giritli, Sabahattin; Horn, Matthias; Haller, Dirk; Clavel, Thomas

2016-09-23

The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users' own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org.

Self-interaction of NPM1 modulates multiple mechanisms of liquid-liquid phase separation.

PubMed

Mitrea, Diana M; Cika, Jaclyn A; Stanley, Christopher B; Nourse, Amanda; Onuchic, Paulo L; Banerjee, Priya R; Phillips, Aaron H; Park, Cheon-Gil; Deniz, Ashok A; Kriwacki, Richard W

2018-02-26

Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid-liquid phase separation (LLPS) via heterotypic interactions with nucleolar components, including ribosomal RNA (rRNA) and proteins which display multivalent arginine-rich linear motifs (R-motifs), and is integral to the liquid-like nucleolar matrix. Here we show that NPM1 can also undergo LLPS via homotypic interactions between its polyampholytic intrinsically disordered regions, a mechanism that opposes LLPS via heterotypic interactions. Using a combination of biophysical techniques, including confocal microscopy, SAXS, analytical ultracentrifugation, and single-molecule fluorescence, we describe how conformational changes within NPM1 control valency and switching between the different LLPS mechanisms. We propose that this newly discovered interplay between multiple LLPS mechanisms may influence the direction of vectorial pre-ribosomal particle assembly within, and exit from the nucleolus as part of the ribosome biogenesis process.

Minimizing preventable trauma deaths in a limited-resource setting: a test-case of a multidisciplinary panel review approach at the Komfo Anokye Teaching Hospital in Ghana.

PubMed

Yeboah, Dominic; Mock, Charles; Karikari, Patrick; Agyei-Baffour, Peter; Donkor, Peter; Ebel, Beth

2014-07-01

Our objectives were to determine the proportion of preventable trauma deaths at a large trauma hospital in Kumasi, Ghana, and to identify opportunities for the improvement of trauma care. A multidisciplinary panel of experts evaluated pre-hospital, hospital, and postmortem data of consecutive trauma patients who died over a 5-month period in 2006-2007 at the Komfo Anokye Teaching Hospital. The panel judged the preventability of each death. For preventable and potentially preventable deaths, deficiencies in care that contributed to their deaths were identified. The panel reviewed 231 trauma deaths. Of these, 84 charts had sufficient information to review preventable factors. The panel determined that 23 % of trauma deaths were definitely preventable, 37 % were potentially preventable, and 40 % were not preventable. One main deficiency in care was identified for each of the 50 definitely preventable and potentially preventable deaths. The most common deficiencies were pre-hospital delays (44 % of the 50 deficiencies), delay in treatment (32 %), and inadequate fluid resuscitation (22 %). Among the 19 definitely preventable deaths, the most common cause of death was hemorrhage (47 %), and the most common deficiencies were inadequate fluid resuscitation (37 % of deficiencies in this group) and pre-hospital delay (37 %). A high proportion of trauma fatalities might have been preventable by decreasing pre-hospital delays, adequate resuscitation in hospital, and earlier initiation of care, including definitive surgical management. The study also showed that preventable death panel reviews are a feasible and useful quality improvement method in the study setting.

Rates and delay times of Type Ia supernovae in the helium-enriched main-sequence donor scenario

NASA Astrophysics Data System (ADS)

Liu, Zheng-Wei; Stancliffe, Richard J.

2018-04-01

The nature of the progenitors of Type Ia supernovae (SNe Ia) remains a mystery. Comparing theoretical rates and delay-time distributions of SNe Ia with those inferred observationally can constrain their progenitor models. In this work, taking thermohaline mixing into account in the helium-enriched main-sequence (HEMS) donor scenario, we address rates and delay times of SNe Ia in this channel by combining the results of self-consistent binary evolution calculations with population synthesis models. We find that the Galactic SN Ia rate from the HEMS donor scenario is around 0.6-1.2 × 10-3 yr-1, which is about 30 per cent of the observed rate. Delay times of SNe Ia in this scenario cover a wide range of 0.1-1.0 Gyr. We also present the pre-explosion properties of companion stars in the HEMS donor scenario, which will be helpful for placing constraints on SN Ia progenitors through analysing their pre-explosion images.

Influence of stimulant medication and response speed on lateralization of movement-related potentials in attention-deficit/hyperactivity disorder.

PubMed

Bender, Stephan; Resch, Franz; Klein, Christoph; Renner, Tobias; Fallgatter, Andreas J; Weisbrod, Matthias; Romanos, Marcel

2012-01-01

Hyperactivity is one of the core symptoms in attention deficit hyperactivity disorder (ADHD). However, it remains unclear in which way the motor system itself and its development are affected by the disorder. Movement-related potentials (MRP) can separate different stages of movement execution, from the programming of a movement to motor post-processing and memory traces. Pre-movement MRP are absent or positive during early childhood and display a developmental increase of negativity. We examined the influences of response-speed, an indicator of the level of attention, and stimulant medication on lateralized MRP in 16 children with combined type ADHD compared to 20 matched healthy controls. We detected a significantly diminished lateralisation of MRP over the pre-motor and primary motor cortex during movement execution (initial motor potential peak, iMP) in patients with ADHD. Fast reactions (indicating increased visuo-motor attention) led to increased lateralized negativity during movement execution only in healthy controls, while in children with ADHD faster reaction times were associated with more positive amplitudes. Even though stimulant medication had some effect on attenuating group differences in lateralized MRP, this effect was insufficient to normalize lateralized iMP amplitudes. A reduced focal (lateralized) motor cortex activation during the command to muscle contraction points towards an immature motor system and a maturation delay of the (pre-) motor cortex in children with ADHD. A delayed maturation of the neuronal circuitry, which involves primary motor cortex, may contribute to ADHD pathophysiology.

A prototype stable RNA identification cassette for monitoring plasmids of genetically engineered microorganisms

NASA Technical Reports Server (NTRS)

Hedenstierna, K. O.; Lee, Y. H.; Yang, Y.; Fox, G. E.

1993-01-01

A prototype stable RNA identification cassette for monitoring genetically engineered plasmids carried by strains of Escherichia coli has been developed. The cassette consists of a Vibrio proteolyticus 5S ribosomal RNA (rRNA) gene surrounded by promoters and terminators from the rrnB operon of Escherischia coli. The identifier RNA is expressed and successfully processed so that approximately 30% of the 5S rRNA isolated from either whole cells or 70S ribosomes is of the V. proteolyticus type. Cells carrying the identifier are readily detectable by hybridization. Accurate measurements show that the identification cassette has little effect on fitness compared to a strain containing an analogous plasmid carrying wild type E. coli 5S rRNA, and the V. proteolyticus 5S rRNA gene is not inactivated after prolonged growth. These results demonstrate the feasibility of developing small standardized identification cassettes that can utilize already existing highly sensitive rRNA detection methods. Cassettes of this type could in principle be incorporated into either the engineered regions of recombinant plasmids or their hosts.

Nonenzymatic microorganism identification based on ribosomal RNA

NASA Astrophysics Data System (ADS)

Ives, Jeffrey T.; Pierini, Alicia M.; Stokes, Jeffrey A.; Wahlund, Thomas M.; Read, Betsy; Bechtel, James H.; Bronk, Burt V.

1999-11-01

Effective defense against biological warfare (BW) agents requires rapid, fieldable and accurate systems. For micro- organisms like bacteria and viruses, ribosomal RNA (rRNA) provides a valuable target with multiple advantages of species specificity and intrinsic target amplification. Vegetative and spore forms of bacteria contain approximately 104 copies of rRNA. Direct detection of rRNA copies can eliminate some of the interference and preparation difficulties involved in enzymatic amplification methods. In order to apply the advantages of rRNA to BW defense, we are developing a fieldable system based on 16S rRNA, physical disruption of the micro-organism, solid phase hybridization, and fluorescence detection. Our goals include species-specific identification, complete operation from raw sample to identification in 15 minutes or less, and compact, fieldable instrumentation. Initial work on this project has investigated the lysis and hybridization steps, the species-specificity of oligonucleotides probes, and the development of a novel electromagnetic method to physically disrupt the micro- organisms. Target bacteria have been Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis). Continuing work includes further development of methods to rapidly disrupt the micro-organisms and release the rRNA, improved integration and processing, and extension to bacterial and mammalian viruses like MS2 and vesicular stomatitis virus.

Optimization of valve opening process for the suppression of impulse exhaust noise

NASA Astrophysics Data System (ADS)

Li, Jingxiang; Zhao, Shengdun

2017-02-01

Impulse exhaust noise generated by the sudden impact of discharging flow of pneumatic systems has significant temporal characteristics including high sound pressure and rapid sound transient. The impulse noise exposures are more hazardous to hearing than the energy equivalent uniform noise exposures. This paper presents a novel approach to suppress the peak sound pressure as a major indicator of impulsiveness of the impulse exhaust noise by an optimization of the opening process of valve. Relationships between exhaust flow and impulse noise are described by thermodynamics and noise generating mechanism. Then an optimized approach by controlling the valve opening process is derived under a constraint of pre-setting exhaust time. A modified servo-direct-driven valve was designed and assembled in a typical pneumatic system for the verification experiments comparing with an original solenoid valve. Experimental results with groups of initial cylinder pressures and pre-setting exhaust times are shown to verify the effects of the proposed optimization. Some indicators of energy-equivalent and impulsiveness are introduced to discuss the effects of the noise suppressions. Relationship between noise reduction and exhaust time delay is also discussed.

EARLINET Single Calculus Chain - technical - Part 1: Pre-processing of raw lidar data

NASA Astrophysics Data System (ADS)

D'Amico, G.; Amodeo, A.; Mattis, I.; Freudenthaler, V.; Pappalardo, G.

2015-10-01

In this paper we describe an automatic tool for the pre-processing of lidar data called ELPP (EARLINET Lidar Pre-Processor). It is one of two calculus modules of the EARLINET Single Calculus Chain (SCC), the automatic tool for the analysis of EARLINET data. The ELPP is an open source module that executes instrumental corrections and data handling of the raw lidar signals, making the lidar data ready to be processed by the optical retrieval algorithms. According to the specific lidar configuration, the ELPP automatically performs dead-time correction, atmospheric and electronic background subtraction, gluing of lidar signals, and trigger-delay correction. Moreover, the signal-to-noise ratio of the pre-processed signals can be improved by means of configurable time integration of the raw signals and/or spatial smoothing. The ELPP delivers the statistical uncertainties of the final products by means of error propagation or Monte Carlo simulations. During the development of the ELPP module, particular attention has been payed to make the tool flexible enough to handle all lidar configurations currently used within the EARLINET community. Moreover, it has been designed in a modular way to allow an easy extension to lidar configurations not yet implemented. The primary goal of the ELPP module is to enable the application of quality-assured procedures in the lidar data analysis starting from the raw lidar data. This provides the added value of full traceability of each delivered lidar product. Several tests have been performed to check the proper functioning of the ELPP module. The whole SCC has been tested with the same synthetic data sets, which were used for the EARLINET algorithm inter-comparison exercise. The ELPP module has been successfully employed for the automatic near-real-time pre-processing of the raw lidar data measured during several EARLINET inter-comparison campaigns as well as during intense field campaigns.

Sequence of the chloroplast 16S rRNA gene and its surrounding regions of Chlamydomonas reinhardii.

PubMed Central

Dron, M; Rahire, M; Rochaix, J D

1982-01-01

The sequence of a 2 kb DNA fragment containing the chloroplast 16S ribosomal RNA gene from Chlamydomonas reinhardii and its flanking regions has been determined. The algal 16S rRNA sequence (1475 nucleotides) and secondary structure are highly related to those found in bacteria and in the chloroplasts of higher plants. In contrast, the flanking regions are very different. In C. reinhardii the 16S rRNA gene is surrounded by AT rich segments of about 180 bases, which are followed by a long stretch of complementary bases separated from each other by 1833 nucleotides. It is likely that these structures play an important role in the folding and processing of the precursor of 16S rRNA. The primary and secondary structures of the binding sites of two ribosomal proteins in the 16SrRNAs of E. coli and C. reinhardii are considerably related. Images PMID:6296784

Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer.

PubMed

Karahan, Gurbet; Sayar, Nilufer; Gozum, Gokcen; Bozkurt, Betul; Konu, Ozlen; Yulug, Isik G

2015-06-01

Ribosomal RNA (rRNA) expression, one of the most important factors regulating ribosome production, is primarily controlled by a CG-rich 45 S rDNA promoter. However, the DNA methylation state of the 45 S rDNA promoter, as well as its effect on rRNA gene expression in types of human cancers is controversial. In the present study we analyzed the methylation status of the rDNA promoter (-380 to +53 bp) as well as associated rRNA expression levels in breast cancer cell lines and breast tumor-normal tissue pairs. We found that the aforementioned regulatory region was extensively methylated (74-96%) in all cell lines and in 68% (13/19 tumor-normal pairs) of the tumors. Expression levels of rRNA transcripts 18 S, 28 S, 5.8 S and 45 S external transcribed spacer (45 S ETS) greatly varied in the breast cancer cell lines regardless of their methylation status. Analyses of rRNA transcript expression levels in the breast tumor and normal matched tissues showed no significant difference when normalized with TBP. On the other hand, using the geometric mean of the rRNA expression values (GM-rRNA) as reference enabled us to identify significant changes in the relative expression of rRNAs in the tissue samples. We propose GM-rRNA normalization as a novel strategy to analyze expression differences between rRNA transcripts. Accordingly, the 18S rRNA/GM-rRNA ratio was significantly higher whereas the 5.8S rRNA/GM-rRNA ratio was significantly lower in breast tumor samples than this ratio in the matched normal samples. Moreover, the 18S rRNA/GM-rRNA ratio was negatively correlated with the 45 S rDNA promoter methylation level in the normal breast tissue samples, yet not in the breast tumors. Significant correlations observed between the expression levels of rRNA transcripts in the normal samples were lost in the tumor samples. We showed that the expression of rRNA transcripts may not be based solely on promoter methylation. Carcinogenesis may cause dysregulation of the correlation between spliced rRNA expression levels, possibly due to changes in rRNA processing, which requires further investigation.

Assessing effects of the e-Chasqui laboratory information system on accuracy and timeliness of bacteriology results in the Peruvian tuberculosis program.

PubMed

Blaya, Joaquin A; Shin, Sonya S; Yagui, Martin J A; Yale, Gloria; Suarez, Carmen; Asencios, Luis; Fraser, Hamish

2007-10-11

We created a web-based laboratory information system, e-Chasqui to connect public laboratories to health centers to improve communication and analysis. After one year, we performed a pre and post assessment of communication delays and found that e-Chasqui maintained the average delay but eliminated delays of over 60 days. Adding digital verification maintained the average delay, but should increase accuracy. We are currently performing a randomized evaluation of the impacts of e-Chasqui.

Delayed-onset PTSD among war veterans: the role of life events throughout the life cycle.

PubMed

Horesh, Danny; Solomon, Z; Zerach, G; Ein-Dor, T

2011-09-01

The underlying mechanisms of delayed-onset PTSD are yet to be understood. This study examines the role of stressful life events throughout the life cycle in delayed-onset PTSD following combat. 675 Israeli veterans from the 1982 Lebanon War, 369 with antecedent combat stress reaction (CSR) and 306 without CSR were assessed prospectively, 1, 2 and 20 years after the war. Veterans were divided into four groups, according to the time of first PTSD onset (first onset at 1983, 1984, and 2002 and no PTSD onset). They were assessed for post-, peri- and pre-traumatic life events, as well as military and socio-demographic characteristics. Our findings indicate that shorter delays in PTSD onset were associated with a higher risk for CSR, a higher number of pre- and post-war life events, more severe subjective battle exposure, greater perceived danger during combat and a more stressful military position. CSR was found to be the most powerful predictor of PTSD onset. A recency effect was also found, with more recent life events proving to be stronger predictors of PTSD onset. First, our findings validate the existence of delayed-onset PTSD, as it was found among a substantial number of participants (16.5%). Second, post-, peri- and pre-traumatic life events are associated with the time of PTSD onset. Thus, practitioners and researchers are encouraged to examine not only the original trauma, but also the stressful experiences throughout the survivors' life cycle. In particular, identification of antecedent CSR may help mental help professionals in targeting high-risk populations.

Variable Delay Element For Jitter Control In High Speed Data Links

DOEpatents

Livolsi, Robert R.

2002-06-11

A circuit and method for decreasing the amount of jitter present at the receiver input of high speed data links which uses a driver circuit for input from a high speed data link which comprises a logic circuit having a first section (1) which provides data latches, a second section (2) which provides a circuit generates a pre-destorted output and for compensating for level dependent jitter having an OR function element and a NOR function element each of which is coupled to two inputs and to a variable delay element as an input which provides a bi-modal delay for pulse width pre-distortion, a third section (3) which provides a muxing circuit, and a forth section (4) for clock distribution in the driver circuit. A fifth section is used for logic testing the driver circuit.

Fast Mapping Word-Learning Abilities of Language-Delayed Preschoolers.

ERIC Educational Resources Information Center

Rice, Mabel L.; And Others

1990-01-01

Twenty language-delayed children (age three to six) viewed a presentation incorporating object, action, attribute, and affective state words into a narrative script. In pre- and postviewing word comprehension measurements, subjects scored lower than children matched for chronological age and children matched for mean length of utterance.…

Student Participation under Random and Delayed Credit Contingencies

ERIC Educational Resources Information Center

Aspiranti, K. B.; McCleary, D. F.; McCleary, L. N.; Ga-lyon, C. E.; Blondin, C. A.; Yaw, J. S.; Williams, R. L.

2013-01-01

The authors examined the effects of randomized and delayed credit on the percentage of college students participating at four pre-defined levels on each class discussion day: non-participation, credit-level participation, frequent participation, and dominant participation. Although the same amount of participation credit was available to students…

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides.

PubMed

Chopyk, Jessica; Moore, Ryan M; DiSpirito, Zachary; Stromberg, Zachary R; Lewis, Gentry L; Renter, David G; Cernicchiaro, Natalia; Moxley, Rodney A; Wommack, K Eric

2016-03-22

Since 1982, specific serotypes of Shiga toxin-producing Escherichia coli (STEC) have been recognized as significant foodborne pathogens acquired from contaminated beef and, more recently, other food products. Cattle are the major reservoir hosts of these organisms, and while there have been advancements in food safety practices and industry standards, STEC still remains prevalent within beef cattle operations with cattle hides implicated as major sources of carcass contamination. To investigate whether the composition of hide-specific microbial communities are associated with STEC prevalence, 16S ribosomal RNA (rRNA) bacterial community profiles were obtained from hide and fecal samples collected from a large commercial feedlot over a 3-month period. These community data were examined amidst an extensive collection of prevalence data on a subgroup of STEC that cause illness in humans, referred to as enterohemorrhagic E. coli (EHEC). Fecal 16S rRNA gene OTUs (operational taxonomic units) were subtracted from the OTUs found within each hide 16S rRNA amplicon library to identify hide-specific bacterial populations. Comparative analysis of alpha diversity revealed a significant correlation between low bacterial diversity and samples positive for the presence of E. coli O157:H7 and/or the non-O157 groups: O26, O111, O103, O121, O45, and O145. This trend occurred regardless of diversity metric or fecal OTU presence. The number of EHEC serogroups present in the samples had a compounding effect on the inverse relationship between pathogen presence and bacterial diversity. Beta diversity data showed differences in bacterial community composition between samples containing O157 and non-O157 populations, with certain OTUs demonstrating significant changes in relative abundance. The cumulative prevalence of the targeted EHEC serogroups was correlated with low bacterial community diversity on pre-harvest cattle hides. Understanding the relationship between indigenous hide bacterial communities and populations may provide strategies to limit EHEC in cattle and provide biomarkers for EHEC risk assessment.

Delayed luminescence in a multiparameter approach to evaluation and reduction of radiobiological risks

NASA Astrophysics Data System (ADS)

Grasso, Rosaria; Cammarata, Francesco Paolo; Minafra, Luigi; Marchese, Valentina; Russo, Giorgio; Manti, Lorenzo; Musumeci, Francesco; Scordino, Agata

2017-07-01

In the framework of the research project ETHICS "Pre-clinical experimental and theoretical studies to improve treatment and protection by charged particles" funded by the National Nuclear Physics Institute, Italy, we studied the phenomenon called delayed luminescence emitted by non-tumorigenic breast epithelial MCF10A cell line after proton irradiation at different doses (0.5, 2, 6, 9 Gy). The aim is to found possible correlations between delayed luminescence and in vitro damaging induced by ion irradiation. The first results of this research show that the delayed luminescence kinetics is proton dose dependent. An interesting correlation between delayed luminescence and clonogenic potential was observed.

Incident Learning and Failure-Mode-and-Effects-Analysis Guided Safety Initiatives in Radiation Medicine

PubMed Central

Kapur, Ajay; Goode, Gina; Riehl, Catherine; Zuvic, Petrina; Joseph, Sherin; Adair, Nilda; Interrante, Michael; Bloom, Beatrice; Lee, Lucille; Sharma, Rajiv; Sharma, Anurag; Antone, Jeffrey; Riegel, Adam; Vijeh, Lili; Zhang, Honglai; Cao, Yijian; Morgenstern, Carol; Montchal, Elaine; Cox, Brett; Potters, Louis

2013-01-01

By combining incident learning and process failure-mode-and-effects-analysis (FMEA) in a structure-process-outcome framework we have created a risk profile for our radiation medicine practice and implemented evidence-based risk-mitigation initiatives focused on patient safety. Based on reactive reviews of incidents reported in our departmental incident-reporting system and proactive FMEA, high safety-risk procedures in our paperless radiation medicine process and latent risk factors were identified. Six initiatives aimed at the mitigation of associated severity, likelihood-of-occurrence, and detectability risks were implemented. These were the standardization of care pathways and toxicity grading, pre-treatment-planning peer review, a policy to thwart delay-rushed processes, an electronic whiteboard to enhance coordination, and the use of six sigma metrics to monitor operational efficiencies. The effectiveness of these initiatives over a 3-years period was assessed using process and outcome specific metrics within the framework of the department structure. There has been a 47% increase in incident-reporting, with no increase in adverse events. Care pathways have been used with greater than 97% clinical compliance rate. The implementation of peer review prior to treatment-planning and use of the whiteboard have provided opportunities for proactive detection and correction of errors. There has been a twofold drop in the occurrence of high-risk procedural delays. Patient treatment start delays are routinely enforced on cases that would have historically been rushed. Z-scores for high-risk procedures have steadily improved from 1.78 to 2.35. The initiatives resulted in sustained reductions of failure-mode risks as measured by a set of evidence-based metrics over a 3-years period. These augment or incorporate many of the published recommendations for patient safety in radiation medicine by translating them to clinical practice. PMID:24380074

Anti-hypertensive treatment prolongs tPA door-to-treatment time: Secondary analysis of the INSTINCT trial.

PubMed Central

Skolarus, Lesli E.; Scott, Phillip A.; Burke, James F.; Adelman, Eric E.; Frederiksen, Shirley M.; Kade, Allison M.; Kalbfleisch, Jack D.; Ford, Andria L.; Meurer, William J.

2012-01-01

Background/Purpose Identifying modifiable tPA treatment delays may improve stroke outcomes. We hypothesized that pre-thrombolytic anti-hypertensive treatment (AHT) may prolong door-to-treatment time (DTT). Methods Analysis of consecutive tPA-treated patients at 24 randomly selected community hospitals in the INSTINCT trial between 2007-2010. DTTs among stroke patients who received pre-thrombolytic AHT were compared to those that did not receive pre-thrombolytic AHT. We then calculated a propensity score for the probability of receiving pre-thrombolytic AHT using logistic regression with demographics, stroke risk factors, home medications, stroke severity (NIHSS), onset-to-door time, admission glucose, pretreatment blood pressure, EMS transport and location at time of stroke as independent variables. A paired t-test was performed to compare the DTTs between the propensity matched groups. Results Of 534 tPA treated stroke patients analyzed, 95 received pre-thrombolytic AHT. In the unmatched cohort, patients who received pre-thrombolytic AHT had a longer DTT (mean increase 9 minutes; 95% confidence interval (CI) 2-16 minutes) than patients who did not. After propensity matching, patients who received pre-thrombolytic AHT had a longer DTT (mean increase 10.4 minutes, 95% CI 1.9 - 18.8) than patients who did not receive pre-thrombolytic AHT. Conclusion Pre-thrombolytic AHT is associated with modest delays in DTT. This represents a potential target for quality improvement initiatives. Further research evaluating optimum pre-thrombolytic hypertension management is warranted. PMID:23033348

Investigation of histone H4 hyperacetylation dynamics in the 5S rRNA genes family by chromatin immunoprecipitation assay.

PubMed

Burlibașa, Liliana; Suciu, Ilinca

2015-12-01

Oogenesis is a critical event in the formation of female gamete, whose role in development is to transfer genomic information to the next generation. During this process, the gene expression pattern changes dramatically concomitant with genome remodelling, while genomic information is stably maintained. The aim of the present study was to investigate the presence of H4 acetylation of the oocyte and somatic 5S rRNA genes in Triturus cristatus, using chromatin immunoprecipitation assay (ChIP). Our findings suggest that some epigenetic mechanisms such as histone acetylation could be involved in the transcriptional regulation of 5S rRNA gene families.

Centering a DDR Strobe in the Middle of a Data Packet

NASA Technical Reports Server (NTRS)

Johnson, Michael; Nelson, Dave; Seefeldt, James; Roper, Weston; Passow, Craig

2014-01-01

The Orion CEV Northstar ASIC (application- specific integrated circuit) project required a DDR (double data rate) memory bus driver/receiver (DDR PHY block) to interface with external DDR memory. The DDR interface (JESD79C) is based on a source synchronous strobe (DQS\\) that is sent along with each packet of data (DQ). New data is provided concurrently with each edge of strobe and is sent irregularly. In order to capture this data, the strobe needs to be delayed and used to latch the data into a register. A circuit solves the need for training a DDR PRY block by incorporating a PVT-compensated delay element in the strobe path. This circuit takes an external reference clock signal and uses the regular clock to calibrate a known delay through a data path. The compensated delay DQS signal is then used to capture the DQ data in a normal register. This register structure can be configured as a FIFO (first in first out), in order to transfer data from the DDR domain to the system clock domain. This design is different in that it does not rely upon the need for training the system response, nor does it use a PLL (phase locked loop) or a DLL (delay locked loop) to provide an offset of the strobe signal. The circuit is created using standard ASIC building blocks, plus the PVT (process, voltage, and temperature) compensated delay line. The design uses a globally available system clock as a reference, alleviating the need to operate synchronously with the remote memory. The reference clock conditions the PVT compensated delay line to provide a pre-determined amount of delay to any data signal that passes through this delay line. The delay line is programmed in degrees of offset, so that one could think of the clock period representing 360deg of delay. In an ideal environment, delaying the strobe 1/4 of a clock cycle (90deg) would place the strobe in the middle of the data packet. This delayed strobe can then be used to clock the data into a register, satisfying setup and hold requirements of the system.

Pubertal Height Velocity and Associations with Pre-pubertal and Adult Heights in Cystic Fibrosis

PubMed Central

Zhang, Zhumin; Lindstrom, Mary J.; Lai, HuiChuan J.

2013-01-01

Objectives To test the hypothesis that pubertal peak height velocity (PHV) in cystic fibrosis (CF) has improved and is influenced by pre-pubertal growth and genetic potential. Study design PHV from 1862 children born in 1984–87 and documented in the 1986–2008 US CF Foundation Registry was determined by statistical modeling and classified into normal, delayed (2-SD > average age), attenuated (magnitude < 5th percentile), or both (D&A). Genetic potential for height was estimated by parental stature. Results PHV averaged 8.4 cm/y at age 14.0 y in boys and 7.0 cm/y at age 12.1 y in girls, ~6 mo delay and ~15% reduction compared with healthy children. PHV was normal in 60%, delayed in 9%, attenuated in 21% and D&A in 5%. Patients with delayed PHV reached similar adult height percentile (boys: 34th, girls: 46th) to those with normal PHV (boys: 33rd, girls: 34th); both were significantly taller than the attenuated (boys: 11th, girls: 19th) and D&A PHV subgroups (boys: 8th, girls: 14th). Pancreatic sufficient patients had taller pre-pubertal and adult heights but similar PHV compared with pancreatic insufficient or meconium ileus patients. Adjusting for genetic potential reduced adult height percentiles more in boys (25th to 16th) than girls (28th to 24th). Height at age 7 y, PHV age and magnitude, and parental stature significantly predicted adult height. Conclusions Pubertal PHV has improved in children with CF born after mid 1980s compared with older cohorts but remains below normal. Suboptimal pre-pubertal and pubertal growth led to adult height below genetic potential in CF. PMID:23535012

Reducing time delays in the management of ischemic stroke patients in Northern Italy.

PubMed

Vidale, Simone; Arnaboldi, Marco; Bezzi, Giacomo; Bono, Giorgio; Grampa, Giampiero; Guidotti, Mario; Perrone, Patrizia; Salmaggi, Andrea; Zarcone, Davide; Zoli, Alberto; Agostoni, Elio

2016-07-15

Thrombolysis represents the best therapy for ischemic stroke but the main limitation of its administration is time. The avoidable delay is a concept reflecting the effectiveness of management pathway. For this reason, we projected a study concerning the detection of main delays with following introduction of corrective factors. In this paper we describe the results after these corrections. Consecutive patients admitted for ischemic stroke during a 3-months period to 35 hospitals of a macro-area of Northern Italy were enrolled. Each time of management was registered, identifying three main intervals: pre-hospital, in-hospital and total times. Previous corrective interventions were: 1.increasing of population awareness to use the Emergency Medical Service (EMS); 2.pre-notification of Emergency Department; 3.use of high urgency codes; 4.use of standardised operational algorithm. Statistical analysis was conducted using time-to-event analysis and Cox proportional hazard regression. 1084 patients were enrolled. EMS was alerted for 56.3% of subjects, mainly in females and severe strokes (p<0.001). Thrombolytic treatment was performed in 4.7% of patients. Median pre-hospital and in-hospital times were 113 and 105min, while total time was 240. High urgency codes at transport contributed to reduce pre-hospital and in-hospital time (p<0.05). EMS use and high urgency codes promoted thrombolysis. Treatment within 4.5hours from symptom onset was performed in 14% of patients more than the first phase of study. The implementation of an organizational system based on EMS and concomitant high urgency codes use was effective to reduce avoidable delay and to increase thrombolysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides.

PubMed

Hia, Fabian; Chionh, Yok Hian; Pang, Yan Ling Joy; DeMott, Michael S; McBee, Megan E; Dedon, Peter C

2015-03-11

A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Improving visual spatial working memory in younger and older adults: effects of cross-modal cues.

PubMed

Curtis, Ashley F; Turner, Gary R; Park, Norman W; Murtha, Susan J E

2017-11-06

Spatially informative auditory and vibrotactile (cross-modal) cues can facilitate attention but little is known about how similar cues influence visual spatial working memory (WM) across the adult lifespan. We investigated the effects of cues (spatially informative or alerting pre-cues vs. no cues), cue modality (auditory vs. vibrotactile vs. visual), memory array size (four vs. six items), and maintenance delay (900 vs. 1800 ms) on visual spatial location WM recognition accuracy in younger adults (YA) and older adults (OA). We observed a significant interaction between spatially informative pre-cue type, array size, and delay. OA and YA benefitted equally from spatially informative pre-cues, suggesting that attentional orienting prior to WM encoding, regardless of cue modality, is preserved with age.  Contrary to predictions, alerting pre-cues generally impaired performance in both age groups, suggesting that maintaining a vigilant state of arousal by facilitating the alerting attention system does not help visual spatial location WM.

Early electrophysiological markers of atypical language processing in prematurely born infants.

PubMed

Paquette, Natacha; Vannasing, Phetsamone; Tremblay, Julie; Lefebvre, Francine; Roy, Marie-Sylvie; McKerral, Michelle; Lepore, Franco; Lassonde, Maryse; Gallagher, Anne

2015-12-01

Because nervous system development may be affected by prematurity, many prematurely born children present language or cognitive disorders at school age. The goal of this study is to investigate whether these impairments can be identified early in life using electrophysiological auditory event-related potentials (AERPs) and mismatch negativity (MMN). Brain responses to speech and non-speech stimuli were assessed in prematurely born children to identify early electrophysiological markers of language and cognitive impairments. Participants were 74 children (41 full-term, 33 preterm) aged 3, 12, and 36 months. Pre-attentional auditory responses (MMN and AERPs) were assessed using an oddball paradigm, with speech and non-speech stimuli presented in counterbalanced order between participants. Language and cognitive development were assessed using the Bayley Scale of Infant Development, Third Edition (BSID-III). Results show that preterms as young as 3 months old had delayed MMN response to speech stimuli compared to full-terms. A significant negative correlation was also found between MMN latency to speech sounds and the BSID-III expressive language subscale. However, no significant differences between full-terms and preterms were found for the MMN to non-speech stimuli, suggesting preserved pre-attentional auditory discrimination abilities in these children. Identification of early electrophysiological markers for delayed language development could facilitate timely interventions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantifying The Food And Drug Administration's rulemaking delays highlights the need for transparency.

PubMed

Hwang, Thomas J; Avorn, Jerry; Carpenter, Daniel; Kesselheim, Aaron S

2014-02-01

The Food and Drug Administration (FDA) frequently uses its rulemaking process to establish or modify the way it regulates drugs, medical devices, and other medical products. The federal agency's rulemaking is controversial because of its perceived complexity, lack of transparency, and lengthy duration. To shed light on the FDA's rulemaking process, we examined the evolution of significant rules that the agency published during 2000-12 for drugs, devices, and other medical products. We found that the rules' median time to finalization was 7.3 years, with the pre-rule phase and postreview deliberation within the FDA accounting for the majority of that time. Rules that involved mandatory cost-benefit analyses were associated with an additional delay of approximately two years. We also found that longer review times were significantly associated with a reduction in the stringency of final rules, compared to the originally proposed versions. We recommend improving FDA's rulemaking by allocating additional resources to increase efficiency and by embarking on initiatives to promote transparency by the FDA and other parts of the executive branch.

Local Stability of AIDS Epidemic Model Through Treatment and Vertical Transmission with Time Delay

NASA Astrophysics Data System (ADS)

Novi W, Cascarilla; Lestari, Dwi

2016-02-01

This study aims to explain stability of the spread of AIDS through treatment and vertical transmission model. Human with HIV need a time to positively suffer AIDS. The existence of a time, human with HIV until positively suffer AIDS can be delayed for a time so that the model acquired is the model with time delay. The model form is a nonlinear differential equation with time delay, SIPTA (susceptible-infected-pre AIDS-treatment-AIDS). Based on SIPTA model analysis results the disease free equilibrium point and the endemic equilibrium point. The disease free equilibrium point with and without time delay are local asymptotically stable if the basic reproduction number is less than one. The endemic equilibrium point will be local asymptotically stable if the time delay is less than the critical value of delay, unstable if the time delay is more than the critical value of delay, and bifurcation occurs if the time delay is equal to the critical value of delay.

Mak5 and Ebp2 Act Together on Early Pre-60S Particles and Their Reduced Functionality Bypasses the Requirement for the Essential Pre-60S Factor Nsa1

PubMed Central

Pratte, Dagmar; Singh, Ujjwala; Murat, Guillaume; Kressler, Dieter

2013-01-01

Ribosomes are the molecular machines that translate mRNAs into proteins. The synthesis of ribosomes is therefore a fundamental cellular process and consists in the ordered assembly of 79 ribosomal proteins (r-proteins) and four ribosomal RNAs (rRNAs) into a small 40S and a large 60S ribosomal subunit that form the translating 80S ribosomes. Most of our knowledge concerning this dynamic multi-step process comes from studies with the yeast Saccharomyces cerevisiae, which have shown that assembly and maturation of pre-ribosomal particles, as they travel from the nucleolus to the cytoplasm, relies on a multitude (>200) of biogenesis factors. Amongst these are many energy-consuming enzymes, including 19 ATP-dependent RNA helicases and three AAA-ATPases. We have previously shown that the AAA-ATPase Rix7 promotes the release of the essential biogenesis factor Nsa1 from late nucleolar pre-60S particles. Here we show that mutant alleles of genes encoding the DEAD-box RNA helicase Mak5, the C/D-box snoRNP component Nop1 and the rRNA-binding protein Nop4 bypass the requirement for Nsa1. Interestingly, dominant-negative alleles of RIX7 retain their phenotype in the absence of Nsa1, suggesting that Rix7 may have additional nuclear substrates besides Nsa1. Mak5 is associated with the Nsa1 pre-60S particle and synthetic lethal screens with mak5 alleles identified the r-protein Rpl14 and the 60S biogenesis factors Ebp2, Nop16 and Rpf1, which are genetically linked amongst each other. We propose that these ’Mak5 cluster’ factors orchestrate the structural arrangement of a eukaryote-specific 60S subunit surface composed of Rpl6, Rpl14 and Rpl16 and rRNA expansion segments ES7L and ES39L. Finally, over-expression of Rix7 negatively affects growth of mak5 and ebp2 mutant cells both in the absence and presence of Nsa1, suggesting that Rix7, at least when excessively abundant, may act on structurally defective pre-60S subunits and may subject these to degradation. PMID:24312670

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes.

PubMed

Xu, Jiajiong; Tang, Wei; Ma, Jun; Wang, Hong

2017-07-01

Drinking water treatment processes remove undesirable chemicals and microorganisms from source water, which is vital to public health protection. The purpose of this study was to investigate the effects of treatment processes and configuration on the microbiome by comparing microbial community shifts in two series of different treatment processes operated in parallel within a full-scale drinking water treatment plant (DWTP) in Southeast China. Illumina sequencing of 16S rRNA genes of water samples demonstrated little effect of coagulation/sedimentation and pre-oxidation steps on bacterial communities, in contrast to dramatic and concurrent microbial community shifts during ozonation, granular activated carbon treatment, sand filtration, and disinfection for both series. A large number of unique operational taxonomic units (OTUs) at these four treatment steps further illustrated their strong shaping power towards the drinking water microbial communities. Interestingly, multidimensional scaling analysis revealed tight clustering of biofilm samples collected from different treatment steps, with Nitrospira, the nitrite-oxidizing bacteria, noted at higher relative abundances in biofilm compared to water samples. Overall, this study provides a snapshot of step-to-step microbial evolvement in multi-step drinking water treatment systems, and the results provide insight to control and manipulation of the drinking water microbiome via optimization of DWTP design and operation.

Skeletal muscle plasticity induced by seasonal acclimatization in carp involves differential expression of rRNA and molecules that epigenetically regulate its synthesis.

PubMed

Fuentes, Eduardo N; Zuloaga, Rodrigo; Nardocci, Gino; Fernandez de la Reguera, Catalina; Simonet, Nicolas; Fumeron, Robinson; Valdes, Juan Antonio; Molina, Alfredo; Alvarez, Marco

2014-01-01

Ribosomal biogenesis controls cellular growth in living organisms, with the rate-limiting step of this process being the transcription of ribosomal DNA (rDNA). Considering that epigenetic mechanisms allow an organism to respond to environmental changes, the expression in muscle of several molecules that regulate epigenetic rRNA synthesis, as well as rDNA transcription, were evaluated during the seasonal acclimatization of the carp. First, the nucleotide sequences encoding the components forming the NoRC (ttf-I, tip5) and eNoSC (sirt1, nml, suv39h1), two chromatin remodeling complexes that silence rRNA synthesis, as well as the sequence of ubf1, a key regulator of rDNA transcription, were obtained. Subsequently the transcriptional regulation of the aforementioned molecules, and other key molecules involved in rRNA synthesis (mh2a1, mh2a2, h2a.z, h2a.z.7, nuc, p80), was assessed. The carp sequences for TTF-I, TIP5, SIRT1, NML, SUV39H1, and UBF1 showed a high conservation of domains and key amino acids in comparison with other fish and higher vertebrates. The mRNA contents in muscle for ttf-I, tip5, sirt1, nml, suv39h1, mh2a1, mh2a.z, and nuc were up-regulated during winter in comparison with summer, whereas the mRNA levels of mh2a2, ubf1, and p80 were down-regulated. Also, the contents of molecules involved in processing the rRNA (snoRNAs) and pRNA, a stabilizer of NoRC complex, were analyzed, finding that these non-coding RNAs were not affected by seasonal acclimatization. These results suggest that variations in the expression of rRNA and the molecules that epigenetically regulate its synthesis are contributing to the muscle plasticity induced by seasonal acclimatization in carp. Copyright © 2014 Elsevier Inc. All rights reserved.

Effects of wrapping time delays on the nutritive value of baled alfalfa silages

USDA-ARS?s Scientific Manuscript database

Baled silages are an attractive forage conservation option, especially for small and mid-sized beef and dairy producers. Our objectives were to test the effects of delayed wrapping on the nutritive value of baled alfalfa silages on a pre- and post-storage basis. A secondary objective was to evaluate...

Delayed Parturition and Altered Myometrial Progesterone Receptor Isoform A Expression in Mice Null for Kruppel-like Factor 9

USDA-ARS?s Scientific Manuscript database

Pre-term and delayed labor conditions are devastating health problems, with currently unknown etiologies. We previously showed that the transcription factor Krüppel-like factor 9 (KLF9) influences the expression and/or transcriptional activity of receptors for estrogen and progesterone in endometria...

Movement Exploration as a Technique for Teaching Pre-Swimming Skills to Students with Developmental Delays.

ERIC Educational Resources Information Center

Buis, Joyce M.; Schane, Catherine S.

1980-01-01

Background, rationale, and techniques for using movement exploration to teach preswimming skills to developmentally delayed persons are given. Objectives (beyond the primary one of safety) of such a program include body awareness, spatial awareness, movement, and perceptual motor functions. Guidelins for activity selection and adaptation are…

Automating individualized coaching and authentic role-play practice for brief intervention training.

PubMed

Hayes-Roth, B; Saker, R; Amano, K

2010-01-01

Brief intervention helps to reduce alcohol abuse, but there is a need for accessible, cost-effective training of clinicians. This study evaluated STAR Workshop , a web-based training system that automates efficacious techniques for individualized coaching and authentic role-play practice. We compared STAR Workshop to a web-based, self-guided e-book and a no-treatment control, for training the Engage for Change (E4C) brief intervention protocol. Subjects were medical and nursing students. Brief written skill probes tested subjects' performance of individual protocol steps, in different clinical scenarios, at three test times: pre-training, post-training, and post-delay (two weeks). Subjects also did live phone interviews with a standardized patient, post-delay. STAR subjects performed significantly better than both other groups. They showed significantly greater improvement from pre-training probes to post-training and post-delay probes. They scored significantly higher on post-delay phone interviews. STAR Workshop appears to be an accessible, cost-effective approach for training students to use the E4C protocol for brief intervention in alcohol abuse. It may also be useful for training other clinical interviewing protocols.

Urea transporter UT-B deletion induces DNA damage and apoptosis in mouse bladder urothelium.

PubMed

Dong, Zixun; Ran, Jianhua; Zhou, Hong; Chen, Jihui; Lei, Tianluo; Wang, Weiling; Sun, Yi; Lin, Guiting; Bankir, Lise; Yang, Baoxue

2013-01-01

Previous studies found that urea transporter UT-B is abundantly expressed in bladder urothelium. However, the dynamic role of UT-B in bladder urothelial cells remains unclear. The objective of this study is to evaluate the physiological roles of UT-B in bladder urothelium using UT-B knockout mouse model and T24 cell line. Urea and NO measurement, mRNA expression micro-array analysis, light and transmission electron microscopy, apoptosis assays, DNA damage and repair determination, and intracellular signaling examination were performed in UT-B null bladders vs wild-type bladders and in vitro T24 epithelial cells. UT-B was highly expressed in mouse bladder urothelium. The genes, Dcaf11, MCM2-4, Uch-L1, Bnip3 and 45 S pre rRNA, related to DNA damage and apoptosis were significantly regulated in UT-B null urothelium. DNA damage and apoptosis highly occurred in UT-B null urothelium. Urea and NO levels were significantly higher in UT-B null urothelium than that in wild-type, which may affect L-arginine metabolism and the intracellular signals related to DNA damage and apoptosis. These findings were consistent with the in vitro study in T24 cells that, after urea loading, exhibited cell cycle delay and apoptosis. UT-B may play an important role in protecting bladder urothelium by balancing intracellular urea concentration. Disruption of UT-B function induces DNA damage and apoptosis in bladder, which can result in bladder disorders.

Urea Transporter UT-B Deletion Induces DNA Damage and Apoptosis in Mouse Bladder Urothelium

PubMed Central

Zhou, Hong; Chen, Jihui; Lei, Tianluo; Wang, Weiling; Sun, Yi; Lin, Guiting; Bankir, Lise; Yang, Baoxue

2013-01-01

Background Previous studies found that urea transporter UT-B is abundantly expressed in bladder urothelium. However, the dynamic role of UT-B in bladder urothelial cells remains unclear. The objective of this study is to evaluate the physiological roles of UT-B in bladder urothelium using UT-B knockout mouse model and T24 cell line. Methodology/Principal Findings Urea and NO measurement, mRNA expression micro-array analysis, light and transmission electron microscopy, apoptosis assays, DNA damage and repair determination, and intracellular signaling examination were performed in UT-B null bladders vs wild-type bladders and in vitro T24 epithelial cells. UT-B was highly expressed in mouse bladder urothelium. The genes, Dcaf11, MCM2-4, Uch-L1, Bnip3 and 45 S pre rRNA, related to DNA damage and apoptosis were significantly regulated in UT-B null urothelium. DNA damage and apoptosis highly occurred in UT-B null urothelium. Urea and NO levels were significantly higher in UT-B null urothelium than that in wild-type, which may affect L-arginine metabolism and the intracellular signals related to DNA damage and apoptosis. These findings were consistent with the in vitro study in T24 cells that, after urea loading, exhibited cell cycle delay and apoptosis. Conclusions/Significance UT-B may play an important role in protecting bladder urothelium by balancing intracellular urea concentration. Disruption of UT-B function induces DNA damage and apoptosis in bladder, which can result in bladder disorders. PMID:24204711

Identification of Lactic Acid Bacteria in Fruit Pulp Processing Byproducts and Potential Probiotic Properties of Selected Lactobacillus Strains

PubMed Central

Garcia, Estefânia F.; Luciano, Winnie A.; Xavier, Danilo E.; da Costa, Whyara C. A.; de Sousa Oliveira, Kleber; Franco, Octávio L.; de Morais Júnior, Marcos A.; Lucena, Brígida T. L.; Picão, Renata C.; Magnani, Marciane; Saarela, Maria; de Souza, Evandro L.

2016-01-01

This study aimed to identify lactic acid bacteria (LAB) in byproducts of fruit (Malpighia glabra L., Mangifera indica L., Annona muricata L., and Fragaria vesca L.) pulp processing. Fifty strains of LAB were identified using matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequence (16S rRNA) analysis. Species belonging to Lactobacillus genus were the predominant LAB in all fruit pulp processing byproducts. The average congruency between the MALDI-TOF MS and 16S rRNA in LAB species identification reached 86%. Isolates of L. plantarum, L. brevis, L. pentosus, L. lactis and L. mesenteroides were identified with 100% congruency. MALDI-TOF MS and 16S rRNA analysis presented 86 and 100% efficiency of LAB species identification, respectively. Further, five selected Lactobacillus strains (L. brevis 59, L. pentosus 129, L. paracasei 108, L. plantarum 49, and L. fermentum 111) were evaluated for desirable probiotic-related properties and growth behavior on two different cultivation media. The exposure to pH 2.0 sharply decreased the counts of the different Lactobacillus strains after a 1 or 2 h incubation, while varied decreases were noted after 3 h of exposure to pH 3.0. Overall, the exposure to pH 5.0 and to bile salts (0.15, 0.30, and 1.00%) did not decrease the counts of the Lactobacillus strains. All tested Lactobacillus strains presented inhibitory activity against Staphylococcus aureus, Salmonella Typhimurium, Salmonella Enteritidis, Listeria monocytogenes and Escherichia coli, and presented variable susceptibility to different antibiotics. The selected Lactobacillus strains presented satisfactory and reproducible growth behavior. In conclusion, MALDI-TOF MS and 16S rRNA analysis revealed high efficiency and congruency for LAB species identification, and the selected Lactobacillus strains may be candidates for further investigation of novel probiotic strains. PMID:27625647

Spouses' conceptions of the pre-hospital phase when their partners suffered an acute myocardial infarction--a qualitative analysis.

PubMed

Johansson, Ingela; Swahn, Eva; Strömberg, Anna

2008-09-01

Delay from onset of acute myocardial infarction symptoms to the delivery of medical care is a major determinant of prognosis. Although studies have explored patient reasons for delay, there are only limited data concerning experiences of the spouse. Was to describe spouses' conceptions of the pre-hospital phase when their partners suffered an acute myocardial infarction. A phenomenographic approach was applied. Fifteen spouses were interviewed <48 h after the partner's hospital admittance. Two categories with underlying sub-categories conceptualised the spouses' experiences. The category being resourceful contained: sharing the experience, having knowledge, understanding the severity, being rational, and consulting others. The category respecting independence contained: accepting the need for control, marital roles and experiences, restraining emotions, and seeking agreement. Our findings suggest that spouses have a strong influence on the course of events. When accepting the partner's need for control through following earlier marital roles and experiences, restraining own emotions and seeking agreement, this seemed to contribute to delay. However, when the spouse was resourceful by sharing the experience, having knowledge, understanding the severity, being rational and consulting others when needed, this seemed to have a positive influence on the pre-hospital time.

Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study.

PubMed

Arboleya, Silvia; Sánchez, Borja; Solís, Gonzalo; Fernández, Nuria; Suárez, Marta; Hernández-Barranco, Ana M; Milani, Christian; Margolles, Abelardo; de Los Reyes-Gavilán, Clara G; Ventura, Marco; Gueimonde, Miguel

2016-04-29

The microbial colonization of the neonatal gut provides a critical stimulus for normal maturation and development. This process of early microbiota establishment, known to be affected by several factors, constitutes an important determinant for later health. We studied the establishment of the microbiota in preterm and full-term infants and the impact of perinatal antibiotics upon this process in premature babies. To this end, 16S rRNA gene sequence-based microbiota assessment was performed at phylum level and functional inference analyses were conducted. Moreover, the levels of the main intestinal microbial metabolites, the short-chain fatty acids (SCFA) acetate, propionate and butyrate, were measured by Gas-Chromatography Flame ionization/Mass spectrometry detection. Prematurity affects microbiota composition at phylum level, leading to increases of Proteobacteria and reduction of other intestinal microorganisms. Perinatal antibiotic use further affected the microbiota of the preterm infant. These changes involved a concomitant alteration in the levels of intestinal SCFA. Moreover, functional inference analyses allowed for identifying metabolic pathways potentially affected by prematurity and perinatal antibiotics use. A deficiency or delay in the establishment of normal microbiota function seems to be present in preterm infants. Perinatal antibiotic use, such as intrapartum prophylaxis, affected the early life microbiota establishment in preterm newborns, which may have consequences for later health.

The Effects of Combinations of Cognitive Impairment and Pre-frailty on Adverse Outcomes from a Prospective Community-Based Cohort Study of Older Chinese People.

PubMed

Yu, Ruby; Morley, John E; Kwok, Timothy; Leung, Jason; Cheung, Osbert; Woo, Jean

2018-01-01

To examine how various combinations of cognitive impairment (overall performance and specific domains) and pre-frailty predict risks of adverse outcomes; and to determine whether cognitive frailty may be defined as the combination of cognitive impairment and the presence of pre-frailty. Community-based cohort study. Chinese men and women ( n  = 3,491) aged 65+ without dementia, Parkinson's disease and/or frailty at baseline. Frailty was characterized using the Cardiovascular Health Study criteria. Overall cognitive impairment was defined by a Cantonese Mini-Mental Status Examination (CMMSE) total score (<21/24/27, depending on participants' educational levels); delayed recall impairment by a CMMSE delayed recall score (<3); and language and praxis impairment by a CMMSE language and praxis score (<9). Adverse outcomes included poor quality of life, physical limitation, increased cumulative hospital stay, and mortality. Compared to those who were robust and cognitively intact at baseline, those who were robust but cognitively impaired were more likely to develop pre-frailty/frailty after 4 years ( P  < 0.01). Compared to participants who were robust and cognitively intact at baseline, those who were pre-frail and with overall cognitive impairment had lower grip strength ( P  < 0.05), lower gait speed ( P  < 0.01), poorer lower limb strength ( P  < 0.01), and poorer delayed recall at year 4 [OR, 1.6; 95% confidence interval (CI), 1.2-2.3]. They were also associated with increased risks of poor quality of life (OR, 1.5; 95% CI, 1.1-2.2) and incident physical limitation at year 4 (OR, 1.8; 95% CI, 1.3-2.5), increased cumulative hospital stay at year 7 (OR, 1.5; 95% CI, 1.1-2.1), and mortality over an average of 12 years (OR, 1.5; 95% CI, 1.0-2.1) after adjustment for covariates. There was no significant difference in risks of adverse outcomes between participants who were pre-frail, with/without cognitive impairment at baseline. Similar results were obtained with delayed recall and language and praxis impairments. Robust and cognitively impaired participants had higher risks of becoming pre-frail/frail over 4 years compared with those with normal cognition. Cognitive impairment characterized by the CMMSE overall score or its individual domain score improved the predictive power of pre-frailty for poor quality of life, incident physical limitation, increased cumulative hospital stay, and mortality. Our findings support to the concept that cognitive frailty may be defined as the occurrence of both cognitive impairment and pre-frailty, not necessarily progressing to dementia.

Acute Ethanol Withdrawal Impairs Contextual Learning and Enhances Cued Learning

PubMed Central

Tipps, Megan E.; Raybuck, Jonathan D.; Buck, Kari J.; Lattal, K. Matthew

2014-01-01

Background Alcohol affects many of the brain regions and neural processes that support learning and memory, and these effects are thought to underlie, at least in part, the development of addiction. Although much work has been done regarding the effects of alcohol intoxication on learning and memory, little is known about the effects of acute withdrawal from a single alcohol exposure. Methods We assess the effects of acute ethanol withdrawal (6 h post-injection with 4 g/kg ethanol) on two forms of fear conditioning (delay and trace fear conditioning) in C57BL/6J and DBA/2J mice. The influence of a number of experimental parameters (pre- and post-training withdrawal exposure; foreground/background processing; training strength; non-associative effects) is also investigated. Results Acute ethanol withdrawal during training had a bidirectional effect on fear conditioned responses, decreasing contextual responses and increasing cued responses. These effects were apparent for both trace and delay conditioning in DBA/2J mice and for trace conditioning in C57BL/6J mice; however, C57BL/6J mice were selectively resistant to the effects of acute withdrawal on delay cued responses. Conclusions Our results show that acute withdrawal from a single, initial ethanol exposure is sufficient to alter long-term learning in mice. In addition, the differences between the strains and conditioning paradigms used suggest that specific learning processes can be differentially affected by acute withdrawal in a manner that is distinct from the reported effects of both alcohol intoxication and withdrawal following chronic alcohol exposure. Thus, our results suggest a unique effect of acute alcohol withdrawal on learning and memory processes. PMID:25684050

Ovarian reaction and estrus manifestation in delayed puberty gilts after treatment with equine chorionic gonadotropin

USDA-ARS?s Scientific Manuscript database

Prolonged pre-insemination anestrus (estrus not detected until 8 mo of age, i.e. delayed puberty) is the major reason for culling about 30% of the total number of gilts selected for reproduction at the large breeding farm units in Vojvodina (Republic of Serbia). It is important to determine whether...

Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations

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

Gupta, Chinmaya; López, José Manuel; Azencott, Robert

Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein. Genetic regulatory networks are therefore frequently modeled as stochastic birth-death processes with delay. Here, we examine the relationship between delay birth-death processes and their appropriate approximating delay chemical Langevin equations. We prove a quantitative bound on the error between the pathwise realizations of these two processes. Our results hold for both fixed delay and distributed delay. Simulations demonstrate that the delay chemicalmore » Langevin approximation is accurate even at moderate system sizes. It captures dynamical features such as the oscillatory behavior in negative feedback circuits, cross-correlations between nodes in a network, and spatial and temporal information in two commonly studied motifs of metastability in biochemical systems. Overall, these results provide a foundation for using delay stochastic differential equations to approximate the dynamics of birth-death processes with delay.« less

Adaptive Pre-FFT Equalizer with High-Precision Channel Estimator for ISI Channels

NASA Astrophysics Data System (ADS)

Yoshida, Makoto

We present an attractive approach for OFDM transmission using an adaptive pre-FFT equalizer, which can select ICI reduction mode according to channel condition, and a degenerated-inverse-matrix-based channel estimator (DIME), which uses a cyclic sinc-function matrix uniquely determined by transmitted subcarriers. In addition to simulation results, the proposed system with an adaptive pre-FFT equalizer and DIME has been laboratory tested by using a software defined radio (SDR)-based test bed. The simulation and experimental results demonstrated that the system at a rate of more than 100Mbps can provide a bit error rate of less than 10-3 for a fast multi-path fading channel that has a moving velocity of more than 200km/h with a delay spread of 1.9µs (a maximum delay path of 7.3µs) in the 5-GHz band.

AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia.

PubMed

Zhou, Fengbiao; Liu, Yi; Rohde, Christian; Pauli, Cornelius; Gerloff, Dennis; Köhn, Marcel; Misiak, Danny; Bäumer, Nicole; Cui, Chunhong; Göllner, Stefanie; Oellerich, Thomas; Serve, Hubert; Garcia-Cuellar, Maria-Paz; Slany, Robert; Maciejewski, Jaroslaw P; Przychodzen, Bartlomiej; Seliger, Barbara; Klein, Hans-Ulrich; Bartenhagen, Christoph; Berdel, Wolfgang E; Dugas, Martin; Taketo, Makoto Mark; Farouq, Daneyal; Schwartz, Schraga; Regev, Aviv; Hébert, Josée; Sauvageau, Guy; Pabst, Caroline; Hüttelmaier, Stefan; Müller-Tidow, Carsten

2017-07-01

Leukaemogenesis requires enhanced self-renewal, which is induced by oncogenes. The underlying molecular mechanisms remain incompletely understood. Here, we identified C/D box snoRNAs and rRNA 2'-O-methylation as critical determinants of leukaemic stem cell activity. Leukaemogenesis by AML1-ETO required expression of the groucho-related amino-terminal enhancer of split (AES). AES functioned by inducing snoRNA/RNP formation via interaction with the RNA helicase DDX21. Similarly, global loss of C/D box snoRNAs with concomitant loss of rRNA 2'-O-methylation resulted in decreased leukaemia self-renewal potential. Genomic deletion of either C/D box snoRNA SNORD14D or SNORD35A suppressed clonogenic potential of leukaemia cells in vitro and delayed leukaemogenesis in vivo. We further showed that AML1-ETO9a, MYC and MLL-AF9 all enhanced snoRNA formation. Expression levels of C/D box snoRNAs in AML patients correlated closely with in vivo frequency of leukaemic stem cells. Collectively, these findings indicate that induction of C/D box snoRNA/RNP function constitutes an important pathway in leukaemogenesis.

Nano- and micro-structuring of fused silica using time-delay adjustable double flash ns-laser radiation

NASA Astrophysics Data System (ADS)

Lorenz, Pierre; Zhao, Xiongtao; Ehrhardt, Martin; Zagoranskiy, Igor; Zimmer, Klaus; Han, Bing

2018-02-01

Large area, high speed, nanopatterning of surfaces by laser ablation is challenging due to the required high accuracy of the optical and mechanical systems fulfilling the precision of nanopatterning process. Utilization of self-organization approaches can provide an alternative decoupling spot precision and field of machining. The laser-induced front side etching (LIFE) and laser-induced back side dry etching (LIBDE) of fused silica were studied using single and double flash nanosecond laser pulses with a wavelength of 532 nm where the time delay Δτ of the double flash laser pulses was adjusted from 50 ns to 10 μs. The fused silica can be etched at both processes assisted by a 10 nm chromium layer where the etching depth Δz at single flash laser pulses is linear to the laser fluence and independent on the number of laser pulses, from 2 to 12 J/cm2, it is Δz = δLIFE/LIBDE . Φ with δLIFE 16 nm/(J/cm2) and δLIBDE 5.2 nm/(J/cm2) 3 . δLIFE. At double flash laser pulses, the Δz is dependent on the time delay Δτ of the laser pulses and the Δz slightly increased at decreasing Δτ. Furthermore, the surface nanostructuring of fused silica using IPSM-LIFE (LIFE using in-situ pre-structured metal layer) method with a single double flash laser pulse was tested. The first pulse of the double flash results in a melting of the metal layer. The surface tension of the liquid metal layer tends in a droplet formation process and dewetting process, respectively. If the liquid phase life time ΔtLF is smaller than the droplet formation time the metal can be "frozen" in an intermediated state like metal bare structures. The second laser treatment results in a evaporation of the metal and in a partial evaporation and melting of the fused silica surface, where the resultant structures in the fused silica surface are dependent on the lateral geometry of the pre-structured metal layer. A successful IPSM-LIFE structuring could be achieved assisted by a 20 nm molybdenum layer at Δτ >= 174 ns. That path the way for the high speed ultra-fast nanostructuring of dielectric surfaces by self-organizing processes. The different surface structures were analyzed by scanning electron microscopy (SEM) and white light interferometry (WLI).

When place and time matter: How to conduct safe inter-hospital transfer of patients

PubMed Central

Sethi, Divya; Subramanian, Shalini

2014-01-01

Inter-hospital transfer (IHT) of patients is often needed for diagnostic or therapeutic interventions. However, the transfer process carries its own risks as a poorly and hastily conducted transfer could lead to adverse events. In this article, we have reviewed literature on the key elements of IHT process including pre-transfer patient stabilization. We have also discussed various modes of transfer, physiological effects of transfer, possible adverse events and how to avoid or mitigate these. Even critically ill-patients can be transported safely by experienced and trained personnel using appropriate equipment. The patient must be maximally stabilized prior to transfer though complete optimization may be possible only at the receiving hospital. Ground or air transport may be employed depending on the urgency, feasibility and availability. Meticulous pre-transfer check and adherence to standard protocols during the transfer will help keep the entire process smooth and event free. The transport team should be trained to anticipate and manage any possible adverse events, medical or technical, during the transfer. Coordination between the referring and receiving hospitals would facilitate prompt transfer to the definitive destination avoiding delay at the emergency or casualty. Documentation of the transfer process and transfer of medical record and investigation reports are important for maintaining continuity of medical care and for medico-legal purposes. PMID:24665250

"Pre-Semantic" Cognition Revisited: Critical Differences between Semantic Aphasia and Semantic Dementia

ERIC Educational Resources Information Center

Jefferies, Elizabeth; Rogers, Timothy T.; Hopper, Samantha; Lambon Ralph, Matthew A.

2010-01-01

Patients with semantic dementia show a specific pattern of impairment on both verbal and non-verbal "pre-semantic" tasks, e.g., reading aloud, past tense generation, spelling to dictation, lexical decision, object decision, colour decision and delayed picture copying. All seven tasks are characterised by poorer performance for items that are…

Different effects of the two types of spatial pre-cueing: what precisely is "attention" in Di Lollo's and Enns' substitution masking theory?

PubMed

Luiga, I; Bachmann, T

2007-11-01

Enns and Di Lollo [Psychological Science, 8 (2), 135-139, 1997] have introduced the object substitution theory of visual masking. Object substitution masking occurs when focusing attention on the target is delayed. However, Posner (Quarterly Journal of Experimental Psychology, 32, 3-25, 1980) has already shown that attention can be directed to a target at least in two ways: intentionally (endogenously) and automatically (exogenously). We conducted two experiments to explore the effects of endogenous and exogenous cues on substitution masking. The results showed that when attention was shifted to the target location automatically (using a local peripheral pre-cue), masking was attenuated. A decrease in target identification dependent on a delay of mask offset, typical to substitution masking, was not observed. However, strong substitution masking occurred when the target location was not pre-cued or when attention was directed to the target location intentionally (using a symbolic pre-cue displayed centrally). The hypothesis of two different mechanisms of attentional control in substitution masking was confirmed.

Revolving Loan Fund: A Novel Approach to Increasing Access to Long-Acting Reversible Contraception Methods in Community Health Centers.

PubMed

Evans, Megan L; Breeze, Janis L; Paulus, Jessica K; Meadows, Audra

The aim of this study was to assess the impact of a revolving loan fund (RLF) on timing of device insertion and long-acting reversible contraception (LARC) access among a high-risk urban population at 3 Boston community health centers. Three health centers were identified to implement a RLF. Each clinic received $5000 from the RLF to purchase LARC devices. Data collected through medical record review retrospectively 1 year prior to start of the RLF and prospectively for 1 year thereafter included patient demographics, type of LARC selected, patient's date of documented interest in a LARC device, and date of insertion. The effect of a RLF on delay to LARC insertion was tested using negative binomial regression, controlling for site and potential confounding variables between the pre- and post-RLF periods. Three urban community health centers. Reproductive-aged women who received family planning services at the 3 participating health centers. Increasing access to LARC and decreasing wait times to LARC insertion after implementation of the RLF. Data on 133 patients in the pre-RLF group and 205 in the post-RLF group were collected. There were no statistically significant differences in demographic or clinical characteristics between the 2 time periods. LARC uptake increased significantly from the pre- to post-RLF period, specifically among implant users. There was a statistically significant decrease in the mean number of days in delay from interest to insertion from the pre- to post-RLF period (pre-RLF: 31.3 ± 50.6 days; post-RLF: 13.6 ± 16.7 days, adjusted P < .001). The reasons for the delay did not differ significantly between the 2 time periods. The RLF decreased wait time for the devices and increased overall insertion rates. This may serve as a promising solution to improve LARC access in community health centers. This project could be expanded to include more health centers, creating a city wide RLF. This expansion could allow for further data analysis, including unintended pregnancy rates with LARC delay, LARC continuation rates, and sustainability of a RLF.

Computational and Experimental Characterization of Ribosomal DNA and RNA G-Quadruplexes

NASA Astrophysics Data System (ADS)

Cho, Samuel

DNA G-quadruplexes in human telomeres and gene promoters are being extensively studied for their role in controlling the growth of cancer cells. Recent studies strongly suggest that guanine (G)-rich genes encoding pre-ribosomal RNA (pre-rRNA) are a potential anticancer target through the inhibition of RNA polymerase I (Pol I) in ribosome biogenesis. However, the structures of ribosomal G-quadruplexes at atomic resolution are unknown, and very little biophysical characterization has been performed on them to date. Here, we have modeled two putative rDNA G-quadruplex structures, NUC 19P and NUC 23P, which we observe via circular dichroism (CD) spectroscopy to adopt a predominantly parallel topology, and their counterpart rRNA. To validate and refine the putative ribosomal G-quadruplex structures, we performed all-atom molecular dynamics (MD) simulations using the CHARMM36 force field in the presence and absence of stabilizing K + or Na + ions. We optimized the CHARMM36 force field K + parameters to be more consistent with quantum mechanical calculations (and the polarizable Drude model force field) so that the K + ion is predominantly in the G-quadruplex channel. Our MD simulations show that the rDNA G-quadruplex have more well-defined, predominantly parallel-topology structures than rRNA and NUC 19P is more structured than NUC 23P, which features extended loops. Our study demonstrates that they are both potential targets for the design of novel chemotherapeutics.

Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites

PubMed Central

Diermeier, Sarah D.; Németh, Attila; Rehli, Michael; Grummt, Ingrid; Längst, Gernot

2013-01-01

Enhancers and promoters often contain multiple binding sites for the same transcription factor, suggesting that homotypic clustering of binding sites may serve a role in transcription regulation. Here we show that clustering of binding sites for the transcription termination factor TTF-I downstream of the pre-rRNA coding region specifies transcription termination, increases the efficiency of transcription initiation and affects the three-dimensional structure of rRNA genes. On chromatin templates, but not on free rDNA, clustered binding sites promote cooperative binding of TTF-I, loading TTF-I to the downstream terminators before it binds to the rDNA promoter. Interaction of TTF-I with target sites upstream and downstream of the rDNA transcription unit connects these distal DNA elements by forming a chromatin loop between the rDNA promoter and the terminators. The results imply that clustered binding sites increase the binding affinity of transcription factors in chromatin, thus influencing the timing and strength of DNA-dependent processes. PMID:24068958

Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation

DOE PAGES

Mitrea, Diana M.; Cika, Jaclyn A.; Stanley, Christopher B.; ...

2018-02-26

Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid–liquid phase separation (LLPS) via heterotypic interactions with nucleolar components, including ribosomal RNA (rRNA) and proteins which display multivalent arginine-rich linear motifs (R-motifs), and is integral to the liquid-like nucleolar matrix. Here we show that NPM1 can also undergo LLPS via homotypic interactions between its polyampholytic intrinsically disordered regions, a mechanism that opposes LLPS via heterotypic interactions. Using a combination of biophysical techniques, including confocal microscopy, SAXS, analytical ultracentrifugation, and single-molecule fluorescence, we describe how conformational changes withinmore » NPM1 control valency and switching between the different LLPS mechanisms. We propose that this newly discovered interplay between multiple LLPS mechanisms may influence the direction of vectorial pre-ribosomal particle assembly within, and exit from the nucleolus as part of the ribosome biogenesis process.« less

Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans

PubMed Central

Holdt, Lesca M.; Stahringer, Anika; Sass, Kristina; Pichler, Garwin; Kulak, Nils A.; Wilfert, Wolfgang; Kohlmaier, Alexander; Herbst, Andreas; Northoff, Bernd H.; Nicolaou, Alexandros; Gäbel, Gabor; Beutner, Frank; Scholz, Markus; Thiery, Joachim; Musunuru, Kiran; Krohn, Knut; Mann, Matthias; Teupser, Daniel

2016-01-01

Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their molecular mechanism in human disease remains obscure. Here we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome 9p21, confers atheroprotection by controlling ribosomal RNA (rRNA) maturation and modulating pathways of atherogenesis. CircANRIL binds to pescadillo homologue 1 (PES1), an essential 60S-preribosomal assembly factor, thereby impairing exonuclease-mediated pre-rRNA processing and ribosome biogenesis in vascular smooth muscle cells and macrophages. As a consequence, circANRIL induces nucleolar stress and p53 activation, resulting in the induction of apoptosis and inhibition of proliferation, which are key cell functions in atherosclerosis. Collectively, these findings identify circANRIL as a prototype of a circRNA regulating ribosome biogenesis and conferring atheroprotection, thereby showing that circularization of long non-coding RNAs may alter RNA function and protect from human disease. PMID:27539542

Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation

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

Mitrea, Diana M.; Cika, Jaclyn A.; Stanley, Christopher B.

Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid–liquid phase separation (LLPS) via heterotypic interactions with nucleolar components, including ribosomal RNA (rRNA) and proteins which display multivalent arginine-rich linear motifs (R-motifs), and is integral to the liquid-like nucleolar matrix. Here we show that NPM1 can also undergo LLPS via homotypic interactions between its polyampholytic intrinsically disordered regions, a mechanism that opposes LLPS via heterotypic interactions. Using a combination of biophysical techniques, including confocal microscopy, SAXS, analytical ultracentrifugation, and single-molecule fluorescence, we describe how conformational changes withinmore » NPM1 control valency and switching between the different LLPS mechanisms. We propose that this newly discovered interplay between multiple LLPS mechanisms may influence the direction of vectorial pre-ribosomal particle assembly within, and exit from the nucleolus as part of the ribosome biogenesis process.« less

16S rRNA beacons for bacterial monitoring during human space missions.

PubMed

Larios-Sanz, Maia; Kourentzi, Katerina D; Warmflash, David; Jones, Jeffrey; Pierson, Duane L; Willson, Richard C; Fox, George E

2007-04-01

Microorganisms are unavoidable in space environments and their presence has, at times, been a source of problems. Concerns about disease during human space missions are particularly important considering the significant changes the immune system incurs during spaceflight and the history of microbial contamination aboard the Mir space station. Additionally, these contaminants may have adverse effects on instrumentation and life-support systems. A sensitive, highly specific system to detect, characterize, and monitor these microbial populations is essential. Herein we describe a monitoring approach that uses 16S rRNA targeted molecular beacons to successfully detect several specific bacterial groupings. This methodology will greatly simplify in-flight monitoring by minimizing sample handling and processing. We also address and provide solutions to target accessibility problems encountered in hybridizations that target 16S rRNA.

Can Early Years Professionals Determine Which Preschoolers Have Comprehension Delays? A Comparison of Two Screening Tools

ERIC Educational Resources Information Center

Seager, Emily; Abbot-Smith, Kirsten

2017-01-01

Language comprehension delays in pre-schoolers are predictive of difficulties in a range of developmental domains. In England, early years practitioners are required to assess the language comprehension of 2-year-olds in their care. Many use a format based on the Early Years Foundation Stage Unique Child Communication Sheet (EYFS:UCCS) in which…

The Effects of Imitation Instruction Using a Mirror on the Emergence of Duplicative Responses by Preschool Students Diagnosed with Developmental Delays

ERIC Educational Resources Information Center

Moreno, Jalene Donica

2012-01-01

Using pre-and post-intervention non-concurrent multiple probe designs across participants, I conducted 2 experiments that tested the effects of imitation instruction using a mirror on the emergence of both basic and advanced forms of generalized imitation (GI) involving physical actions with preschool students diagnosed with developmental delays.…

Fabrication of viable and functional pre-vascularized modular bone tissues by coculturing MSCs and HUVECs on microcarriers in spinner flasks.

PubMed

Zhang, Songjie; Zhou, Min; Ye, Zhaoyang; Zhou, Yan; Tan, Wen-Song

2017-08-01

Slow vascularization often impedes the viability and function of engineered bone replacements. Prevascularization is a promising way to solve this problem. In this study, a new process was developed by integrating microcarrier culture and coculture to fabricate pre-vascularized bone microtissues with mesenchymal stem cells (MSCs) and human umbilical vein endothelial cells (HUVECs). Initially, coculture medium and cell ratio between MSCs and HUVECs were optimized in tissue culture plates concerning cell proliferation, osteogenesis and angiogenesis. Subsequently, cells were seeded onto CultiSpher S microcarriers in spinner flasks and subjected to a two-stage (proliferative-osteogenic) culture process for four weeks. Both cells proliferated and functioned well in chosen medium and a 1 : 1 ratio between MSCs and HUVECs was chosen for better angiogenesis. After four weeks of culture in spinner flasks, the microtissues were formed with high cellularity, evenly distributed cells and tube formation ability. While coculture with HUVECs exerted an inhibitory effect on osteogenic differentiation of MSCs, with downregulated alkaline phosphatase activity, mineralization and gene expression of COLI, RUNX2 and OCN, this could be attenuated by employing a delayed seeding strategy of HUVECs against MSCs during the microtissue fabrication process. Collectively, this work established an effective method to fabricate pre-vascularized bone microtissues, which would lay a solid foundation for subsequent development of vascularized tissue grafts for bone regeneration. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatial organization and dynamics of RNase E and ribosomes in Caulobacter crescentus.

PubMed

Bayas, Camille A; Wang, Jiarui; Lee, Marissa K; Schrader, Jared M; Shapiro, Lucy; Moerner, W E

2018-04-17

We report the dynamic spatial organization of Caulobacter crescentus RNase E (RNA degradosome) and ribosomal protein L1 (ribosome) using 3D single-particle tracking and superresolution microscopy. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. These results contrast with RNase E and ribosome distribution in Escherichia coli , where RNase E colocalizes with the cytoplasmic membrane and ribosomes accumulate in polar nucleoid-free zones. For both RNase E and ribosomes in Caulobacter , we observed a decrease in confinement and clustering upon transcription inhibition and subsequent depletion of nascent RNA, suggesting that RNA substrate availability for processing, degradation, and translation facilitates confinement and clustering. Importantly, RNase E cluster positions correlated with the subcellular location of chromosomal loci of two highly transcribed rRNA genes, suggesting that RNase E's function in rRNA processing occurs at the site of rRNA synthesis. Thus, components of the RNA degradosome and ribosome assembly are spatiotemporally organized in Caulobacter , with chromosomal readout serving as the template for this organization.

Joint Transmit and Receive Filter Optimization for Sub-Nyquist Delay-Doppler Estimation

NASA Astrophysics Data System (ADS)

Lenz, Andreas; Stein, Manuel S.; Swindlehurst, A. Lee

2018-05-01

In this article, a framework is presented for the joint optimization of the analog transmit and receive filter with respect to a parameter estimation problem. At the receiver, conventional signal processing systems restrict the two-sided bandwidth of the analog pre-filter $B$ to the rate of the analog-to-digital converter $f_s$ to comply with the well-known Nyquist-Shannon sampling theorem. In contrast, here we consider a transceiver that by design violates the common paradigm $B\\leq f_s$. To this end, at the receiver, we allow for a higher pre-filter bandwidth $B>f_s$ and study the achievable parameter estimation accuracy under a fixed sampling rate when the transmit and receive filter are jointly optimized with respect to the Bayesian Cram\\'{e}r-Rao lower bound. For the case of delay-Doppler estimation, we propose to approximate the required Fisher information matrix and solve the transceiver design problem by an alternating optimization algorithm. The presented approach allows us to explore the Pareto-optimal region spanned by transmit and receive filters which are favorable under a weighted mean squared error criterion. We also discuss the computational complexity of the obtained transceiver design by visualizing the resulting ambiguity function. Finally, we verify the performance of the optimized designs by Monte-Carlo simulations of a likelihood-based estimator.

Community-based early intervention for language delay: a preliminary investigation.

PubMed

Ciccone, Natalie; Hennessey, Neville; Stokes, Stephanie F

2012-01-01

A trial parent-focused early intervention (PFEI) programme for children with delayed language development is reported in which current research evidence was translated and applied within the constraints of available of clinical resources. The programme, based at a primary school, was run by a speech-language pathologist with speech-language pathology students. To investigate the changes in child language development and parent and child interactions following attendance at the PFEI. Eighteen parents and their children attended six, weekly group sessions in which parents were provided with strategies to maximize language learning in everyday contexts. Pre- and post-programme assessments of vocabulary size and measures of parent-child interaction were collected. Parents and children significantly increased their communicative interactions from pre- to post-treatment. Children's expressive vocabulary size and language skills increased significantly. Large-effect sizes were observed. The positive outcomes of the intervention programme contribute to the evidence base of intervention strategies and forms of service delivery for children at risk of language delay. © 2012 Royal College of Speech and Language Therapists.

Change or Durability? The Contribution of Metaconceptual Awareness in Preservice Early Childhood Teachers' Learning of Science Concepts

NASA Astrophysics Data System (ADS)

Saçkes, Mesut; Trundle, Kathy Cabe

2017-06-01

This longitudinal study examined the role of metaconceptual awareness in the change and the durability of preservice teachers' conceptual understandings over the course of several months. Sixteen preservice early childhood teachers participated in the study. Semi-structured interviews were conducted to reveal the participants' conceptual understandings of lunar phases (pre, post, and delayed-post) and level of metaconceptual awareness (delayed-post only). Based on the change and stability in participants' conceptual understandings from pre to post and from post to delayed-post interviews, participants' conceptual understandings were assigned into three groups that described the profile of their long-term conceptual understandings: " decay or stability", " continuous growth", and " growth and stability". The results indicated that participants in the " continuous growth" and " growth and stability" groups had significantly higher metaconceptual awareness scores than participants in the " decay or stability" group. The results provided evidence that metaconceptual awareness plays a more decisive role in the restructuring of conceptual understandings than the durability of conceptual understandings.

Twins and virtual twins: Do genetic (as well as experiential) factors affect developmental risks?

PubMed

Segal, Nancy L; Tan, Tony Xing; Graham, Jamie L

2015-08-01

Factors underlying developmental delays and psychosocial risks are of interest to international adoption communities. The current study administered a Pre-Adoption Adversity (PAA) Questionnaire to mostly American parents raising (a) adopted Chinese twins or (b) same-age unrelated adopted siblings. A goal was to replicate earlier analyses of pre-adoption adversity/adjustment among adopted preschool-age Chinese girls. A second goal was to conduct genetic analyses of four content areas (Developmental Delays at Adoption, Initial Adaptation to Adoption, Crying/Clinging, and Refusal/Avoidance) derived from the PAA Questionnaire. A key finding was that age at adoption added less than other predictors to adoptees' externalizing and internalizing behaviors. Family factors (e.g., parental education) contributed significantly to behavioral outcomes among the adopted Chinese twins. Genetic effects were indicated for all four content areas, with shared environmental effects evident for Developmental Delays at Adoption and Crying/Clinging. Future investigators should consider incorporating genetically sensitive designs into developmental research programs. Copyright © 2015 Elsevier Inc. All rights reserved.

A novel RNase G mutant that is defective in degradation of adhE mRNA but proficient in the processing of 16S rRNA precursor.

PubMed

Wachi, M; Kaga, N; Umitsuki, G; Clark, D P; Nagai, K

2001-12-21

Escherichia coli RNase G, encoded by the rng gene, is involved in both the processing of 16S rRNA precursor and the degradation of adhE mRNA. Consequently, defects in RNase G result in elevation of AdhE levels. Furthermore, the adhR430 mutant strain, DC430, is reported to overproduce the AdhE protein in a manner dependent on the adhC81 mutation. We found that overproduction of AdhE by DC430 was reversed to wild-type levels by introduction of a plasmid carrying the wild-type allele of rng. Mapping by P1-phage-mediated transduction also indicated that a mutation involved in AdhE overproduction was located around the rng region in DC430. DNA sequencing of the rng region revealed that DC430 indeed had a mutation in the rng gene: a G1022 to A transition that caused substitution of Gly341 with Ser and which was named rng430. This lies in the highly conserved region of the RNase E/RNase G family, called high similarity region 2 (HSR2). However, very interestingly, rng430 mutant strains did not accumulate the 16.3S precursor of 16S rRNA unlike rng::cat mutants. We also found that the Rng1 mutant protein, which is truncated in its C-terminal domain encompassing HSR2, exhibited a residual processing activity against the 16S rRNA precursor, when overproduced. These results indicate that the HSR2 of RNase G plays an important role in substrate recognition and/or ribonucleolytic action.

Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

PubMed

Maus, Irena; Kim, Yong Sung; Wibberg, Daniel; Stolze, Yvonne; Off, Sandra; Antonczyk, Sebastian; Pühler, Alfred; Scherer, Paul; Schlüter, Andreas

2017-02-28

Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic autofluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality. In this study, four different BGPs were investigated. The results indicated stable process performance in the mesophilic BGPs and in the thermophilic reactor. Bacterial subcommunity characterization revealed significant differences between the four BGPs. Most remarkably, the genera Defluviitoga and Halocella dominated the thermophilic bacterial subcommunity, whereas members of another taxon, Syntrophaceticus , were found to be abundant in the mesophilic BGP. The domain Archaea was dominated by the genus Methanoculleus in all four BGPs, followed by Methanosaeta in BGP1 and BGP3. In contrast, Methanothermobacter members were highly abundant in the thermophilic BGP4. Furthermore, a high consistency between the sequencing approach and the QMF method was shown, especially for the thermophilic BGP. The differences elucidated that using this biphasic approach for mesophilic BGPs provided novel insights regarding disaggregated single cells of Methanosarcina and Methanosaeta species. Both dominated the archaeal subcommunity and replaced coccoid Methanoculleus members belonging to the same group of Methanomicrobiales that have been frequently observed in similar BGPs. This work demonstrates that combining QMF and 16S rRNA gene amplicon sequencing is a complementary strategy to describe archaeal community structures within biogas processes.

Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

NASA Astrophysics Data System (ADS)

Antonielli, Livio; Sessitsch, Angela

2016-04-01

Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

Improving perioperative performance: the use of operations management and the electronic health record.

PubMed

Foglia, Robert P; Alder, Adam C; Ruiz, Gardito

2013-01-01

Perioperative services require the orchestration of multiple staff, space and equipment. Our aim was to identify whether the implementation of operations management and an electronic health record (EHR) improved perioperative performance. We compared 2006, pre operations management and EHR implementation, to 2010, post implementation. Operations management consisted of: communication to staff of perioperative vision and metrics, obtaining credible data and analysis, and the implementation of performance improvement processes. The EHR allows: identification of delays and the accountable service or person, collection and collation of data for analysis in multiple venues, including operational, financial, and quality. Metrics assessed included: operative cases, first case on time starts; reason for delay, and operating revenue. In 2006, 19,148 operations were performed (13,545 in the Main Operating Room (OR) area, and 5603, at satellite locations); first case on time starts were 12%; reasons for first case delay were not identifiable; and operating revenue was $115.8M overall, with $78.1M in the Main OR area. In 2010, cases increased to 25,856 (+35%); Main OR area increased to 13,986 (+3%); first case on time starts improved to 46%; operations outside the Main OR area increased to 11,870 (112%); case delays were ascribed to nurses 7%, anesthesiologists 22%, surgeons 33%, and other (patient, hospital) 38%. Five surgeons (7%) accounted for 29% of surgical delays and 4 anesthesiologists (8%) for 45% of anesthesiology delays; operating revenue increased to $177.3M (+53%) overall, and in the Main OR area rose to $101.5M (+30%). The use of operations management and EHR resulted in improved processes, credible data, promptly sharing the metrics, and pinpointing individual provider performance. Implementation of these strategies allowed us to shift cases between facilities, reallocate OR blocks, increase first case on time starts four fold and operative cases by 35%, and these changes were associated with a 53% increase in operating revenue. The fact that revenue increase was greater than case volume (53% vs. 35%) speaks for improved performance. Copyright © 2013 Elsevier Inc. All rights reserved.

Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome.

PubMed

Pontvianne, Frédéric; Carpentier, Marie-Christine; Durut, Nathalie; Pavlištová, Veronika; Jaške, Karin; Schořová, Šárka; Parrinello, Hugues; Rohmer, Marine; Pikaard, Craig S; Fojtová, Miloslava; Fajkus, Jiří; Sáez-Vásquez, Julio

2016-08-09

The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS) and identified nucleolus-associated chromatin domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Cognitive stimulation therapy (CST): neuropsychological mechanisms of change.

PubMed

Hall, Louise; Orrell, Martin; Stott, Joshua; Spector, Aimee

2013-03-01

Cognitive stimulation therapy (CST) is an evidence-based psychosocial intervention for people with dementia consisting of 14 group sessions aiming to stimulate various areas of cognition. This study examined the effects of CST on specific cognitive domains and explored the neuropsychological processes underpinning any effects. A total of 34 participants with mild to moderate dementia were included. A one-group pretest-posttest design was used. Participants completed a battery of neuropsychological tests in the week before and after the manualised seven-week CST programme. There were significant improvement pre- to post-CST group on measures of delayed verbal recall (WMS III logical memory subtest - delayed), visual memory (WMS III visual reproduction subtest - delayed), orientation (WMS III information and orientation subscale), and auditory comprehension (Token Test). There were no significant changes on measures of naming (Boston Naming Test-2), attention (Trail Making Test A/Digit Span), executive function (DKEFS verbal fluency/Trail Making Test B), praxis (WMS III visual reproduction - immediate) or on a general cognitive screen (MMSE). Memory, comprehension of syntax, and orientation appear to be the cognitive domains most impacted by CST. One hypothesis is that the language-based nature of CST enhances neural pathways responsible for processing of syntax, possibly also aiding verbal recall. Another is that the reduction in negative self-stereotypes due to the de-stigmatising effect of CST may impact on language and memory, domains that are the primary focus of CST. Further research is required to substantiate these hypotheses.

Analysis of STAT laboratory turnaround times before and after conversion of the hospital information system.

PubMed

Lowe, Gary R; Griffin, Yolanda; Hart, Michael D

2014-08-01

Modern electronic health record systems (EHRS) reportedly offer advantages including improved quality, error prevention, cost reduction, and increased efficiency. This project reviewed the impact on specimen turnaround times (TAT) and percent compliance for specimens processed in a STAT laboratory after implementation of an upgraded EHRS. Before EHRS implementation, laboratory personnel received instruction and training for specimen processing. One laboratory member per shift received additional training. TAT and percent compliance data sampling occurred 4 times monthly for 13 months post-conversion and were compared with the mean of data collected for 3 months pre-conversion. Percent compliance was gauged using a benchmark of reporting 95% of all specimens within 7 min from receipt. Control charts were constructed for TAT and percent compliance with control limits set at 2 SD and applied continuously through the data collection period. TAT recovered to pre-conversion levels by the 6th month post-conversion. Percent compliance consistently returned to pre-conversion levels by the 10th month post-conversion. Statistical analyses revealed the TAT were significantly longer for 3 months post-conversion (P < .001) compared with pre-conversion levels. Statistical significance was not observed for subsequent groups. Percent compliance results were significantly lower for 6 months post-conversion (P < .001). Statistical significance was not observed for subsequent groups. Extensive efforts were made to train and prepare personnel for challenges expected after the EHRS upgrade. Specific causes identified with the upgraded EHRS included multiple issues involving personnel and the EHRS. These data suggest that system and user issues contributed to delays in returning to pre-conversion TAT and percent compliance levels following the upgrade in the EHRS.

Clinorotation influences rDNA and NopA100 localization in nucleoli

NASA Astrophysics Data System (ADS)

Sobol, M. A.; González-Camacho, F.; Rodríguez-Vilariño, V.; Kordyum, E. L.; Medina, F. J.

The nucleolus is the transcription site of rRNA genes as well as the site of processing and initial packaging of their transcripts. The plant nucleolin homologue NopA100 is involved in the regulation of r-chromatin condensation/expansion and rDNA transcription as well as in rRNA processing. We have investigated with immunogold electron microscopy the location of nucleolar DNA and NopA100 in cress root meristematic cells grown under slow horizontal clinorotation, reproducing an important feature of microgravity, namely the absence of an orienting action of a gravity vector, compared to control conditions. We demonstrate redistribution of both rDNA and NopA100 in nucleolar subcomponents induced by clinorotation. Ribosomal DNA concentrated predominantly in fibrillar centers in the form of condensed r-chromatin inclusions and internal non condensed fibrils, redistributing from the dense fibrillar component and the transition zone between fibrillar centers and the dense fibrillar component, recognized as the loci of rDNA transcription. The content of NopA100 was much higher in the inner space of fibrillar centers and reduced in the dense fibrillar component as compared to the control. Based on these data, an effect of slow horizontal clinorotation in lowering the level of rDNA transcription as well as rRNA processing is suggested.

The origin of the 5S ribosomal RNA molecule could have been caused by a single inverse duplication: strong evidence from its sequences.

PubMed

Branciamore, Sergio; Di Giulio, Massimo

2012-04-01

The secondary structure of the 5S ribosomal RNA (5S rRNA) molecule shows a high degree of symmetry. In order to explain the origin of this symmetry, it has been conjectured that one half of the 5S rRNA molecule was its precursor and that an indirect duplication of this precursor created the other half and thus the current symmetry of the molecule. Here, we have subjected to an empirical test both the indirect duplication model, analysing a total of 684 5S rRNA sequences for complementarity between the two halves of the 5S rRNA, and the direct duplication model analysing in this case the similarity between the two halves of this molecule. In intra- and inter-molecule and intra- and inter-domain comparisons, we find a high statistical support to the hypothesis of a complementarity relationship between the two halves of the 5S rRNA molecule, denying vice versa the hypothesis of similarity between these halves. Therefore, these observations corroborate the indirect duplication model at the expense of the direct duplication model, as reason of the origin of the 5S rRNA molecule. More generally, we discuss and favour the hypothesis that all RNAs and proteins, which present symmetry, did so through gene duplication and not by gradualistic accumulation of few monomers or segments of molecule into a gradualistic growth process. This would be the consequence of the very high propensity that nucleic acids have to be subjected to duplications.

Dual Role of a SAS10/C1D Family Protein in Ribosomal RNA Gene Expression and Processing Is Essential for Reproduction in Arabidopsis thaliana

PubMed Central

Chen, Ying-Jiun C.; Wang, Huei-Jing

2016-01-01

In eukaryotic cells, ribosomal RNAs (rRNAs) are transcribed, processed, and assembled with ribosomal proteins in the nucleolus. Regulatory mechanisms of rRNA gene (rDNA) transcription and processing remain elusive in plants, especially their connection to nucleolar organization. We performed an in silico screen for essential genes of unknown function in Arabidopsis thaliana and identified Thallo (THAL) encoding a SAS10/C1D family protein. THAL disruption caused enlarged nucleoli in arrested embryos, aberrant processing of precursor rRNAs at the 5’ External Transcribed Spacer, and repression of the major rDNA variant (VAR1). THAL overexpression lines showed de-repression of VAR1 and overall reversed effects on rRNA processing sites. Strikingly, THAL overexpression also induced formation of multiple nucleoli per nucleus phenotypic of mutants of heterochromatin factors. THAL physically associated with histone chaperone Nucleolin 1 (NUC1), histone-binding NUC2, and histone demethylase Jumonji 14 (JMJ14) in bimolecular fluorescence complementation assay, suggesting that it participates in chromatin regulation. Furthermore, investigation of truncated THAL proteins revealed that the SAS10 C-terminal domain is likely important for its function in chromatin configuration. THAL also interacted with putative Small Subunit processome components, including previously unreported Arabidopsis homologue of yeast M Phase Phosphoprotein 10 (MPP10). Our results uncovering the dual role of THAL in transcription and processing events critical for proper rRNA biogenesis and nucleolar organization during reproduction are the first to define the function of SAS10/C1D family members in plants. PMID:27792779

In-Field Spatial Variability in the Degradation of the Phenyl-Urea Herbicide Isoproturon Is the Result of Interactions between Degradative Sphingomonas spp. and Soil pH

PubMed Central

Bending, Gary D.; Lincoln, Suzanne D.; Sørensen, Sebastian R.; Morgan, J. Alun W.; Aamand, Jens; Walker, Allan

2003-01-01

Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the Sphingomonas group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the Sphingomonas group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading Sphingomonas sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of Sphingomonas spp. could largely account for the spatial variation of IPU degradation rates across the field. PMID:12571001

Dissociating the Role of the pre-SMA in Response Inhibition and Switching: A Combined Online and Offline TMS Approach

PubMed Central

Obeso, Ignacio; Robles, Noemí; Marrón, Elena M.; Redolar-Ripoll, Diego

2013-01-01

The pre-supplementary motor area (pre-SMA) is considered to be a key node in the cognitive control of actions that require rapid updating, inhibition, or switching, as well as working memory. It is now recognized that the pre-SMA is part of a “cognitive control” network involving the inferior frontal gyrus (IFG) and subcortical regions, such as the striatum and subthalamic nucleus. However, two important questions remain to be addressed. First, it is not clear if the main role of the pre-SMA in cognitive control lies in inhibition or switching of actions. From imaging evidence, the right pre-SMA is consistently recruited during inhibition and switching, but the extent to which it participates specifically in either of these processes is unknown. Secondly, the pre-SMA may perform inhibition and switching alone or as part of a larger brain network. The present study used online and offline transcranial magnetic stimulation (TMS) to dissociate the roles of pre-SMA in cognitive control, but also to investigate the potential contribution of connectivity between the pre-SMA and IFG. We applied continuous theta burst stimulation (cTBS) over the right IFG before participants performed a stop switching task while receiving single TMS pulses over the right pre-SMA. The results were compared to a sham cTBS session and pulses applied over the vertex region. Significant worsening of inhibition as well as response adaptation during inhibition was found when applying pulses over the pre-SMA. However, no such worsening was observed in switch trials. Additionally, after cTBS over the IFG, inhibition was also delayed, suggesting its critical necessity in stopping of actions. The results reveal a key contribution of the pre-SMA in inhibition and could suggest a dissociative role in the switching of actions. These findings indicate there is an essential union between IFG and pre-SMA during inhibition. PMID:23616761

Expression profile of Rab5, Rab7, tryptophan aspartate-containing coat protein, leprae lipoarabinomannan, and phenolic glycolipid-1 on the failure of the phagolysosome process in macrophages of leprosy patients as a viability marker of Mycobacterium leprae.

PubMed

Prakoeswa, Cita Rosita Sigit; Wahyuni, Ratna; Iswahyudi; Adriaty, Dinar; Yusuf, Irawan; Sutjipto; Agusni, Indropo; Izumi, Shinzo

2016-06-01

Phagolysosome process in macrophage of leprosy patients' is important in the early phase of eliminating Mycobacterium leprae invasion. This study was to clarify the involvement of Rab5, Rab7, and trytophan aspartate-containing coat protein (TACO) from host macrophage and leprae lipoarabinomannan (Lep-LAM) and phenolic glycolipid-1 (PGL-1) from M. leprae cell wall as the reflection of phagolysosome process in relation to 16 subunit ribosomal RNA (16S rRNA) M. leprae as a marker of viability of M. leprae. Using a cross sectional design study, skin biopsies were obtained from 47 newly diagnosed, untreated leprosy at Dr Soetomo Hospital, Surabaya, Indonesia. RNA isolation and complementary DNA synthesis were performed. Samples were divided into two groups: 16S rRNA M. leprae-positive and 16S rRNA M. leprae-negative. The expressions of Rab5, Rab7, TACO, Lep-LAM, and PGL-1 were assessed with an immunohistochemistry technique. Using Mann-Whitney U analysis, a significant difference in the expression profile of Rab5, Rab7, Lep-LAM, and PGL-1 was found (p<.05), but there was no significant difference of TACO between the two groups (p>.05). Spearman analysis revealed that there was a significant correlation between the score of Rab5, Rab7, Lep-LAM, and PGL-1 and the score of 16S rRNA M. leprae (p<.05). In M. leprae infection, Rab5, Rab7, and Lep-LAM play important roles in the failure of phagolysosome process via a membrane trafficking pathway, while PGL-1 plays a role via blocking lysosomal activities. These inventions might be used for the development of an early diagnostic device in the future. Copyright © 2016 Asian-African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem.

PubMed

Brazelton, William J; Schrenk, Matthew O; Kelley, Deborah S; Baross, John A

2006-09-01

Hydrothermal venting and the formation of carbonate chimneys in the Lost City hydrothermal field (LCHF) are driven predominantly by serpentinization reactions and cooling of mantle rocks, resulting in a highly reducing, high-pH environment with abundant dissolved hydrogen and methane. Phylogenetic and terminal restriction fragment length polymorphism analyses of 16S rRNA genes in fluids and carbonate material from this site indicate the presence of organisms similar to sulfur-oxidizing, sulfate-reducing, and methane-oxidizing Bacteria as well as methanogenic and anaerobic methane-oxidizing Archaea. The presence of these metabolic groups indicates that microbial cycling of sulfur and methane may be the dominant biogeochemical processes active within this ultramafic rock-hosted environment. 16S rRNA gene sequences grouping within the Methylobacter and Thiomicrospira clades were recovered from a chemically diverse suite of carbonate chimney and fluid samples. In contrast, 16S rRNA genes corresponding to the Lost City Methanosarcinales phylotype were found exclusively in high-temperature chimneys, while a phylotype of anaerobic methanotrophic Archaea (ANME-1) was restricted to lower-temperature, less vigorously venting sites. A hyperthermophilic habitat beneath the LCHF may be reflected by 16S rRNA gene sequences belonging to Thermococcales and uncultured Crenarchaeota identified in vent fluids. The finding of a diverse microbial ecosystem supported by the interaction of high-temperature, high-pH fluids resulting from serpentinization reactions in the subsurface provides insight into the biogeochemistry of what may be a pervasive process in ultramafic subseafloor environments.

Word Recognition and Cognitive Profiles of Chinese Pre-School Children at Risk for Dyslexia through Language Delay or Familial History of Dyslexia

ERIC Educational Resources Information Center

McBride-Chang, Catherine; Lam, Fanny; Lam, Catherine; Doo, Sylvia; Wong, Simpson W. L.; Chow, Yvonne Y. Y.

2008-01-01

Background: This study sought to identify cognitive abilities that might distinguish Hong Kong Chinese kindergarten children at risk for dyslexia through either language delay or familial history of dyslexia from children who were not at risk and to examine how these abilities were associated with Chinese word recognition. The cognitive skills of…

Assessing the Effects of the "McGraw Hill Phonemic Awareness" Program with Preschool Children with Developmental Delays: A Case Study

ERIC Educational Resources Information Center

Isakson, Lisa; Marchand-Martella, Nancy; Martella, Ronald C.

2011-01-01

This study assessed the effects of "McGraw Hill Phonemic Awareness" on the phonemic awareness skills of 5 preschool children with developmental delays. The children received 60 of the 110 lessons included in this program over 5 months. They were pre- and posttested using the kindergarten level Initial Sound Fluency and Phoneme…

40 CFR 63.140 - Process wastewater provisions-delay of repair.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 10 2014-07-01 2014-07-01 false Process wastewater provisions-delay of... Manufacturing Industry for Process Vents, Storage Vessels, Transfer Operations, and Wastewater § 63.140 Process wastewater provisions—delay of repair. (a) Delay of repair of equipment for which a control equipment failure...

40 CFR 63.140 - Process wastewater provisions-delay of repair.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 10 2012-07-01 2012-07-01 false Process wastewater provisions-delay of... Manufacturing Industry for Process Vents, Storage Vessels, Transfer Operations, and Wastewater § 63.140 Process wastewater provisions—delay of repair. (a) Delay of repair of equipment for which a control equipment failure...

40 CFR 63.140 - Process wastewater provisions-delay of repair.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 9 2011-07-01 2011-07-01 false Process wastewater provisions-delay of... Manufacturing Industry for Process Vents, Storage Vessels, Transfer Operations, and Wastewater § 63.140 Process wastewater provisions—delay of repair. (a) Delay of repair of equipment for which a control equipment failure...

40 CFR 63.140 - Process wastewater provisions-delay of repair.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 10 2013-07-01 2013-07-01 false Process wastewater provisions-delay of... Manufacturing Industry for Process Vents, Storage Vessels, Transfer Operations, and Wastewater § 63.140 Process wastewater provisions—delay of repair. (a) Delay of repair of equipment for which a control equipment failure...

Parents' and speech and language therapists' explanatory models of language development, language delay and intervention.

PubMed

Marshall, Julie; Goldbart, Juliet; Phillips, Julie

2007-01-01

Parental and speech and language therapist (SLT) explanatory models may affect engagement with speech and language therapy, but there has been dearth of research in this area. This study investigated parents' and SLTs' views about language development, delay and intervention in pre-school children with language delay. The aims were to describe, explore and explain the thoughts, understandings, perceptions, beliefs, knowledge and feelings held by: a group of parents from East Manchester, UK, whose pre-school children had been referred with suspected language delay; and SLTs working in the same area, in relation to language development, language delay and language intervention. A total of 24 unstructured interviews were carried out: 15 with parents whose children had been referred for speech and language therapy and nine with SLTs who worked with pre-school children. The interviews were transcribed verbatim and coded using Atlas/ti. The data were analysed, subjected to respondent validation, and grounded theories and principled descriptions developed to explain and describe parents' and SLTs' beliefs and views. Parent and SLT data are presented separately. There are commonalities and differences between the parents and the SLTs. Both groups believe that language development and delay are influenced by both external and internal factors. Parents give more weight to the role of gender, imitation and personality and value television and videos, whereas the SLTs value the 'right environment' and listening skills and consider that health/disability and socio-economic factors are important. Parents see themselves as experts on their child and have varied ideas about the role of SLTs, which do not always accord with SLTs' views. The parents and SLTs differ in their views of the roles of imitation and play in intervention. Parents typically try strategies before seeing an SLT. These data suggest that parents' ideas vary and that, although parents and SLTs may share some views, there are some important differences. These views have implications for the provision of appropriate services. Although this is a small sample from one group in the UK, the results indicate the need to investigate the views of other groups of parents.

Systemic delay propagation in the US airport network

PubMed Central

Fleurquin, Pablo; Ramasco, José J.; Eguiluz, Victor M.

2013-01-01

Technologically driven transport systems are characterized by a networked structure connecting operation centers and by a dynamics ruled by pre-established schedules. Schedules impose serious constraints on the timing of the operations, condition the allocation of resources and define a baseline to assess system performance. Here we study the performance of an air transportation system in terms of delays. Technical, operational or meteorological issues affecting some flights give rise to primary delays. When operations continue, such delays can propagate, magnify and eventually involve a significant part of the network. We define metrics able to quantify the level of network congestion and introduce a model that reproduces the delay propagation patterns observed in the U.S. performance data. Our results indicate that there is a non-negligible risk of systemic instability even under normal operating conditions. We also identify passenger and crew connectivity as the most relevant internal factor contributing to delay spreading. PMID:23362459

Enhanced water window x-ray emission from in situ formed carbon clusters irradiated by intense ultra-short laser pulses

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

Chakravarty, U.; Rao, B. S.; Arora, V.

Enhanced water window x-ray emission (23–44 Å) from carbon clusters, formed in situ using a pre-pulse, irradiated by intense (I > 10{sup 17} W/cm{sup 2}) ultra-short laser pulse, is demonstrated. An order of magnitude x-ray enhancement over planar graphite target is observed in carbon clusters, formed by a sub-ns pre-pulse, interacting with intense main pulse after a delay. The effect of the delay and the duration of the main pulse is studied for optimizing the x-ray emission in the water window region. This x-ray source has added advantages of being an efficient, high repetition rate, and low debris x-ray source.

Pre-operative urinary tract infection: is it a risk factor for early surgical site infection with hip fracture surgery? A retrospective analysis.

PubMed

Yassa, Rafik Rd; Khalfaoui, Mahdi Y; Veravalli, Karunakar; Evans, D Alun

2017-03-01

The aims of the current study were to determine whether pre-operative urinary tract infections in patients presenting acutely with neck of femur fractures resulted in a delay to surgery and whether such patients were at increased risk of developing post-operative surgical site infections. A retrospective review of all patients presenting with a neck of femur fracture, at a single centre over a one-year period. The hospital hip fracture database was used as the main source of data. UK University Teaching Hospital. All patients ( n  = 460) presenting across a single year study period with a confirmed hip fracture. The presence of pre-operative urinary tract infection, the timing of surgical intervention, the occurrence of post-operative surgical site infection and the pathogens identified. A total of 367 patients were operated upon within 24 hours of admission. Urinary infections were the least common cause of delay. A total of 99 patients (21.5%) had pre-operative urinary tract infection. Post-operatively, a total of 57 (12.4%) patients developed a surgical site infection. Among the latter, 31 (54.4%) did not have a pre-operative urinary infection, 23 (40.4%) patients had a pre-operative urinary tract infection, 2 had chronic leg ulcers and one patient had a pre-operative chest infection. Statistically, there was a strong relationship between pre-operative urinary tract infection and the development of post-operative surgical site infection ( p -value: 0.0005). The results of our study indicate that pre-operative urinary tract infection has a high prevalence amongst those presenting with neck of femur fractures, and this is a risk factor for the later development of post-operative surgical site infection.

5SRNAdb: an information resource for 5S ribosomal RNAs.

PubMed

Szymanski, Maciej; Zielezinski, Andrzej; Barciszewski, Jan; Erdmann, Volker A; Karlowski, Wojciech M

2016-01-04

Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA-protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analysis of vaccination status of preschool children in Teresina (PI), Brazil.

PubMed

Fernandes, Ana Catharina Nunes; Gomes, Keila Rejane Oliveira; de Araújo, Telma Maria Evangelista; Moreira-Araújo, Regilda Saraiva dos Reis

2015-01-01

Immunization is a priority action of the Ministry of Health for contributing to reducing child mortality; however, studies show increased vaccination delays and non-vaccination. This study aims to analyze the immunization status of preschool children in Teresina - PI. Cross-sectional study involving 542 children, aged 2-6 years, enrolled in local public schools in four Municipal Childhood Education Centers selected at random, following the proportional division by regions of the city. Data were collected through a pre-coded and pre-tested form, in addition to scanning the children's vaccination card. For univariate descriptive statistical analysis, Pearson's χ2 Test and Fisher's Exact Test were used, and for multivariate analysis, multiple logistic regression was conducted using SPSS version 17.0. The study complied with the ethical aspects in accordance with current legislation. The frequency of delayed vaccination/non-vaccination was 24.9%. The average of non-administered vaccines was 1.7 (SD ± 1.2) and of delayed vaccines was 3.3 (SD ± 1.6). The binomial logistic regression model showed a significant association (p < 0.05) between young caregivers (under 24 years) and low frequency in childcare consultations with delayed vaccination/non-vaccination. There was no association with the variables related to the experience of children in the vaccination room and with the implementation of the Family Health Strategy. Ensuring and strengthening primary healthcare actions are essential tools to reduce non-vaccination and vaccine delays. Professionals who care for children in vaccination rooms need to sensitize themselves to guide and encourage parents/caregivers to meet the vaccination schedules without delays or errors.

Dynamics and three-dimensional localization of ribosomal RNA within the nucleolus.

PubMed Central

Thiry, M; Cheutin, T; O'Donohue, M F; Kaplan, H; Ploton, D

2000-01-01

Although rRNA synthesis, maturation, and assembly into preribosomal particles occur within the nucleolus, the route taken by pre-rRNAs from their synthetic sites toward the cytoplasm remains largely unexplored. Here, we employed a nondestructive method for the incorporation of BrUTP into the RNA of living cells. By using pulse-chase experiments, three-dimensional image reconstructions of confocal optical sections, and electron microscopy analysis of ultrathin sections, we were able to describe topological and spatial dynamics of rRNAs within the nucleolus. We identified the precise location and the volumic organization of four typical subdomains, in which rRNAs are successively moving towards the nucleolar periphery during their synthesis and processing steps. The incorporation of BrUTP takes place simultaneously within several tiny spheres, centered on the fibrillar centers. Then, the structures containing the newly synthesized RNAs enlarge and appear as compact ringlets disposed around the fibrillar centers. Later, they form hollow spheres surrounding the latter components and begin to fuse together. Finally, these structures widen and form large rings reaching the limits of the nucleoli. These results clearly show that the transport of pre-rRNAs within the nucleolus does not occur randomly, but appears as a radial flow starting from the fibrillar centers that form concentric rings, which finally fuse together as they progress toward the nucleolar periphery. PMID:11142375

The methane production of poultry slaughtering residues and effects of pre-treatments on the methane production of poultry feather.

PubMed

Salminen, E; Einola, J; Rintala, J

2003-09-01

The biological methane production rate and yield of different poultry slaughtering residues were studied. Poultry offal, blood, and bonemeal were rich in proteins and lipids and showed high methane yields, 0.7-0.9, 0.5, and 0.6-0.7 m3 kg(-1) volatile solids(added), respectively (270-340, 100, and 150-170 m3 ton(-1) wet weight). Blood and bonemeal produced methane rapidly, whereas the methane production of offal was more delayed probably due to long-chain fatty acid inhibition. The length of delay depended on the source and concentration of inoculum and incubation temperature, sewage sludge at 35 degrees C having the shortest delay of a few days, while granular sludge did not produce methane within 94 days of incubation. Feather showed a somewhat lower methane yield, 0.21 m3 kg(-1) volatile solids(added) (50 m3 ton(-1) wet weight). Combined thermal (120 degrees C, 5 min) and enzymatic (commercial alkaline endopeptidase, 2-10 g l(-1)) pre-treatments increased its methane yield by 37 to 51%. Thermal (70-120 degrees C, 5-60 min), chemical (NaOH 2-10 g l(-1), 2-24 h), and enzymatic pre-treatments were less effective, with methane yield increasing by 5 to 32%. Based on the present results, anaerobic digestion of the studied poultry slaughtering residues appears a promising possibility because of the high methane yield and nitrogen content of these residues (8 to 14% N of total solids), whereas pre-treatments were shown to improve the methane production of feather.

Early onset of industrial-era warming across the oceans and continents.

PubMed

Abram, Nerilie J; McGregor, Helen V; Tierney, Jessica E; Evans, Michael N; McKay, Nicholas P; Kaufman, Darrell S

2016-08-25

The evolution of industrial-era warming across the continents and oceans provides a context for future climate change and is important for determining climate sensitivity and the processes that control regional warming. Here we use post-ad 1500 palaeoclimate records to show that sustained industrial-era warming of the tropical oceans first developed during the mid-nineteenth century and was nearly synchronous with Northern Hemisphere continental warming. The early onset of sustained, significant warming in palaeoclimate records and model simulations suggests that greenhouse forcing of industrial-era warming commenced as early as the mid-nineteenth century and included an enhanced equatorial ocean response mechanism. The development of Southern Hemisphere warming is delayed in reconstructions, but this apparent delay is not reproduced in climate simulations. Our findings imply that instrumental records are too short to comprehensively assess anthropogenic climate change and that, in some regions, about 180 years of industrial-era warming has already caused surface temperatures to emerge above pre-industrial values, even when taking natural variability into account.

A Role of Oral Bacteria in Bisphosphonate-induced Osteonecrosis of the Jaw

PubMed Central

Mawardi, H.; Giro, G.; Kajiya, M.; Ohta, K.; Almazrooa, S.; Alshwaimi, E.; Woo, S.-B.; Nishimura, I.; Kawai, T.

2011-01-01

No consensus has yet been reached to associate oral bacteria conclusively with the etio-pathogenesis of bisphosphonate-induced osteonecrosis of the jaw (BONJ). Therefore, the present study examined the effects of oral bacteria on the development of BONJ-like lesions in a mouse model. In the pamidronate (Pam)-treated mice, but not control non-drug-treated mice, tooth extraction followed by oral infection with Fusobacterium nucleatum caused BONJ-like lesions and delayed epithelial healing, both of which were completely suppressed by a broad-spectrum antibiotic cocktail. Furthermore, in both in vitro and in vivo experiments, the combination of Pam and Fusobacterium nucleatum caused the death of gingival fibroblasts (GFs) and down-regulated their production of keratinocyte growth factor (KGF), which induces epithelial cell growth and migration. Therefore, in periodontal tissues pre-exposed to bisphosphonate, bacterial infection at tooth extraction sites caused diminished KGF expression in GFs, leading to a delay in the epithelial wound-healing process that was mitigated by antibiotics. PMID:21921248

Dynamics of a pre-lens tear film after a blink: Model, evolution, and rupture

NASA Astrophysics Data System (ADS)

Usha, R.; Anjalaiah, Sanyasiraju, Y. V. S. S.

2013-11-01

A mathematical model is developed to investigate the dynamics and rupture of a pre-lens tear film on a contact lens. The contact lens is modeled as a saturated porous medium of constant, finite thickness and is described by the Darcy-Brinkman equations with stress-jump condition at the interface. The model incorporates the influence of capillarity, gravitational drainage, contact lens properties such as the permeability, the porosity, and the thickness of the contact lens on the evolution and rupture of a pre-lens tear film, when the eyelid has opened after a blink. Two models are derived for the evolution of a pre-lens tear film thickness using lubrication theory and are solved numerically; the first uses shear-free surface condition and the second, the tangentially immobile free surface condition. The results reveal that life span of a pre-lens tear film is longer on a thinner contact lens for all values of permeability and porosity parameter considered. An increase in permeability of contact lens, porosity or stress-jump parameter increases the rate of thinning of the film and advances the rupture time. The viscous-viscous interaction between the porous contact lens and the pre-lens tear film increases the resistance offered by the frictional forces to the rate of thinning of pre-lens tear film. This slows down the thinning process and hence delays the rupture of the film as compared to that predicted by the models of Nong and Anderson [SIAM. J. Appl. Math. 70, 2771-2795 (2010)] derived in the framework of Darcy model.

The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot.

PubMed

Sardana, Richa; Liu, Xin; Granneman, Sander; Zhu, Jieyi; Gill, Michael; Papoulas, Ophelia; Marcotte, Edward M; Tollervey, David; Correll, Carl C; Johnson, Arlen W

2015-02-01

In eukaryotes, the highly conserved U3 small nucleolar RNA (snoRNA) base-pairs to multiple sites in the pre-ribosomal RNA (pre-rRNA) to promote early cleavage and folding events. Binding of the U3 box A region to the pre-rRNA is mutually exclusive with folding of the central pseudoknot (CPK), a universally conserved rRNA structure of the small ribosomal subunit essential for protein synthesis. Here, we report that the DEAH-box helicase Dhr1 (Ecm16) is responsible for displacing U3. An active site mutant of Dhr1 blocked release of U3 from the pre-ribosome, thereby trapping a pre-40S particle. This particle had not yet achieved its mature structure because it contained U3, pre-rRNA, and a number of early-acting ribosome synthesis factors but noticeably lacked ribosomal proteins (r-proteins) that surround the CPK. Dhr1 was cross-linked in vivo to the pre-rRNA and to U3 sequences flanking regions that base-pair to the pre-rRNA including those that form the CPK. Point mutations in the box A region of U3 suppressed a cold-sensitive mutation of Dhr1, strongly indicating that U3 is an in vivo substrate of Dhr1. To support the conclusions derived from in vivo analysis we showed that Dhr1 unwinds U3-18S duplexes in vitro by using a mechanism reminiscent of DEAD box proteins.

The DEAH-box Helicase Dhr1 Dissociates U3 from the Pre-rRNA to Promote Formation of the Central Pseudoknot

PubMed Central

Granneman, Sander; Zhu, Jieyi; Gill, Michael; Papoulas, Ophelia; Marcotte, Edward M.; Tollervey, David; Correll, Carl C.; Johnson, Arlen W.

2015-01-01

In eukaryotes, the highly conserved U3 small nucleolar RNA (snoRNA) base-pairs to multiple sites in the pre-ribosomal RNA (pre-rRNA) to promote early cleavage and folding events. Binding of the U3 box A region to the pre-rRNA is mutually exclusive with folding of the central pseudoknot (CPK), a universally conserved rRNA structure of the small ribosomal subunit essential for protein synthesis. Here, we report that the DEAH-box helicase Dhr1 (Ecm16) is responsible for displacing U3. An active site mutant of Dhr1 blocked release of U3 from the pre-ribosome, thereby trapping a pre-40S particle. This particle had not yet achieved its mature structure because it contained U3, pre-rRNA, and a number of early-acting ribosome synthesis factors but noticeably lacked ribosomal proteins (r-proteins) that surround the CPK. Dhr1 was cross-linked in vivo to the pre-rRNA and to U3 sequences flanking regions that base-pair to the pre-rRNA including those that form the CPK. Point mutations in the box A region of U3 suppressed a cold-sensitive mutation of Dhr1, strongly indicating that U3 is an in vivo substrate of Dhr1. To support the conclusions derived from in vivo analysis we showed that Dhr1 unwinds U3-18S duplexes in vitro by using a mechanism reminiscent of DEAD box proteins. PMID:25710520

DEAD-Box RNA Helicase Dbp4 Is Required for Small-Subunit Processome Formation and Function

PubMed Central

Soltanieh, Sahar; Osheim, Yvonne N.; Spasov, Krasimir; Trahan, Christian; Beyer, Ann L.

2014-01-01

DEAD-box RNA helicase Dbp4 is required for 18S rRNA synthesis: cellular depletion of Dbp4 impairs the early cleavage reactions of the pre-rRNA and causes U14 small nucleolar RNA (snoRNA) to remain associated with pre-rRNA. Immunoprecipitation experiments (IPs) carried out with whole-cell extracts (WCEs) revealed that hemagglutinin (HA)-tagged Dbp4 is associated with U3 snoRNA but not with U14 snoRNA. IPs with WCEs also showed association with the U3-specific protein Mpp10, which suggests that Dbp4 interacts with the functionally active U3 RNP; this particle, called the small-subunit (SSU) processome, can be observed at the 5′ end of nascent pre-rRNA. Electron microscopy analyses indicated that depletion of Dbp4 compromised SSU processome formation and cotranscriptional cleavage of the pre-rRNA. Sucrose density gradient analyses revealed that depletion of U3 snoRNA or the Mpp10 protein inhibited the release of U14 snoRNA from pre-rRNA, just as was seen with Dbp4-depleted cells, indicating that alteration of SSU processome components has significant consequences for U14 snoRNA dynamics. We also found that the C-terminal extension flanking the catalytic core of Dbp4 plays an important role in the release of U14 snoRNA from pre-rRNA. PMID:25535329

Impact of resistance exercise on ribosome biogenesis is acutely regulated by post-exercise recovery strategies.

PubMed

Figueiredo, Vandré C; Roberts, Llion A; Markworth, James F; Barnett, Matthew P G; Coombes, Jeff S; Raastad, Truls; Peake, Jonathan M; Cameron-Smith, David

2016-02-01

Muscle hypertrophy occurs following increased protein synthesis, which requires activation of the ribosomal complex. Additionally, increased translational capacity via elevated ribosomal RNA (rRNA) synthesis has also been implicated in resistance training-induced skeletal muscle hypertrophy. The time course of ribosome biogenesis following resistance exercise (RE) and the impact exerted by differing recovery strategies remains unknown. In the present study, the activation of transcriptional regulators, the expression levels of pre-rRNA, and mature rRNA components were measured through 48 h after a single-bout RE. In addition, the effects of either low-intensity cycling (active recovery, ACT) or a cold-water immersion (CWI) recovery strategy were compared. Nine male subjects performed two bouts of high-load RE randomized to be followed by 10 min of either ACT or CWI. Muscle biopsies were collected before RE and at 2, 24, and 48 h after RE. RE increased the phosphorylation of the p38-MNK1-eIF4E axis, an effect only evident with ACT recovery. Downstream, cyclin D1 protein, total eIF4E, upstream binding factor 1 (UBF1), and c-Myc proteins were all increased only after RE with ACT. This corresponded with elevated abundance of the pre-rRNAs (45S, ITS-28S, ITS-5.8S, and ETS-18S) from 24 h after RE with ACT. In conclusion, coordinated upstream signaling and activation of transcriptional factors stimulated pre-rRNA expression after RE. CWI, as a recovery strategy, markedly blunted these events, suggesting that suppressed ribosome biogenesis may be one factor contributing to the impaired hypertrophic response observed when CWI is used regularly after exercise. © 2016 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

False Context Fear Memory in Rats

ERIC Educational Resources Information Center

Bae, Sarah; Holmes, Nathan M.; Westbrook, R. Frederick

2015-01-01

Four experiments used rats to study false context fear memories. In Experiment 1, rats were pre-exposed to a distinctive chamber (context A) or to a control environment (context C), shocked after a delay in a second chamber (context B) and tested either in B or A. Rats pre-exposed to A froze just as much as control rats in B but more than control…

Brief Report: The Relationship between Language Skills, Adaptive Behavior, and Emotional and Behavior Problems in Pre-Schoolers with Autism

ERIC Educational Resources Information Center

Park, Carlie J.; Yelland, Gregory W.; Taffe, John R.; Gray, Kylie M.

2012-01-01

This study investigated the relationship between structural language skills, and communication skills, adaptive behavior, and emotional and behavior problems in pre-school children with autism. Participants were aged 3-5 years with autism (n = 27), and two comparison groups of children with developmental delay without autism (n = 12) and typically…

Improving the Quality of Host Country Ethical Oversight of International Research: The Use of a Collaborative 'Pre-Review' Mechanism for a Study of Fexinidazole for Human African Trypanosomiasis.

PubMed

Coleman, Carl H; Ardiot, Chantal; Blesson, Séverine; Bonnin, Yves; Bompart, Francois; Colonna, Pierre; Dhai, Ames; Ecuru, Julius; Edielu, Andrew; Hervé, Christian; Hirsch, François; Kouyaté, Bocar; Mamzer-Bruneel, Marie-France; Maoundé, Dionko; Martinent, Eric; Ntsiba, Honoré; Pelé, Gérard; Quéva, Gilles; Reinmund, Marie-Christine; Sarr, Samba Cor; Sepou, Abdoulaye; Tarral, Antoine; Tetimian, Djetodjide; Valverde, Olaf; Van Nieuwenhove, Simon; Strub-Wourgaft, Nathalie

2015-12-01

Developing countries face numerous barriers to conducting effective and efficient ethics reviews of international collaborative research. In addition to potentially overlooking important scientific and ethical considerations, inadequate or insufficiently trained ethics committees may insist on unwarranted changes to protocols that can impair a study's scientific or ethical validity. Moreover, poorly functioning review systems can impose substantial delays on the commencement of research, which needlessly undermine the development of new interventions for urgent medical needs. In response to these concerns, the Drugs for Neglected Diseases Initiative (DNDi), an independent nonprofit organization founded by a coalition of public sector and international organizations, developed a mechanism to facilitate more effective and efficient host country ethics review for a study of the use of fexinidazole for the treatment of late stage African Trypanosomiasis (HAT). The project involved the implementation of a novel 'pre-review' process of ethical oversight, conducted by an ad hoc committee of ethics committee representatives from African and European countries, in collaboration with internationally recognized scientific experts. This article examines the process and outcomes of this collaborative process. © 2014 The Authors. Developing World Bioethics published by John Wiley & Sons Ltd.

Nonlinear friction dynamics on polymer surface under accelerated movement

NASA Astrophysics Data System (ADS)

Aita, Yuuki; Asanuma, Natsumi; Takahashi, Akira; Mayama, Hiroyuki; Nonomura, Yoshimune

2017-04-01

Nonlinear phenomena on the soft material surface are one of the most exciting topics of chemical physics. However, only a few reports exist on the friction phenomena under accelerated movement, because friction between two solid surfaces is considered a linear phenomenon in many cases. We aim to investigate how nonlinear accelerated motion affects friction on solid surfaces. In the present study, we evaluate the frictional forces between two polytetrafluoroethylene (PTFE) resins using an advanced friction evaluation system. On PTFE surfaces, the normalized delay time δ, which is the time lag in the response of the friction force to the accelerated movement, is observed in the pre-sliding friction process. Under high-velocity conditions, kinetic friction increases with velocity. Based on these experimental results, we propose a two-phase nonlinear model including a pre-sliding process (from the beginning of sliding of a contact probe to the establishment of static friction) and a kinetic friction process. The present model consists of several factors including velocity, acceleration, stiffness, viscosity, and vertical force. The findings reflecting the viscoelastic properties of soft material is useful for various fields such as in the fabrication of clothes, cosmetics, automotive materials, and virtual reality systems as well as for understanding friction phenomena on soft material surfaces.

Ribosome Biogenesis in African Trypanosomes Requires Conserved and Trypanosome-Specific Factors

PubMed Central

Umaer, Khan; Ciganda, Martin

2014-01-01

Large ribosomal subunit protein L5 is responsible for the stability and trafficking of 5S rRNA to the site of eukaryotic ribosomal assembly. In Trypanosoma brucei, in addition to L5, trypanosome-specific proteins P34 and P37 also participate in this process. These two essential proteins form a novel preribosomal particle through interactions with both the ribosomal protein L5 and 5S rRNA. We have generated a procyclic L5 RNA interference cell line and found that L5 itself is a protein essential for trypanosome growth, despite the presence of other 5S rRNA binding proteins. Loss of L5 decreases the levels of all large-subunit rRNAs, 25/28S, 5.8S, and 5S rRNAs, but does not alter small-subunit 18S rRNA. Depletion of L5 specifically reduced the levels of the other large ribosomal proteins, L3 and L11, whereas the steady-state levels of the mRNA for these proteins were increased. L5-knockdown cells showed an increase in the 40S ribosomal subunit and a loss of the 60S ribosomal subunits, 80S monosomes, and polysomes. In addition, L5 was involved in the processing and maturation of precursor rRNAs. Analysis of polysomal fractions revealed that unprocessed rRNA intermediates accumulate in the ribosome when L5 is depleted. Although we previously found that the loss of P34 and P37 does not result in a change in the levels of L5, the loss of L5 resulted in an increase of P34 and P37 proteins, suggesting the presence of a compensatory feedback loop. This study demonstrates that ribosomal protein L5 has conserved functions, in addition to nonconserved trypanosome-specific features, which could be targeted for drug intervention. PMID:24706018

Nucleolus-like bodies of fully-grown mouse oocytes contain key nucleolar proteins but are impoverished for rRNA.

PubMed

Shishova, Kseniya V; Lavrentyeva, Elena A; Dobrucki, Jurek W; Zatsepina, Olga V

2015-01-15

It is well known that fully-grown mammalian oocytes, rather than typical nucleoli, contain prominent but structurally homogenous bodies called "nucleolus-like bodies" (NLBs). NLBs accumulate a vast amount of material, but their biochemical composition and functions remain uncertain. To clarify the composition of the NLB material in mouse GV oocytes, we devised an assay to detect internal oocyte proteins with fluorescein-5-isothiocyanate (FITC) and applied the fluorescent RNA-binding dye acridine orange to examine whether NLBs contain RNA. Our results unequivocally show that, similarly to typical nucleoli, proteins and RNA are major constituents of transcriptionally active (or non-surrounded) NLBs as well as of transcriptionally silent (or surrounded) NLBs. We also show, by exposing fixed oocytes to a mild proteinase K treatment, that the NLB mass in oocytes of both types contains nucleolar proteins that are involved in all major steps of ribosome biogenesis, including rDNA transcription (UBF), early rRNA processing (fibrillarin), and late rRNA processing (NPM1/nucleophosmin/B23, nucleolin/C23), but none of the nuclear proteins tested, including SC35, NOBOX, topoisomerase II beta, HP1α, and H3. The ribosomal RPL26 protein was detected within the NLBs of NSN-type oocytes but is virtually absent from NLBs of SN-type oocytes. Taking into account that the major class of nucleolar RNA is ribosomal RNA (rRNA), we applied fluorescence in situ hybridization with oligonucleotide probes targeting 18S and 28S rRNAs. The results show that, in contrast to active nucleoli, NLBs of fully-grown oocytes are impoverished for the rRNAs, which is consistent with the absence of transcribed ribosomal genes in the NLB mass. Overall, the results of this study suggest that NLBs of fully-grown mammalian oocytes serve for storing major nucleolar proteins but not rRNA. Copyright © 2014 Elsevier Inc. All rights reserved.

The Differential Effects of the Use of Handwriting without Tears® Modified Gray Block Paper to Teach Two Preschool Students with Developmental Delays Capital Letter Writing Skills

ERIC Educational Resources Information Center

Griffith, Jessica; McLaughlin, T. F.; Neyman, Jen; Donica, Denise K.; Robison, Milena

2013-01-01

The purpose of this study was to evaluate and measure the effectiveness of Handwriting Without Tears (HWT) modified gray block paper with letter writing on two preschool students diagnosed with developmental delays in pre-academics. Two students were selected from a self-contained special education preschool classroom in the Pacific Northwest. All…

COURSES OF MISRECALL OVER LONG-TERM RETENTION INTERVALS AS RELATED TO STRENGTH OF PRE-EXPERIMENTAL HABITS OF WORD ASSOCIATION.

ERIC Educational Resources Information Center

BILODEAU, EDWARD A.; BLICK, KENNETH A.

THIS STUDY WAS MADE TO COMPARE THE EFFECTS OF STIMULATION AND NONSTIMULATION ON RECALL OF WORDS FOLLOWING TIME-DELAY PERIODS. THE SUBJECTS (670 AIRMEN) WERE TRAINED WITH AN EXAMPLE WORD LIST AND TWO WORD LISTS CONTAINING FIVE OF THE SECONDARY WORDS ASSOCIATED WITH RUSSELL-JENKINS STIMULUS WORDS. AFTER TIME DELAYS OF 2 MINUTES, 20 MINUTES, 2 DAYS,…

A systematic approach to designing reliable VV optimization methodology: assessment of internal validity of echocardiographic, electrocardiographic and haemodynamic optimization of cardiac resynchronization therapy.

PubMed

Kyriacou, Andreas; Li Kam Wa, Matthew E; Pabari, Punam A; Unsworth, Beth; Baruah, Resham; Willson, Keith; Peters, Nicholas S; Kanagaratnam, Prapa; Hughes, Alun D; Mayet, Jamil; Whinnett, Zachary I; Francis, Darrel P

2013-08-10

In atrial fibrillation (AF), VV optimization of biventricular pacemakers can be examined in isolation. We used this approach to evaluate internal validity of three VV optimization methods by three criteria. Twenty patients (16 men, age 75 ± 7) in AF were optimized, at two paced heart rates, by LVOT VTI (flow), non-invasive arterial pressure, and ECG (minimizing QRS duration). Each optimization method was evaluated for: singularity (unique peak of function), reproducibility of optimum, and biological plausibility of the distribution of optima. The reproducibility (standard deviation of the difference, SDD) of the optimal VV delay was 10 ms for pressure, versus 8 ms (p=ns) for QRS and 34 ms (p<0.01) for flow. Singularity of optimum was 85% for pressure, 63% for ECG and 45% for flow (Chi(2)=10.9, p<0.005). The distribution of pressure optima was biologically plausible, with 80% LV pre-excited (p=0.007). The distributions of ECG (55% LV pre-excitation) and flow (45% LV pre-excitation) optima were no different to random (p=ns). The pressure-derived optimal VV delay is unaffected by the paced rate: SDD between slow and fast heart rate is 9 ms, no different from the reproducibility SDD at both heart rates. Using non-invasive arterial pressure, VV delay optimization by parabolic fitting is achievable with good precision, satisfying all 3 criteria of internal validity. VV optimum is unaffected by heart rate. Neither QRS minimization nor LVOT VTI satisfy all validity criteria, and therefore seem weaker candidate modalities for VV optimization. AF, unlinking interventricular from atrioventricular delay, uniquely exposes resynchronization concepts to experimental scrutiny. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Modeling the influence of the VV delay for CRT on the electrical activation patterns in absence of conduction through the AV node

NASA Astrophysics Data System (ADS)

Romero, D. A.; Sebastián, Rafael; Plank, Gernot; Vigmond, Edward J.; Frangi, Alejandro F.

2008-03-01

From epidemiological studies, it has been shown that 0.2% of men and 0.1% of women suffer from a degree of atrioventricular (AV) block. In recent years, the palliative treatment for third degree AV block has included Cardiac Resynchronization Therapy (CRT). It was found that patients show more clinical improvement in the long term with CRT compared with single chamber devices. Still, an important group of patients does not improve their hemodynamic function as much as could be expected. A better understanding of the basis for optimizing the devices settings (among which the VV delay) will help to increase the number of responders. In this work, a finite element model of the left and right ventricles was generated using an atlas-based approach for their segmentation, which includes fiber orientation. The electrical activity was simulated with the electrophysiological solver CARP, using the Ten Tusscher et al. ionic model for the myocardium, and the DiFrancesco-Noble for Purkinje fibers. The model is representative of a patient without dilated or ischemic cardiomyopathy. The simulation results were analyzed for total activation times and latest activated regions at different VV delays and pre-activations (RV pre-activated, LV pre-activated). To optimize the solution, simulations are compared against the His-Purkinje network activation (normal physiological conduction), and interventricular septum activation (as collision point for the two wave fronts). The results were analyzed using Pearson's coefficient of correlation for point to point comparisons between simulation cases. The results of this study contribute to gain insight on the VV delay and how its adjustment might influence response to CRT and how it can be used to optimize the treatment.

A non-catalytic role for inositol 1,3,4,5,6-pentakisphosphate 2-kinase in the synthesis of ribosomal RNA

PubMed Central

Brehm, Maria A.; Wundenberg, Torsten; Williams, Jason; Mayr, Georg W.; Shears, Stephen B.

2013-01-01

Summary Fundamental to the life and destiny of every cell is the regulation of protein synthesis through ribosome biogenesis, which begins in the nucleolus with the production of ribosomal RNA (rRNA). Nucleolar organization is a highly dynamic and tightly regulated process; the structural factors that direct nucleolar assembly and disassembly are just as important in controlling rRNA synthesis as are the catalytic activities that synthesize rRNA. Here, we report that a signaling enzyme, inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IP5K) is also a structural component in the nucleolus. We demonstrate that IP5K has functionally significant interactions with three proteins that regulate rRNA synthesis: protein kinase CK2, TCOF1 and upstream-binding-factor (UBF). Through molecular modeling and mutagenic studies, we identified an Arg-Lys-Lys tripeptide located on the surface of IP5K that mediates its association with UBF. Nucleolar IP5K spatial dynamics were sensitive to experimental procedures (serum starvation or addition of actinomycin D) that inhibited rRNA production. We show that IP5K makes stoichiometrically sensitive contributions to the architecture of the nucleoli in intact cells, thereby influencing the degree of rRNA synthesis. Our study adds significantly to the biological significance of IP5K; previously, it was the kinase activity of this protein that had attracted attention. Our demonstration that IP5K ‘moonlights’ as a molecular scaffold offers an unexpected new example of how the biological sophistication of higher organisms can arise from gene products acquiring multiple functions, rather than by an increase in gene number. PMID:23203802

A non-catalytic role for inositol 1,3,4,5,6-pentakisphosphate 2-kinase in the synthesis of ribosomal RNA.

PubMed

Brehm, Maria A; Wundenberg, Torsten; Williams, Jason; Mayr, Georg W; Shears, Stephen B

2013-01-15

Fundamental to the life and destiny of every cell is the regulation of protein synthesis through ribosome biogenesis, which begins in the nucleolus with the production of ribosomal RNA (rRNA). Nucleolar organization is a highly dynamic and tightly regulated process; the structural factors that direct nucleolar assembly and disassembly are just as important in controlling rRNA synthesis as are the catalytic activities that synthesize rRNA. Here, we report that a signaling enzyme, inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IP5K) is also a structural component in the nucleolus. We demonstrate that IP5K has functionally significant interactions with three proteins that regulate rRNA synthesis: protein kinase CK2, TCOF1 and upstream-binding-factor (UBF). Through molecular modeling and mutagenic studies, we identified an Arg-Lys-Lys tripeptide located on the surface of IP5K that mediates its association with UBF. Nucleolar IP5K spatial dynamics were sensitive to experimental procedures (serum starvation or addition of actinomycin D) that inhibited rRNA production. We show that IP5K makes stoichiometrically sensitive contributions to the architecture of the nucleoli in intact cells, thereby influencing the degree of rRNA synthesis. Our study adds significantly to the biological significance of IP5K; previously, it was the kinase activity of this protein that had attracted attention. Our demonstration that IP5K 'moonlights' as a molecular scaffold offers an unexpected new example of how the biological sophistication of higher organisms can arise from gene products acquiring multiple functions, rather than by an increase in gene number.

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters

PubMed Central

Wilkins, David; Lu, Xiao-Ying; Shen, Zhiyong; Chen, Jiapeng

2014-01-01

Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the mcrA genes suggested that these digesters were dominated by acetoclastic methanogens, particularly Methanosarcinales, while the other digesters were dominated by hydrogenotrophic Methanomicrobiales. The proposed euryarchaeotal order Methanomassiliicoccales and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential mcrA genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the mcrA gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of mcrA transcripts in digesters treating sludge and wastewater samples, supporting the mcrA gene as a biomarker for methane yield. PMID:25381241

Short-term sleep disturbance-induced stress does not affect basal pain perception, but does delay postsurgical pain recovery

PubMed Central

Wang, Po-Kai; Cao, Jing; Wang, Hongzhen; Liang, Lingli; Zhang, Jun; Lutz, Brianna Marie; Shieh, Kun-Ruey; Bekker, Alex; Tao, Yuan-Xiang

2015-01-01

Chronic sleep disturbance-induced stress is known to increase basal pain sensitivity. However, most surgical patients frequently report short-term sleep disturbance/deprivation during pre- and post-operation periods and have normal pain perception pre-surgery. Whether this short-term sleep disturbance affects postsurgical pain is elusive. We here reported that pre- or post-exposure to rapid eye movement sleep disturbance (REMSD) 6 h daily for 3 consecutive days did not alter basal responses to mechanical, heat, and cold stimuli, but did delay recovery in incision-induced reductions in paw withdrawal threshold to mechanical stimulation and paw withdrawal latencies to heat and cold stimuli on the ipsilateral side of male or female rats. This short-term REMSD led to stress evidenced by an increase in swim immobility time, a decrease in sucrose consumption, and an elevation in the level of corticosterone in serum. Blocking this stress via intrathecal RU38486 or bilateral adrenalectomy abolished REMSD-caused delay in recovery of incision-induced reductions in behavioral responses to mechanical, heat, and cold stimuli. Moreover, this short-term REMSD produced significant reductions in the levels of mu opioid receptor and kappa opioid receptor, but not Kv1.2, in the ipsilateral L4/5 spinal cord and dorsal root ganglia on day 9 post-incision (but not post-sham surgery). PMID:26342649

A randomized controlled trial of high-fidelity simulation versus lecture-based education in preclinical medical students.

PubMed

Alluri, Ram Kiran; Tsing, Pamela; Lee, Edward; Napolitano, Jason

2016-01-01

The purpose of this study was to compare the efficacy of simulation versus lecture-based education among preclinical medical students. Twenty medical students participated in this randomized, controlled crossover study. Students were randomized to four groups. Each group received two simulations and two lectures covering four different topics. Students were administered a pre-test, post-test and delayed post-test. The mean percentage of questions answered correctly on each test was calculated. The mean of each student's change in score across the three tests was used to compare simulation- versus lecture-based education. Students in both the simulation and lecture groups demonstrated improvement between the pre-test and post-test (p < 0.05). Students in the simulation group demonstrated improvement between the immediate post-test and delayed post-test (p < 0.05), while students in the lecture group did not demonstrate improvement (p > 0.05). When comparing interventions, the change in score between the pre-test and post-test was similar among both the groups (p > 0.05). The change in score between the post-test and delayed post-test was greater in the simulation group (p < 0.05). High-fidelity simulation may serve as a viable didactic platform for preclinical medical education. Our study demonstrated equivalent immediate knowledge gain and superior long-term knowledge retention in comparison to lectures.

Response of end tidal CO2 pressure to impulse exercise.

PubMed

Yano, T; Afroundeh, R; Yamanak, R; Arimitsu, T; Lian, C-S; Shirkawa, K; Yunoki, T

2014-03-01

The purpose of the present study was to examine how end tidal CO(2) pressure (PETCO(2)) is controlled in impulse exercise. After pre-exercise at 25 watts for 5 min, impulse exercise for 10 sec with 200 watts followed by post exercise at 25 watts was performed. Ventilation (VE) significantly increased until the end of impulse exercise and significantly re-increased after a sudden decrease. Heart rate (HR) significantly increased until the end of impulse exercise and then decreased to the pre-exercise level. PETCO(2) remained constant during impulse exercise. PETCO(2) significantly increased momentarily after impulse exercise and then significantly decreased to the pre-exercise level. PETCO(2) showed oscillation. The average peak frequency of power spectral density in PETCO(2) appeared at 0.0078 Hz. Cross correlations were obtained after impulse exercise. The peak cross correlations between VE and PETCO(2), HR and PETCO(2), and VE and HR were 0.834 with a time delay of -7 sec, 0.813 with a time delay of 7 sec and 0.701 with a time delay of -15 sec, respectively. We demonstrated that PETCO(2) homeodynamics was interactively maintained by PETCO(2) itself, CO(2) transportation (product of cardiac output and mixed venous CO(2) content) into the lungs by heart pumping and CO(2) elimination by ventilation, and it oscillates as a result of their interactions.

Can we improve the prevention and detection of congenital abnormalities? An audit of early pregnancy care in New Zealand.

PubMed

Arroll, Nicola; Sadler, Lynn; Stone, Peter; Masson, Vicki; Farquhar, Cindy

2013-08-16

To determine whether there were "quality gaps" in the provision of care during pregnancies that resulted in a perinatal death due to congenital abnormality. Perinatal deaths from congenital cardiovascular, central nervous system or chromosomal abnormality in 2010 were identified retrospectively. Data were extracted by retrospective clinical note review and obtained by independent review of ultrasound scans. There were 137 perinatal deaths due to a congenital cardiovascular (35), central nervous system (29) or chromosomal abnormality (73). First contact with a health professional during pregnancy was predominantly with a general practitioner. First contact occurred within 14 weeks in 85% of pregnancies and there was often a significant delay before booking. Folate supplements were taken by 7% pre-conceptually and 54% of women in the antenatal period. There were 20 perinatal deaths from neural tube defects that could potentially have been prevented through the use of pre-conceptual folate. Antenatal screening was offered to 75% of the women who presented prior to 20 weeks and 84% of these undertook at least one of the available antenatal screening tests. Review of ultrasound images found five abnormalities could have been detected earlier. Delay in booking or failure to offer screening early were the most common reasons for delay in diagnosis of screen detectable abnormalities. The preventative value and timing of (pre-conceptual) folate needs emphasis.

Evolution of introns in the archaeal world.

PubMed

Tocchini-Valentini, Giuseppe D; Fruscoloni, Paolo; Tocchini-Valentini, Glauco P

2011-03-22

The self-splicing group I introns are removed by an autocatalytic mechanism that involves a series of transesterification reactions. They require RNA binding proteins to act as chaperones to correctly fold the RNA into an active intermediate structure in vivo. Pre-tRNA introns in Bacteria and in higher eukaryote plastids are typical examples of self-splicing group I introns. By contrast, two striking features characterize RNA splicing in the archaeal world. First, self-splicing group I introns cannot be found, to this date, in that kingdom. Second, the RNA splicing scenario in Archaea is uniform: All introns, whether in pre-tRNA or elsewhere, are removed by tRNA splicing endonucleases. We suggest that in Archaea, the protein recruited for splicing is the preexisting tRNA splicing endonuclease and that this enzyme, together with the ligase, takes over the task of intron removal in a more efficient fashion than the ribozyme. The extinction of group I introns in Archaea would then be a consequence of recruitment of the tRNA splicing endonuclease. We deal here with comparative genome analysis, focusing specifically on the integration of introns into genes coding for 23S rRNA molecules, and how this newly acquired intron has to be removed to regenerate a functional RNA molecule. We show that all known oligomeric structures of the endonuclease can recognize and cleave a ribosomal intron, even when the endonuclease derives from a strain lacking rRNA introns. The persistence of group I introns in mitochondria and chloroplasts would be explained by the inaccessibility of these introns to the endonuclease.

Spotlight-Mode Synthetic Aperture Radar Processing for High-Resolution Lunar Mapping

NASA Technical Reports Server (NTRS)

Harcke, Leif; Weintraub, Lawrence; Yun, Sang-Ho; Dickinson, Richard; Gurrola, Eric; Hensley, Scott; Marechal, Nicholas

2010-01-01

During the 2008-2009 year, the Goldstone Solar System Radar was upgraded to support radar mapping of the lunar poles at 4 m resolution. The finer resolution of the new system and the accompanying migration through resolution cells called for spotlight, rather than delay-Doppler, imaging techniques. A new pre-processing system supports fast-time Doppler removal and motion compensation to a point. Two spotlight imaging techniques which compensate for phase errors due to i) out of focus-plane motion of the radar and ii) local topography, have been implemented and tested. One is based on the polar format algorithm followed by a unique autofocus technique, the other is a full bistatic time-domain backprojection technique. The processing system yields imagery of the specified resolution. Products enabled by this new system include topographic mapping through radar interferometry, and change detection techniques (amplitude and coherent change) for geolocation of the NASA LCROSS mission impact site.

Let it go: the flexible engagement and disengagement of monitoring processes in a non-focal prospective memory task.

PubMed

Cohen, Anna-Lisa; Gordon, Aliza; Jaudas, Alexander; Hefer, Carmen; Dreisbach, Gesine

2017-03-01

Remembering to perform a delayed intention is referred to as prospective memory (PM). In two studies, participants performed an Eriksen flanker task with an embedded PM task (they had to remember to press F1 if a pre-specified cue appeared). In study 1, participants performed a flanker task with either a concurrent PM task or a delayed PM task (instructed to carry out the intention in a later different task). In the delayed PM condition, the PM cues appeared unexpectedly early and we examined whether attention would be captured by the PM cue even though they were not relevant. Results revealed ongoing task costs solely in the concurrent PM condition but no significant task costs in the delayed PM condition showing that attention was not captured by the PM cue when it appeared in an irrelevant context. In study 2, we compared a concurrent PM condition (exactly as in Study 1) to a PM forget condition in which participants were told at a certain point during the flanker task that they no longer had to perform the PM task. Analyses revealed that participants were able to switch off attending to PM cues when instructed to forget the PM task. Results from both studies demonstrate the flexibility of monitoring as evidenced by the presence versus absence of costs in the ongoing flanker task implying that selective attention, like a lens, can be adjusted to attend or ignore, depending on intention relevance.

Geometric pre-patterning based tuning of the period doubling onset strain during thin film wrinkling

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

Saha, Sourabh K.

Wrinkling of supported thin films is an easy-to-implement and low-cost fabrication technique for generation of stretch-tunable periodic micro and nano-scale structures. However, the tunability of such structures is often limited by the emergence of an undesirable period doubled mode at high strains. Predictively tuning the onset strain for period doubling via existing techniques requires one to have extensive knowledge about the nonlinear pattern formation behavior. Herein, a geometric pre-patterning based technique is introduced to delay the onset of period doubling that can be implemented to predictively tune the onset strain even with limited system knowledge. The technique comprises pre-patterning themore » film/base bilayer with a sinusoidal pattern that has the same period as the natural wrinkle period of the system. The effectiveness of this technique has been verified via physical and computational experiments on the polydimethylsiloxane/glass bilayer system. It is observed that the period doubling onset strain can be increased from the typical value of 20% for flat films to greater than 30% with a modest pre-pattern aspect ratio (2∙amplitude/period) of 0.15. In addition, finite element simulations reveal that (i) the onset strain can be increased up to a limit by increasing the amplitude of the pre-patterns and (ii) the delaying effect can be captured entirely by the pre-pattern geometry. As a result, one can implement this technique even with limited system knowledge, such as material properties or film thickness, by simply replicating pre-existing wrinkled patterns to generate prepatterned bilayers. Thus, geometric pre-patterning is a practical scheme to suppress period doubling that can increase the operating range of stretch-tunable wrinkle-based devices by at least 50%.« less

Pre-hospital electrocardiogram triage with telemedicine near halves time to treatment in STEMI: A meta-analysis and meta-regression analysis of non-randomized studies.

PubMed

Brunetti, Natale Daniele; De Gennaro, Luisa; Correale, Michele; Santoro, Francesco; Caldarola, Pasquale; Gaglione, Antonio; Di Biase, Matteo

2017-04-01

A shorter time to treatment has been shown to be associated with lower mortality rates in acute myocardial infarction (AMI). Several strategies have been adopted with the aim to reduce any delay in diagnosis of AMI: pre-hospital triage with telemedicine is one of such strategies. We therefore aimed to measure the real effect of pre-hospital triage with telemedicine in case of AMI in a meta-analysis study. We performed a meta-analysis of non-randomized studies with the aim to quantify the exact reduction of time to treatment achieved by pre-hospital triage with telemedicine. Data were pooled and compared by relative time reduction and 95% C.I.s. A meta-regression analysis was performed in order to find possible predictors of shorter time to treatment. Eleven studies were selected and finally evaluated in the study. The overall relative reduction of time to treatment with pre-hospital triage and telemedicine was -38/-40% (p<0.001). Absolute time reduction was significantly correlated to time to treatment in the control groups (p<0.001), while relative time reduction was independent. A non-significant trend toward shorter relative time reductions was observed over years. Pre-hospital triage with telemedicine is associated with a near halved time to treatment in AMI. The benefit is larger in terms of absolute time to treatment reduction in populations with larger delays to treatment. Copyright © 2017 Elsevier B.V. All rights reserved.

Protein-Protein Interactions within Late Pre-40S Ribosomes

PubMed Central

Campbell, Melody G.; Karbstein, Katrin

2011-01-01

Ribosome assembly in eukaryotic organisms requires more than 200 assembly factors to facilitate and coordinate rRNA transcription, processing, and folding with the binding of the ribosomal proteins. Many of these assembly factors bind and dissociate at defined times giving rise to discrete assembly intermediates, some of which have been partially characterized with regards to their protein and RNA composition. Here, we have analyzed the protein-protein interactions between the seven assembly factors bound to late cytoplasmic pre-40S ribosomes using recombinant proteins in binding assays. Our data show that these factors form two modules: one comprising Enp1 and the export adaptor Ltv1 near the beak structure, and the second comprising the kinase Rio2, the nuclease Nob1, and a regulatory RNA binding protein Dim2/Pno1 on the front of the head. The GTPase-like Tsr1 and the universally conserved methylase Dim1 are also peripherally connected to this second module. Additionally, in an effort to further define the locations for these essential proteins, we have analyzed the interactions between these assembly factors and six ribosomal proteins: Rps0, Rps3, Rps5, Rps14, Rps15 and Rps29. Together, these results and previous RNA-protein crosslinking data allow us to propose a model for the binding sites of these seven assembly factors. Furthermore, our data show that the essential kinase Rio2 is located at the center of the pre-ribosomal particle and interacts, directly or indirectly, with every other assembly factor, as well as three ribosomal proteins required for cytoplasmic 40S maturation. These data suggest that Rio2 could play a central role in regulating cytoplasmic maturation steps. PMID:21283762

Protein-protein interactions within late pre-40S ribosomes.

PubMed

Campbell, Melody G; Karbstein, Katrin

2011-01-20

Ribosome assembly in eukaryotic organisms requires more than 200 assembly factors to facilitate and coordinate rRNA transcription, processing, and folding with the binding of the ribosomal proteins. Many of these assembly factors bind and dissociate at defined times giving rise to discrete assembly intermediates, some of which have been partially characterized with regards to their protein and RNA composition. Here, we have analyzed the protein-protein interactions between the seven assembly factors bound to late cytoplasmic pre-40S ribosomes using recombinant proteins in binding assays. Our data show that these factors form two modules: one comprising Enp1 and the export adaptor Ltv1 near the beak structure, and the second comprising the kinase Rio2, the nuclease Nob1, and a regulatory RNA binding protein Dim2/Pno1 on the front of the head. The GTPase-like Tsr1 and the universally conserved methylase Dim1 are also peripherally connected to this second module. Additionally, in an effort to further define the locations for these essential proteins, we have analyzed the interactions between these assembly factors and six ribosomal proteins: Rps0, Rps3, Rps5, Rps14, Rps15 and Rps29. Together, these results and previous RNA-protein crosslinking data allow us to propose a model for the binding sites of these seven assembly factors. Furthermore, our data show that the essential kinase Rio2 is located at the center of the pre-ribosomal particle and interacts, directly or indirectly, with every other assembly factor, as well as three ribosomal proteins required for cytoplasmic 40S maturation. These data suggest that Rio2 could play a central role in regulating cytoplasmic maturation steps.

The essential nature of YqfG, a YbeY homologue required for 3' maturation of Bacillus subtilis 16S ribosomal RNA is suppressed by deletion of RNase R.

PubMed

Baumgardt, Kathrin; Gilet, Laetitia; Figaro, Sabine; Condon, Ciarán

2018-06-05

Ribosomal RNAs are processed from primary transcripts containing 16S, 23S and 5S rRNAs in most bacteria. Maturation generally occurs in a two-step process, consisting of a first crude separation of the major species by RNase III during transcription, followed by precise trimming of 5' and 3' extensions on each species upon accurate completion of subunit assembly. The various endo- and exoribonucleases involved in the final processing reactions are strikingly different in Escherichia coli and Bacillus subtilis, the two best studied representatives of Gram-negative and Gram-positive bacteria, respectively. Here, we show that the one exception to this rule is the protein involved in the maturation of the 3' end of 16S rRNA. Cells depleted for the essential B. subtilis YqfG protein, a homologue of E. coli YbeY, specifically accumulate 16S rRNA precursors bearing 3' extensions. Remarkably, the essential nature of YqfG can be suppressed by deleting the ribosomal RNA degrading enzyme RNase R, i.e. a ΔyqfG Δrnr mutant is viable. Our data suggest that 70S ribosomes containing 30S subunits with 3' extensions of 16S rRNA are functional to a degree, but become substrates for degradation by RNase R and are eliminated.

Diagnosis and treatment delays among elderly breast cancer patients with pre-existing mental illness.

PubMed

Iglay, Kristy; Santorelli, Melissa L; Hirshfield, Kim M; Williams, Jill M; Rhoads, George G; Lin, Yong; Demissie, Kitaw

2017-11-01

This study aimed to compare diagnosis and treatment delays in elderly breast cancer patients with and without pre-existing mental illness. A retrospective cohort study was conducted using the Surveillance, Epidemiology and End Results-Medicare data including 16,636 women 68+ years, who were diagnosed with stage I-IIIa breast cancer in the United States from 2005 to 2007. Mental illness was identified using International Classification of Diseases, Ninth Revision, Clinical Modification codes recorded on inpatient and outpatient claims during the 3 years prior to breast cancer diagnosis. Patients were classified as having no mental illness, anxiety, depression, anxiety and depression, or severe mental illness (bipolar disorder, schizophrenia, and other psychotic disorder). Multivariable binomial regression was used to assess the association between mental illness and delays of ≥60 and ≥90 days after adjustment for confounders. Patients with comorbid anxiety and depression had an increased risk for diagnosis delay of ≥90 days from symptom recognition (RR 1.11; 95% CI 1.00, 1.23), and those with severe mental illness had an increased risk for initial treatment delay of ≥60 days from diagnosis (RR 1.36; 95% CI 1.06, 1.74). Patients with any mental illness experienced an increased risk for adjuvant chemotherapy delay of ≥90 days from last operation (RR 1.13; 95% CI 1.01, 1.26) and each category of mental illness, except depression, showed a non-significant trend for this association. Breast cancer patients with mental illness should be closely managed by a cross-functional care team, including a psychiatrist, a primary care physician, and an oncologist, to ensure adequate care is received within an appropriate timeframe.

Opioids delay healing of spinal fusion: a rabbit posterolateral lumbar fusion model.

PubMed

Jain, Nikhil; Himed, Khaled; Toth, Jeffrey M; Briley, Karen C; Phillips, Frank M; Khan, Safdar N

2018-04-19

Opioid use is prevalent for management of pre- and post-operative pain in patients undergoing spinal fusion. There is evidence that opioids downregulate osteoblasts in-vitro, and one previous study found that morphine delays the maturation and remodeling of callus in a rat femur fracture model. However, the effect of opioids on healing of spinal fusion has not been investigated before. Isolating the effect of opioid exposure in humans would be limited by the numerous confounding factors that affect fusion healing. Therefore, we have used a well-established rabbit model to study the process of spinal fusion healing that closely mimics humans. To study the effect of systemic opioids on the process of healing of spinal fusion in a rabbit posterolateral spinal fusion model. Pre-clinical animal study. 24 adult New Zealand white rabbits were studied in two groups after approval from the Institutional Animal Care and Use Committee (IACUC). The opioid group (n=12) received four-weeks pre-operative and six-weeks post-operative transdermal fentanyl. Serum fentanyl levels were measured just before surgery and four-weeks post-operatively to ensure adequate levels. The control group (n=12) received only peri-operative pain control as necessary. All animals received a bilateral L5-L6 posterolateral spinal fusion using iliac crest autograft. Animals were euthanized at the six-week post-operative time point, and assessment of fusion was done by manual palpation, plain radiographs, micro-computed tomography (microCT), and histology. 12 animals in control group and 11 animals in the opioid group were available for analysis at the end of six weeks. The fusion scores on manual palpation, radiographs, and microCT were not statistically different. Three-dimensional microCT morphometry found that the fusion mass in the opioid group had a lower bone volume (p=0.09), lower trabecular number (p=0.02) and higher trabecular separation (p=0.02) as compared to control. Histological analysis found areas of incorporation of autograft, and unincorporated graft fragments in both groups. In the control group, there was remodeling of de-novo woven bone to lamellar organization with incorporation of osteocytes, formation of mature marrow, and relative paucity of hypertrophied osteoblasts lining new bone. Sections from the opioid group showed formation of de-novo woven bone, and hypertrophied osteoblasts seen lining the new bone. There were no sections showing lamellar organization and development of mature marrow elements in the opioid group. Less dense trabeculae on microCT correlated with histological findings of relatively immature fusion mass in the opioid group. Systemic opioids led to an inferior quality fusion mass with delay in maturation and remodeling at six-weeks in this rabbit spinal fusion model. These preliminary results lay foundation for further research to investigate underlying cellular mechanisms, temporal fusion process, and dose-duration relationship of opioids responsible for our findings. Copyright © 2018 Elsevier Inc. All rights reserved.

Evaluation of a Public Child Eye Health Tertiary Facility for Pediatric Cataract in Southern Nigeria I: Visual Acuity Outcome

PubMed Central

Duke, Roseline E.; Adio, Adedayo; Oparah, Sidney K.; Odey, Friday; Eyo, Okon A.

2016-01-01

Purpose: A retrospective study of the outcome of congenital and developmental cataract surgery was conducted in a public child eye health tertiary facility in children <16 years of age in Southern Nigeria, as part of an evaluation. Materials and Method: Manual Small Incision Cataract Surgery with or without anterior vitrectomy was performed. The outcome measures were visual acuity (VA) and change (gain) in visual acuity. The age of the child at onset, duration of delay in presentation, ocular co-morbidity, non ocular co-morbidity, gender, and pre operative visual acuity were matched with postoperative visual acuity. A total of 66 children were studied for a period of six weeks following surgery. Results: Forty eight (72.7%) children had bilateral congenital cataracts and 18 (27.3%) children had bilateral developmental cataracts. There were 38(57.6%) males and 28 (42.4%) females in the study. Thirty Five (53%) children had good visual outcome (normal vision range 6/6/ -6/18) post-operatively. The number of children with blindness (vision <3/60) decreased from 61 (92.4%) pre-operatively to 4 (6.1%) post-operatively. Post operative complication occurred in 6.8% of cases six week after surgery. Delayed presentation had an inverse relationship with change (gain) in visual acuity (r = - 0.342; p-value = 0.005). Pre-operative visual acuity had a positive relationship with post operative change (gain) in visual acuity (r = 0.618; p-value = 0.000). Conclusion: Predictors of change in visual acuity in our study were; delayed presentation and pre-operative VA. Cataract surgery in children showed clinical benefit. PMID:27347247

Prehospital system delay in ST-segment elevation myocardial infarction care: a novel linkage of emergency medicine services and in hospital registry data.

PubMed

Fosbøl, Emil L; Granger, Christopher B; Peterson, Eric D; Lin, Li; Lytle, Barbara L; Shofer, Frances S; Lohmeier, Chad; Mears, Greg D; Garvey, J Lee; Corbett, Claire C; Jollis, James G; Glickman, Seth W

2013-03-01

Emergency medical services (EMS) are critical in the treatment of ST-segment elevation myocardial infarction (STEMI). Prehospital system delays are an important target for improving timely STEMI care, yet few limited data are available. Using a deterministic approach, we merged EMS data from the North Carolina Pre-hospital Medical Information System (PreMIS) with data from the Reperfusion of Acute Myocardial Infarction in Carolina Emergency Departments-Emergency Response (RACE-ER) Project. Our sample included all patients with STEMI from June 2008 to October 2010 who arrived by EMS and who had primary percutaneous coronary intervention (PCI). Prehospital system delays were compared using both RACE-ER and PreMIS to examine agreement between the 2 data sources. Overall, 8,680 patients with STEMI in RACE-ER arrived at a PCI hospital by EMS; 21 RACE-ER hospitals and 178 corresponding EMS agencies across the state were represented. Of these, 6,010 (69%) patients were successfully linked with PreMIS. Linked and notlinked patients were similar. Overall, 2,696 patients were treated with PCI only and were taken directly to a PCI-capable hospital by EMS; 1,750 were transferred from a non-PCI facility. For those being transported directly to a PCI center, 53% reached the 90-minute target guideline goal. For those transferred from a non-PCI facility, 24% reached the 120-minute target goal for primary PCI. We successfully linked prehospital EMS data with in hospital clinical data. With this linked STEMI cohort, less than half of patients reach goals set by guidelines. Such a data source could be used for future research and quality improvement interventions. Copyright © 2013 Mosby, Inc. All rights reserved.

Degradation of a Polyadenylated rRNA Maturation By-Product Involves One of the Three RRP6-Like Proteins in Arabidopsis thaliana▿

PubMed Central

Lange, Heike; Holec, Sarah; Cognat, Valérie; Pieuchot, Laurent; Le Ret, Monique; Canaday, Jean; Gagliardi, Dominique

2008-01-01

Yeast Rrp6p and its human counterpart, PM/Scl100, are exosome-associated proteins involved in the degradation of aberrant transcripts and processing of precursors to stable RNAs, such as the 5.8S rRNA, snRNAs, and snoRNAs. The activity of yeast Rrp6p is stimulated by the polyadenylation of its RNA substrates. We identified three RRP6-like proteins in Arabidopsis thaliana: AtRRP6L3 is restricted to the cytoplasm, whereas AtRRP6L1 and -2 have different intranuclear localizations. Both nuclear RRP6L proteins are functional, since AtRRP6L1 complements the temperature-sensitive phenotype of a yeast rrp6Δ strain and mutation of AtRRP6L2 leads to accumulation of an rRNA maturation by-product. This by-product corresponds to the excised 5′ part of the 18S-5.8S-25S rRNA precursor and accumulates as a polyadenylated transcript, suggesting that RRP6L2 is involved in poly(A)-mediated RNA degradation in plant nuclei. Interestingly, the rRNA maturation by-product is a substrate of AtRRP6L2 but not of AtRRP6L1. This result and the distinctive subcellular distribution of AtRRP6L1 to -3 indicate a specialization of RRP6-like proteins in Arabidopsis. PMID:18285452

Berry Flesh and Skin Ripening Features in Vitis vinifera as Assessed by Transcriptional Profiling

PubMed Central

Grimplet, Jérôme; Bravo, Gema; Flores, Pilar; Fenoll, José; Hellín, Pilar; Oliveros, Juan Carlos; Martínez-Zapater, José M.

2012-01-01

Background Ripening of fleshy fruit is a complex developmental process involving the differentiation of tissues with separate functions. During grapevine berry ripening important processes contributing to table and wine grape quality take place, some of them flesh- or skin-specific. In this study, transcriptional profiles throughout flesh and skin ripening were followed during two different seasons in a table grape cultivar ‘Muscat Hamburg’ to determine tissue-specific as well as common developmental programs. Methodology/Principal Findings Using an updated GrapeGen Affymetrix GeneChip® annotation based on grapevine 12×v1 gene predictions, 2188 differentially accumulated transcripts between flesh and skin and 2839 transcripts differentially accumulated throughout ripening in the same manner in both tissues were identified. Transcriptional profiles were dominated by changes at the beginning of veraison which affect both pericarp tissues, although frequently delayed or with lower intensity in the skin than in the flesh. Functional enrichment analysis identified the decay on biosynthetic processes, photosynthesis and transport as a major part of the program delayed in the skin. In addition, a higher number of functional categories, including several related to macromolecule transport and phenylpropanoid and lipid biosynthesis, were over-represented in transcripts accumulated to higher levels in the skin. Functional enrichment also indicated auxin, gibberellins and bHLH transcription factors to take part in the regulation of pre-veraison processes in the pericarp, whereas WRKY and C2H2 family transcription factors seems to more specifically participate in the regulation of skin and flesh ripening, respectively. Conclusions/Significance A transcriptomic analysis indicates that a large part of the ripening program is shared by both pericarp tissues despite some components are delayed in the skin. In addition, important tissue differences are present from early stages prior to the ripening onset including tissue-specific regulators. Altogether, these findings provide key elements to understand berry ripening and its differential regulation in flesh and skin. PMID:22768087

Time delay and noise explaining the behaviour of the cell growth in fermentation process

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

Ayuobi, Tawfiqullah; Rosli, Norhayati; Bahar, Arifah

2015-02-03

This paper proposes to investigate the interplay between time delay and external noise in explaining the behaviour of the microbial growth in batch fermentation process. Time delay and noise are modelled jointly via stochastic delay differential equations (SDDEs). The typical behaviour of cell concentration in batch fermentation process under this model is investigated. Milstein scheme is applied for solving this model numerically. Simulation results illustrate the effects of time delay and external noise in explaining the lag and stationary phases, respectively for the cell growth of fermentation process.

Time delay and noise explaining the behaviour of the cell growth in fermentation process

NASA Astrophysics Data System (ADS)

Ayuobi, Tawfiqullah; Rosli, Norhayati; Bahar, Arifah; Salleh, Madihah Md

2015-02-01

This paper proposes to investigate the interplay between time delay and external noise in explaining the behaviour of the microbial growth in batch fermentation process. Time delay and noise are modelled jointly via stochastic delay differential equations (SDDEs). The typical behaviour of cell concentration in batch fermentation process under this model is investigated. Milstein scheme is applied for solving this model numerically. Simulation results illustrate the effects of time delay and external noise in explaining the lag and stationary phases, respectively for the cell growth of fermentation process.

Management of umbilical cord clamping.

PubMed

Webbon, Lucy

2013-02-01

The Royal College of Midwives (RCM) has updated its third stage of labour guidelines (RCM 2012) to be clearly supportive of a delay in umbilical cord clamping, although specific guidance on timing is yet to be announced. It is therefore imperative that both midwives and student midwives understand and are able to integrate delaying into their practice, as well as communicating to women the benefits; only in this way can we give women fully informed choices on this aspect of care. The main benefit of delayed cord clamping is the protection it can provide in reducing childhood anaemia, which is a major issue, especially in poorer countries. A review of the evidence found no risks linked to delayed clamping, and no evidence that it cannot be used in combination with the administration of uterotonic drugs. Delayed cord clamping can be especially beneficial for pre term and compromised babies.

Ancient Mitochondrial DNA Analyses of Ascaris Eggs Discovered in Coprolites from Joseon Tomb

PubMed Central

Oh, Chang Seok; Seo, Min; Hong, Jong Ha; Chai, Jong-Yil; Oh, Seung Whan; Park, Jun Bum; Shin, Dong Hoon

2015-01-01

Analysis of ancient DNA (aDNA) extracted from Ascaris is very important for understanding the phylogenetic lineage of the parasite species. When aDNAs obtained from a Joseon tomb (SN2-19-1) coprolite in which Ascaris eggs were identified were amplified with primers for cytochrome b (cyt b) and 18S small subunit ribosomal RNA (18S rRNA) gene, the outcome exhibited Ascaris specific amplicon bands. By cloning, sequencing, and analysis of the amplified DNA, we obtained information valuable for comprehending genetic lineage of Ascaris prevalent among pre-modern Joseon peoples. PMID:25925186

TDLAS-based sensors for in situ measurement of syngas composition in a pressurized, oxygen-blown, entrained flow coal gasifier

NASA Astrophysics Data System (ADS)

Sur, Ritobrata; Sun, Kai; Jeffries, Jay B.; Hanson, Ronald K.; Pummill, Randy J.; Waind, Travis; Wagner, David R.; Whitty, Kevin J.

2014-07-01

Tunable diode laser absorption spectroscopy based in situ sensors for CO (2.33 μm), CO2 (2.02 μm), CH4 (2.29 μm) and H2O (1.35 μm) were deployed in a pilot-scale (1 ton/day), high-pressure (up to 18 atm), entrained flow, oxygen-blown, slagging coal gasifier at the University of Utah. Measurements of species mole fraction with 3-s time resolution were taken at the pre- and post-filtration stages of the gasifier synthesis gas (called here syngas) output flow. Although particulate scattering makes pre-filter measurements more difficult, this location avoids the time delay of flow through the filtration devices. With the measured species and known N2 concentrations, the H2 content was obtained via balance. The lower heating value and the Wobbe index of the gas mixture were estimated using the measured gas composition. The sensors demonstrated here show promise for monitoring and control of the gasification process.

Photocatalytic ozonation of urban wastewater and surface water using immobilized TiO2 with LEDs: Micropollutants, antibiotic resistance genes and estrogenic activity.

PubMed

Moreira, Nuno F F; Sousa, José M; Macedo, Gonçalo; Ribeiro, Ana R; Barreiros, Luisa; Pedrosa, Marta; Faria, Joaquim L; Pereira, M Fernando R; Castro-Silva, Sérgio; Segundo, Marcela A; Manaia, Célia M; Nunes, Olga C; Silva, Adrián M T

2016-05-01

Photocatalytic ozonation was employed for the first time in continuous mode with TiO2-coated glass Raschig rings and light emitting diodes (LEDs) to treat urban wastewater as well as surface water collected from the supply area of a drinking water treatment plant (DWTP). Different levels of contamination and types of contaminants were considered in this work, including chemical priority substances (PSs) and contaminants of emerging concern (CECs), as well as potential human opportunistic antibiotic resistant bacteria and their genes (ARB&ARG). Photocatalytic ozonation was more effective than single ozonation (or even than TiO2 catalytic ozonation) in the degradation of typical reaction by-products (such as oxalic acid), and more effective than photocatalysis to remove the parent micropollutants determined in urban wastewater. In fact, only fluoxetine, clarithromycin, erythromycin and 17-alpha-ethinylestradiol (EE2) were detected after photocatalytic ozonation, by using solid-phase extraction (SPE) pre-concentration and LC-MS/MS analysis. In surface water, this treatment allowed the removal of all determined micropollutants to levels below the limit of detection (0.01-0.20 ng L(-1)). The efficiency of this process was then assessed based on the capacity to remove different groups of cultivable microorganisms and housekeeping (16S rRNA) and antibiotic resistance or related genes (intI1, blaTEM, qnrS, sul1). Photocatalytic ozonation was observed to efficiently remove microorganisms and ARGs. Although after storage total heterotrophic and ARB (to ciprofloxacin, gentamicin, meropenem), fungi, and the genes 16S rRNA and intI1, increased to values close to the pre-treatment levels, the ARGs (blaTEM, qnrS and sul1) were reduced to levels below/close to the quantification limit even after 3-days storage of treated surface water or wastewater. Yeast estrogen screen (YES), thiazolyl blue tetrazolium reduction (MTT) and lactate dehydrogenase (LDH) assays were also performed before and after photocatalytic ozonation to evaluate the potential estrogenic activity, the cellular metabolic activity and the cell viability. Compounds with estrogenic effects and significant differences concerning cell viability were not observed in any case. A slight cytotoxicity was only detected for Caco-2 and hCMEC/D3 cell lines after treatment of the urban wastewater, but not for L929 fibroblasts. Copyright © 2016 Elsevier Ltd. All rights reserved.

MXD1 localizes in the nucleolus, binds UBF and impairs rRNA synthesis.

PubMed

Lafita-Navarro, Maria Del Carmen; Blanco, Rosa; Mata-Garrido, Jorge; Liaño-Pons, Judit; Tapia, Olga; García-Gutiérrez, Lucía; García-Alegría, Eva; Berciano, María T; Lafarga, Miguel; León, Javier

2016-10-25

MXD1 is a protein that interacts with MAX, to form a repressive transcription factor. MXD1-MAX binds E-boxes. MXD1-MAX antagonizes the transcriptional activity of the MYC oncoprotein in most models. It has been reported that MYC overexpression leads to augmented RNA synthesis and ribosome biogenesis, which is a relevant activity in MYC-mediated tumorigenesis. Here we describe that MXD1, but not MYC or MNT, localizes to the nucleolus in a wide array of cell lines derived from different tissues (carcinoma, leukemia) as well as in embryonic stem cells. MXD1 also localizes in the nucleolus of primary tissue cells as neurons and Sertoli cells. The nucleolar localization of MXD1 was confirmed by co-localization with UBF. Co-immunoprecipitation experiments showed that MXD1 interacted with UBF and proximity ligase assays revealed that this interaction takes place in the nucleolus. Furthermore, chromatin immunoprecipitation assays showed that MXD1 was bound in the transcribed rDNA chromatin, where it co-localizes with UBF, but also in the ribosomal intergenic regions. The MXD1 involvement in rRNA synthesis was also suggested by the nucleolar segregation upon rRNA synthesis inhibition by actinomycin D. Silencing of MXD1 with siRNAs resulted in increased synthesis of pre-rRNA while enforced MXD1 expression reduces it. The results suggest a new role for MXD1, which is the control of ribosome biogenesis. This new MXD1 function would be important to curb MYC activity in tumor cells.

MXD1 localizes in the nucleolus, binds UBF and impairs rRNA synthesis

PubMed Central

Lafita-Navarro, Maria del Carmen; Blanco, Rosa; Mata-Garrido, Jorge; Liaño-Pons, Judit; Tapia, Olga; García-Gutiérrez, Lucía; García-Alegría, Eva; Berciano, María T.; Lafarga, Miguel; León, Javier

2016-01-01

MXD1 is a protein that interacts with MAX, to form a repressive transcription factor. MXD1-MAX binds E-boxes. MXD1-MAX antagonizes the transcriptional activity of the MYC oncoprotein in most models. It has been reported that MYC overexpression leads to augmented RNA synthesis and ribosome biogenesis, which is a relevant activity in MYC-mediated tumorigenesis. Here we describe that MXD1, but not MYC or MNT, localizes to the nucleolus in a wide array of cell lines derived from different tissues (carcinoma, leukemia) as well as in embryonic stem cells. MXD1 also localizes in the nucleolus of primary tissue cells as neurons and Sertoli cells. The nucleolar localization of MXD1 was confirmed by co-localization with UBF. Co-immunoprecipitation experiments showed that MXD1 interacted with UBF and proximity ligase assays revealed that this interaction takes place in the nucleolus. Furthermore, chromatin immunoprecipitation assays showed that MXD1 was bound in the transcribed rDNA chromatin, where it co-localizes with UBF, but also in the ribosomal intergenic regions. The MXD1 involvement in rRNA synthesis was also suggested by the nucleolar segregation upon rRNA synthesis inhibition by actinomycin D. Silencing of MXD1 with siRNAs resulted in increased synthesis of pre-rRNA while enforced MXD1 expression reduces it. The results suggest a new role for MXD1, which is the control of ribosome biogenesis. This new MXD1 function would be important to curb MYC activity in tumor cells. PMID:27588501

An Alternative Approach to "Identification of Unknowns": Designing a Protocol to Verify the Identities of Nitrogen Fixing Bacteria.

PubMed

Martinez-Vaz, Betsy M; Denny, Roxanne; Young, Nevin D; Sadowsky, Michael J

2015-12-01

Microbiology courses often include a laboratory activity on the identification of unknown microbes. This activity consists of providing students with microbial cultures and running biochemical assays to identify the organisms. This approach lacks molecular techniques such as sequencing of genes encoding 16S rRNA, which is currently the method of choice for identification of unknown bacteria. A laboratory activity was developed to teach students how to identify microorganisms using 16S rRNA polymerase chain reaction (PCR) and validate microbial identities using biochemical techniques. We hypothesized that designing an experimental protocol to confirm the identity of a bacterium would improve students' knowledge of microbial identification techniques and the physiological characteristics of bacterial species. Nitrogen-fixing bacteria were isolated from the root nodules of Medicago truncatula and prepared for 16S rRNA PCR analysis. Once DNA sequencing revealed the identity of the organisms, the students designed experimental protocols to verify the identity of rhizobia. An assessment was conducted by analyzing pre- and posttest scores and by grading students' verification protocols and presentations. Posttest scores were higher than pretest scores at or below p = 0.001. Normalized learning gains (G) showed an improvement of students' knowledge of microbial identification methods (LO4, G = 0.46), biochemical properties of nitrogen-fixing bacteria (LO3, G = 0.45), and the events leading to the establishment of nitrogen-fixing symbioses (LO1&2, G = 0.51, G = 0.37). An evaluation of verification protocols also showed significant improvement with a p value of less than 0.001.

Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays

NASA Astrophysics Data System (ADS)

Thanh, Vo Hong; Priami, Corrado; Zunino, Roberto

2014-10-01

We propose a new exact stochastic rejection-based simulation algorithm for biochemical reactions and extend it to systems with delays. Our algorithm accelerates the simulation by pre-computing reaction propensity bounds to select the next reaction to perform. Exploiting such bounds, we are able to avoid recomputing propensities every time a (delayed) reaction is initiated or finished, as is typically necessary in standard approaches. Propensity updates in our approach are still performed, but only infrequently and limited for a small number of reactions, saving computation time and without sacrificing exactness. We evaluate the performance improvement of our algorithm by experimenting with concrete biological models.

Influence of age on delayed surgical treatment of proximal femoral fractures

PubMed Central

Gomes, Lisiane Pinto; do Nascimento, Leandra Delfim; Campos, Tulio Vinicius de Oliveira; Paiva, Edson Barreto; de Andrade, Marco Antonio Percope; Guimarães, Henrique Cerqueira

2015-01-01

ABSTRACT OBJECTIVE : To investigate the influence of patients' age on the delay between diagnosis and surgical treatment of proximal femoral fractures METHODS : This is a retrospective study, con-ducted at a tertiary university hospital, including all patients admitted with proximal femoral fractures between March 2013 and March 2014. The participants were categorized into four groups according to age levels. The groups were compared according to demographics, comorbidities, fracture type, trau-ma circumstances, and time between diagnosis and surgical procedure RESULTS : One hundred and sixty one patients were included, 37 adults and 124 elderly. Among adults, the mean delay between diagnosis and surgical procedure was 6.4±5.3 days; among elderly the delay was 9.5±7.6 days. There was a progressive increase in the delay from the young-adults group through the elderly individuals (Kruskal-Wallis: 13.7; p=0.003) CONCLUSION : In spite of being the patients most susceptible to complications due to surgical delay, the elderly individuals pre-sented the longest delays from admission to surgical treatment. Level of Evidence III, Retrospective Study. PMID:27057145

Vehicle Position Estimation Based on Magnetic Markers: Enhanced Accuracy by Compensation of Time Delays.

PubMed

Byun, Yeun-Sub; Jeong, Rag-Gyo; Kang, Seok-Won

2015-11-13

The real-time recognition of absolute (or relative) position and orientation on a network of roads is a core technology for fully automated or driving-assisted vehicles. This paper presents an empirical investigation of the design, implementation, and evaluation of a self-positioning system based on a magnetic marker reference sensing method for an autonomous vehicle. Specifically, the estimation accuracy of the magnetic sensing ruler (MSR) in the up-to-date estimation of the actual position was successfully enhanced by compensating for time delays in signal processing when detecting the vertical magnetic field (VMF) in an array of signals. In this study, the signal processing scheme was developed to minimize the effects of the distortion of measured signals when estimating the relative positional information based on magnetic signals obtained using the MSR. In other words, the center point in a 2D magnetic field contour plot corresponding to the actual position of magnetic markers was estimated by tracking the errors between pre-defined reference models and measured magnetic signals. The algorithm proposed in this study was validated by experimental measurements using a test vehicle on a pilot network of roads. From the results, the positioning error was found to be less than 0.04 m on average in an operational test.

Vehicle Position Estimation Based on Magnetic Markers: Enhanced Accuracy by Compensation of Time Delays

PubMed Central

Byun, Yeun-Sub; Jeong, Rag-Gyo; Kang, Seok-Won

2015-01-01

The real-time recognition of absolute (or relative) position and orientation on a network of roads is a core technology for fully automated or driving-assisted vehicles. This paper presents an empirical investigation of the design, implementation, and evaluation of a self-positioning system based on a magnetic marker reference sensing method for an autonomous vehicle. Specifically, the estimation accuracy of the magnetic sensing ruler (MSR) in the up-to-date estimation of the actual position was successfully enhanced by compensating for time delays in signal processing when detecting the vertical magnetic field (VMF) in an array of signals. In this study, the signal processing scheme was developed to minimize the effects of the distortion of measured signals when estimating the relative positional information based on magnetic signals obtained using the MSR. In other words, the center point in a 2D magnetic field contour plot corresponding to the actual position of magnetic markers was estimated by tracking the errors between pre-defined reference models and measured magnetic signals. The algorithm proposed in this study was validated by experimental measurements using a test vehicle on a pilot network of roads. From the results, the positioning error was found to be less than 0.04 m on average in an operational test. PMID:26580622

DEAD-box RNA helicase Dbp4 is required for small-subunit processome formation and function.

PubMed

Soltanieh, Sahar; Osheim, Yvonne N; Spasov, Krasimir; Trahan, Christian; Beyer, Ann L; Dragon, François

2015-03-01

DEAD-box RNA helicase Dbp4 is required for 18S rRNA synthesis: cellular depletion of Dbp4 impairs the early cleavage reactions of the pre-rRNA and causes U14 small nucleolar RNA (snoRNA) to remain associated with pre-rRNA. Immunoprecipitation experiments (IPs) carried out with whole-cell extracts (WCEs) revealed that hemagglutinin (HA)-tagged Dbp4 is associated with U3 snoRNA but not with U14 snoRNA. IPs with WCEs also showed association with the U3-specific protein Mpp10, which suggests that Dbp4 interacts with the functionally active U3 RNP; this particle, called the small-subunit (SSU) processome, can be observed at the 5' end of nascent pre-rRNA. Electron microscopy analyses indicated that depletion of Dbp4 compromised SSU processome formation and cotranscriptional cleavage of the pre-rRNA. Sucrose density gradient analyses revealed that depletion of U3 snoRNA or the Mpp10 protein inhibited the release of U14 snoRNA from pre-rRNA, just as was seen with Dbp4-depleted cells, indicating that alteration of SSU processome components has significant consequences for U14 snoRNA dynamics. We also found that the C-terminal extension flanking the catalytic core of Dbp4 plays an important role in the release of U14 snoRNA from pre-rRNA. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Increased 5S rRNA oxidation in Alzheimer's disease.

PubMed

Ding, Qunxing; Zhu, Haiyan; Zhang, Bing; Soriano, Augusto; Burns, Roxanne; Markesbery, William R

2012-01-01

It is widely accepted that oxidative stress is involved in neurodegenerative disorders such as Alzheimer's disease (AD). Ribosomal RNA (rRNA) is one of the most abundant molecules in most cells and is affected by oxidative stress in the human brain. Previous data have indicated that total rRNA levels were decreased in the brains of subjects with AD and mild cognitive impairment concomitant with an increase in rRNA oxidation. In addition, level of 5S rRNA, one of the essential components of the ribosome complex, was significantly lower in the inferior parietal lobule (IP) brain area of subjects with AD compared with control subjects. To further evaluate the alteration of 5S rRNA in neurodegenerative human brains, multiple brain regions from both AD and age-matched control subjects were used in this study, including IP, superior and middle temporal gyro, temporal pole, and cerebellum. Different molecular pools including 5S rRNA integrated into ribosome complexes, free 5S rRNA, cytoplasmic 5S rRNA, and nuclear 5S rRNA were studied. Free 5S rRNA levels were significantly decreased in the temporal pole region of AD subjects and the oxidation of ribosome-integrated and free 5S rRNA was significantly increased in multiple brain regions in AD subjects compared with controls. Moreover, a greater amount of oxidized 5S rRNA was detected in the cytoplasm and nucleus of AD subjects compared with controls. These results suggest that the increased oxidation of 5S rRNA, especially the oxidation of free 5S rRNA, may be involved in the neurodegeneration observed in AD.

A Genetic Cascade of let-7-ncl-1-fib-1 Modulates Nucleolar Size and rRNA Pool in Caenorhabditis elegans

PubMed Central

Chiou, Pey-Tsyr; Chen, Po-Hsiang; Lee, Ching-Ming; Chu, Yu-De; Yu, Hsiang; Hsiung, Kuei-Ching; Tsai, Yi-Tzang; Lee, Chi-Chang; Chang, Yu-Sun; Chan, Shih-Peng; Tan, Bertrand Chin-Ming; Lo, Szecheng J.

2015-01-01

Ribosome biogenesis takes place in the nucleolus, the size of which is often coordinated with cell growth and development. However, how metazoans control nucleolar size remains largely unknown. Caenorhabditis elegans provides a good model to address this question owing to distinct tissue distribution of nucleolar sizes and a mutant, ncl-1, which exhibits larger nucleoli than wild-type worms. Here, through a series of loss-of-function analyses, we report that the nucleolar size is regulated by a circuitry composed of microRNA let-7, translation repressor NCL-1, and a major nucleolar pre-rRNA processing protein FIB-1/fibrillarin. In cooperation with RNA binding proteins PUF and NOS, NCL-1 suppressed the translation of FIB-1/fibrillarin, while let-7 targeted the 3’UTR of ncl-1 and inhibited its expression. Consequently, the abundance of FIB-1 is tightly controlled and correlated with the nucleolar size. Together, our findings highlight a novel genetic cascade by which post-transcriptional regulators interplay in developmental control of nucleolar size and function. PMID:26492166

Mrd1p binds to pre-rRNA early during transcription independent of U3 snoRNA and is required for compaction of the pre-rRNA into small subunit processomes.

PubMed

Segerstolpe, Asa; Lundkvist, Pär; Osheim, Yvonne N; Beyer, Ann L; Wieslander, Lars

2008-08-01

In Saccharomyces cerevisiae, synthesis of the small ribosomal subunit requires assembly of the 35S pre-rRNA into a 90S preribosomal complex. SnoRNAs, including U3 snoRNA, and many trans-acting proteins are required for the ordered assembly and function of the 90S preribosomal complex. Here, we show that the conserved protein Mrd1p binds to the pre-rRNA early during transcription and is required for compaction of the pre-18S rRNA into SSU processome particles. We have exploited the fact that an Mrd1p-GFP fusion protein is incorporated into the 90S preribosomal complex, where it acts as a partial loss-of-function mutation. When associated with the pre-rRNA, Mrd1p-GFP functionally interacts with the essential Pwp2, Mpp10 and U3 snoRNP subcomplexes that are functionally interconnected in the 90S preribosomal complex. The fusion protein can partially support 90S preribosome-mediated cleavages at the A(0)-A(2) sites. At the same time, on a substantial fraction of transcripts, the composition and/or structure of the 90S preribosomal complex is perturbed by the fusion protein in such a way that cleavage of the 35S pre-rRNA is either blocked or shifted to aberrant sites. These results show that Mrd1p is required for establishing productive structures within the 90S preribosomal complex.

Composition, Diversity and Abundance of Gut Microbiome in Prediabetes and Type 2 Diabetes.

PubMed

Lambeth, Stacey M; Carson, Trechelle; Lowe, Janae; Ramaraj, Thiruvarangan; Leff, Jonathan W; Luo, Li; Bell, Callum J; Shah, Vallabh O

2015-12-26

Association between type 2 diabetes (T2DM) and compositional changes in the gut micro biota is established, however little is known about the dysbiosis in early stages of Prediabetes (preDM). The purpose of this investigation is to elucidate the characteristics of the gut micro biome in preDM and T2DM, compared to Non-Diabetic (nonDM) subjects. Forty nine subjects were recruited for this study, 15 nonDM, 20 preDM and 14 T2DM. Bacterial community composition and diversity were investigated in fecal DNA samples using Illumina sequencing of the V4 region within the 16S rRNA gene. The five most abundant phyla identified were: Bacteroidetes, Firmicutes, Proteobacteria, Verrucomicrobia , and Actinobacteria . Class Chloracido bacteria was increased in preDM compared to T2DM (p = 0.04). An unknown genus from family Pseudonocardiaceae was significantly present in preDM group compared to the others (p = 0.04). Genus Collinsella , and an unknown genus belonging to family Enterobacteriaceae were both found to be significantly increased in T2DM compared to the other groups (Collinsella, and p = 0.03, Enterobacteriaceae genus p = 0.02). PERMANOVA and Mantel tests performed did not reveal a relationship between overall composition and diagnosis group or HbA1C level. This study identified dysbiosis associated with both preDM and T2DM, specifically at the class and genus levels suggesting that earlier treatment in preDM could possibly have an impact on the intestinal micro flora transitioning to T2DM.

The Effectiveness of the Constant Time Delay Procedure in Teaching Pre-School Academic Skills to Children with Developmental Disabilities in a Small Group Teaching Arrangement

ERIC Educational Resources Information Center

Aldemir, Ozgul; Gursel, Oguz

2014-01-01

Children with developmental disabilities are trained using different teaching arrangements. One of these arrangements is called small-group teaching. It has been ascertained that a small-group teaching arrangement is more effective than a one-to-one teaching arrangement. In that sense, teaching academic skills to pre-school children in small-group…

Implications of delayed initiation of radiotherapy: accelerated repopulation after induction chemotherapy for stage III non-small cell lung cancer.

PubMed

Chen, Chien P; Weinberg, Vivian K; Jahan, Thierry M; Jablons, David M; Yom, Sue S

2011-11-01

For patients with stage III non-small cell lung cancer treated with induction chemotherapy (ICT), delayed initiation of subsequent radiotherapy (RT) may allow for repopulation in the interval between treatment modalities and during the early phase of RT. We quantified the impact of postinduction RT timing by evaluating the pace of tumor regrowth. Institutionally approved retrospective review identified 21 analyzable patients with stage III non-small cell lung cancer who had platinum-based ICT followed by RT+/- chemotherapy from 2002 to 2009. Radiographic response was determined by RECIST criteria and the volume of the single largest tumor mass on the pre-ICT, post-ICT, and RT-planning computed tomography scans. After ICT, the median percent volume change from pre-ICT baseline was -41% (range -86 to +86%). By the RT-planning computed tomography scan, the median percent volume change from the post-ICT timepoint was +40% (range -11 to +311%) and the median volume change was +20 ml (range -4 to 102 ml); these changes were significant (p = 0.0002). Similar results were seen for tumor diameter. A correlation was observed between the amount of delay and degree of regrowth for percent volume (p = 0.0006) and percent diameter change (p = 0.003). A delay greater than 21 days produced greater increases in percent volume change (p = 0.002) and percent diameter (p = 0.055) than lesser delays. After ICT, tumor regrowth can occur within a few weeks. Radiation treatment planning should begin as soon as possible after the administration of ICT to maximize the benefits of cytoreduction.

CDC Kerala 7: Effect of early language intervention among children 0-3 y with speech and language delay.

PubMed

Nair, M K C; Mini, A O; Leena, M L; George, Babu; Harikumaran Nair, G S; Bhaskaran, Deepa; Russell, Paul Swamidhas Sudhakar

2014-12-01

To assess the effect of systematic clinic and home based early language intervention program in children reporting to the early language intervention clinic with full partnership of specially trained developmental therapist and the parents. All babies between 0 and 3 y referred to Child Development Centre (CDC) Kerala for suspected speech/language delay were assessed and those without hearing impairment were screened first using Language Evaluation Scale Trivandrum (LEST) and assessed in detail using Receptive Expressive Emergent Language Scale (REELS). Those having language delay are enrolled into the early language intervention program for a period of 6 mo, 1 h at the CDC clinic once every month followed by home stimulation for rest of the month by the mother trained at CDC. Out of the total 455 children between 0 and 3 y, who successfully completed 6 mo intervention, the mean pre and post intervention language quotient (LQ) were 60.79 and 70.62 respectively and the observed 9.83 increase was statistically significant. The developmental diagnosis included developmental delay (62.4%), global developmental delay (18.5%), Trisomy and other chromosomal abnormalities (10.5%), microcephaly and other brain problems (9.9%), misarticulation (8.4%), autistic features (5.3%) and cleft palate and lip (3.3%) in the descending order. In the present study among 455 children between 0 and 3 y without hearing impairment, who successfully completed 6 mo early language intervention, the mean pre and post intervention LQ were 60.79 and 70.62 respectively and the observed 9.83 increase was statistically significant.

Pre-hospital treatment of STEMI patients. A scientific statement of the Working Group Acute Cardiac Care of the European Society of Cardiology.

PubMed

Tubaro, M; Danchin, N; Goldstein, P; Filippatos, G; Hasin, Y; Heras, M; Jansky, P; Norekval, T M; Swahn, E; Thygesen, K; Vrints, C; Zahger, D; Arntz, H R; Bellou, A; De La Coussaye, J E; De Luca, L; Huber, K; Lambert, Y; Lettino, M; Lindahl, B; McLean, S; Nibbe, L; Peacock, W F; Price, S; Quinn, T; Spaulding, C; Tatu-Chitoiu, G; Van De Werf, F

2011-06-01

In ST-elevation myocardial infarction (STEMI) the pre-hospital phase is the most critical, as the administration of the most appropriate treatment in a timely manner is instrumental for mortality reduction. STEMI systems of care based on networks of medical institutions connected by an efficient emergency medical service are pivotal. The first steps are devoted to minimize the patient's delay in seeking care, rapidly dispatch a properly staffed and equipped ambulance to make the diagnosis on scene, deliver initial drug therapy and transport the patient to the most appropriate (not necessarily the closest) cardiac facility. Primary PCI is the treatment of choice, but thrombolysis followed by coronary angiography and possibly PCI is a valid alternative, according to patient's baseline risk, time from symptoms onset and primary PCI-related delay. Paramedics and nurses have an important role in pre-hospital STEMI care and their empowerment is essential to increase the effectiveness of the system. Strong cooperation between cardiologists and emergency medicine doctors is mandatory for optimal pre-hospital STEMI care. Scientific societies have an important role in guideline implementation as well as in developing quality indicators and performance measures; health care professionals must overcome existing barriers to optimal care together with political and administrative decision makers.

Immune Adjuvant Activity of Pre-Resectional Radiofrequency Ablation Protects against Local and Systemic Recurrence in Aggressive Murine Colorectal Cancer.

PubMed

Ito, Fumito; Ku, Amy W; Bucsek, Mark J; Muhitch, Jason B; Vardam-Kaur, Trupti; Kim, Minhyung; Fisher, Daniel T; Camoriano, Marta; Khoury, Thaer; Skitzki, Joseph J; Gollnick, Sandra O; Evans, Sharon S

2015-01-01

While surgical resection is a cornerstone of cancer treatment, local and distant recurrences continue to adversely affect outcome in a significant proportion of patients. Evidence that an alternative debulking strategy involving radiofrequency ablation (RFA) induces antitumor immunity prompted the current investigation of the efficacy of performing RFA prior to surgical resection (pre-resectional RFA) in a preclinical mouse model. Therapeutic efficacy and systemic immune responses were assessed following pre-resectional RFA treatment of murine CT26 colon adenocarcinoma. Treatment with pre-resectional RFA significantly delayed tumor growth and improved overall survival compared to sham surgery, RFA, or resection alone. Mice in the pre-resectional RFA group that achieved a complete response demonstrated durable antitumor immunity upon tumor re-challenge. Failure to achieve a therapeutic benefit in immunodeficient mice confirmed that tumor control by pre-resectional RFA depends on an intact adaptive immune response rather than changes in physical parameters that make ablated tumors more amenable to a complete surgical excision. RFA causes a marked increase in intratumoral CD8+ T lymphocyte infiltration, thus substantially enhancing the ratio of CD8+ effector T cells: FoxP3+ regulatory T cells. Importantly, pre-resectional RFA significantly increases the number of antigen-specific CD8+ T cells within the tumor microenvironment and tumor-draining lymph node but had no impact on infiltration by myeloid-derived suppressor cells, M1 macrophages or M2 macrophages at tumor sites or in peripheral lymphoid organs (i.e., spleen). Finally, pre-resectional RFA of primary tumors delayed growth of distant tumors through a mechanism that depends on systemic CD8+ T cell-mediated antitumor immunity. Improved survival and antitumor systemic immunity elicited by pre-resectional RFA support the translational potential of this neoadjuvant treatment for cancer patients with high-risk of local and systemic recurrence.

The Effects of Test Trial and Processing Level on Immediate and Delayed Retention.

PubMed

Chang, Sau Hou

2017-03-01

The purpose of the present study was to investigate the effects of test trial and processing level on immediate and delayed retention. A 2 × 2 × 2 mixed ANOVAs was used with two between-subject factors of test trial (single test, repeated test) and processing level (shallow, deep), and one within-subject factor of final recall (immediate, delayed). Seventy-six college students were randomly assigned first to the single test (studied the stimulus words three times and took one free-recall test) and the repeated test trials (studied the stimulus words once and took three consecutive free-recall tests), and then to the shallow processing level (asked whether each stimulus word was presented in capital letter or in small letter) and the deep processing level (whether each stimulus word belonged to a particular category) to study forty stimulus words. The immediate test was administered five minutes after the trials, whereas the delayed test was administered one week later. Results showed that single test trial recalled more words than repeated test trial in immediate final free-recall test, participants in deep processing performed better than those in shallow processing in both immediate and delayed retention. However, the dominance of single test trial and deep processing did not happen in delayed retention. Additional study trials did not further enhance the delayed retention of words encoded in deep processing, but did enhance the delayed retention of words encoded in shallow processing.

The Effects of Test Trial and Processing Level on Immediate and Delayed Retention

PubMed Central

Chang, Sau Hou

2017-01-01

The purpose of the present study was to investigate the effects of test trial and processing level on immediate and delayed retention. A 2 × 2 × 2 mixed ANOVAs was used with two between-subject factors of test trial (single test, repeated test) and processing level (shallow, deep), and one within-subject factor of final recall (immediate, delayed). Seventy-six college students were randomly assigned first to the single test (studied the stimulus words three times and took one free-recall test) and the repeated test trials (studied the stimulus words once and took three consecutive free-recall tests), and then to the shallow processing level (asked whether each stimulus word was presented in capital letter or in small letter) and the deep processing level (whether each stimulus word belonged to a particular category) to study forty stimulus words. The immediate test was administered five minutes after the trials, whereas the delayed test was administered one week later. Results showed that single test trial recalled more words than repeated test trial in immediate final free-recall test, participants in deep processing performed better than those in shallow processing in both immediate and delayed retention. However, the dominance of single test trial and deep processing did not happen in delayed retention. Additional study trials did not further enhance the delayed retention of words encoded in deep processing, but did enhance the delayed retention of words encoded in shallow processing. PMID:28344679

The Timing and Effort of Lexical Access in Natural and Degraded Speech

PubMed Central

Wagner, Anita E.; Toffanin, Paolo; Başkent, Deniz

2016-01-01

Understanding speech is effortless in ideal situations, and although adverse conditions, such as caused by hearing impairment, often render it an effortful task, they do not necessarily suspend speech comprehension. A prime example of this is speech perception by cochlear implant users, whose hearing prostheses transmit speech as a significantly degraded signal. It is yet unknown how mechanisms of speech processing deal with such degraded signals, and whether they are affected by effortful processing of speech. This paper compares the automatic process of lexical competition between natural and degraded speech, and combines gaze fixations, which capture the course of lexical disambiguation, with pupillometry, which quantifies the mental effort involved in processing speech. Listeners’ ocular responses were recorded during disambiguation of lexical embeddings with matching and mismatching durational cues. Durational cues were selected due to their substantial role in listeners’ quick limitation of the number of lexical candidates for lexical access in natural speech. Results showed that lexical competition increased mental effort in processing natural stimuli in particular in presence of mismatching cues. Signal degradation reduced listeners’ ability to quickly integrate durational cues in lexical selection, and delayed and prolonged lexical competition. The effort of processing degraded speech was increased overall, and because it had its sources at the pre-lexical level this effect can be attributed to listening to degraded speech rather than to lexical disambiguation. In sum, the course of lexical competition was largely comparable for natural and degraded speech, but showed crucial shifts in timing, and different sources of increased mental effort. We argue that well-timed progress of information from sensory to pre-lexical and lexical stages of processing, which is the result of perceptual adaptation during speech development, is the reason why in ideal situations speech is perceived as an undemanding task. Degradation of the signal or the receiver channel can quickly bring this well-adjusted timing out of balance and lead to increase in mental effort. Incomplete and effortful processing at the early pre-lexical stages has its consequences on lexical processing as it adds uncertainty to the forming and revising of lexical hypotheses. PMID:27065901

Motor skill delays in pre-school children with leukemia one year after treatment: Hematopoietic stem cell transplantation therapy as an important risk factor.

PubMed

Taverna, Livia; Tremolada, Marta; Bonichini, Sabrina; Tosetto, Barbara; Basso, Giuseppe; Messina, Chiara; Pillon, Marta

2017-01-01

CNS-directed therapies for the treatment of leukemia can adversely affect the acquisition of new skills, such as reading/writing and math. Two years after the end of treatments, children show gross and fine motor skill delays that may persist even when patients are considered healed. The goal of the present study was to assess motor skills difficulties in pre-school children with leukemia one year after treatment. Particular attention has been paid to those patients who had undergone Hematopoietic Stem Cell Transplantation (HSCT) and to the relationship between motor delays and age bands. Participants were 60 children (median age of 5; inter quartile range: 3.07-5.76), including 31 females and 29 males, 91.7% of them were affected by acute lymphoblastic leukemia (ALL), and 8.3% by acute myeloid leukemia (AML). Five children had undergone HCST. Parents were interviewed by Vineland Adaptive Behavior Scales (VABS) on children's motor skills and filled in the Italian Temperament Questionnaire (QUIT). VABS's total scores were converted into equivalent mental age scores (EMA). A score difference of at least three months between current age and equivalent mental age was considered a developmental delay. Non-parametric analyses were run to understand if HSCT treatment and a specific age band influence children's motor skills. Significant delays were found in global motor skills (56.7%) as well as in fine and gross motor domains. Mann Whitney U tests showed that children with HSCT were reported to have lower gross motor mean ranks (U = 62; p = 0.004; Mean rank = 15.40) than peers without HSCT (Mean rank = 31.87) and lower mean rank values on motor temperament scale (U = 9; p = 0.003; HSCT Mean rank = 4.75 versus no HSCT Mean rank = 27.81). Kruskal Wallis' tests identified the high risk treatment showing that HSCT experience negatively impacted the motor skills and temperamental motor activity of pre-school children one year after the diagnosis of leukemia.

Motor skill delays in pre-school children with leukemia one year after treatment: Hematopoietic stem cell transplantation therapy as an important risk factor

PubMed Central

Bonichini, Sabrina; Tosetto, Barbara; Basso, Giuseppe; Messina, Chiara; Pillon, Marta

2017-01-01

CNS-directed therapies for the treatment of leukemia can adversely affect the acquisition of new skills, such as reading/writing and math. Two years after the end of treatments, children show gross and fine motor skill delays that may persist even when patients are considered healed. The goal of the present study was to assess motor skills difficulties in pre-school children with leukemia one year after treatment. Particular attention has been paid to those patients who had undergone Hematopoietic Stem Cell Transplantation (HSCT) and to the relationship between motor delays and age bands. Participants were 60 children (median age of 5; inter quartile range: 3.07–5.76), including 31 females and 29 males, 91.7% of them were affected by acute lymphoblastic leukemia (ALL), and 8.3% by acute myeloid leukemia (AML). Five children had undergone HCST. Parents were interviewed by Vineland Adaptive Behavior Scales (VABS) on children’s motor skills and filled in the Italian Temperament Questionnaire (QUIT). VABS’s total scores were converted into equivalent mental age scores (EMA). A score difference of at least three months between current age and equivalent mental age was considered a developmental delay. Non-parametric analyses were run to understand if HSCT treatment and a specific age band influence children’s motor skills. Significant delays were found in global motor skills (56.7%) as well as in fine and gross motor domains. Mann Whitney U tests showed that children with HSCT were reported to have lower gross motor mean ranks (U = 62; p = 0.004; Mean rank = 15.40) than peers without HSCT (Mean rank = 31.87) and lower mean rank values on motor temperament scale (U = 9; p = 0.003; HSCT Mean rank = 4.75 versus no HSCT Mean rank = 27.81). Kruskal Wallis’ tests identified the high risk treatment showing that HSCT experience negatively impacted the motor skills and temperamental motor activity of pre-school children one year after the diagnosis of leukemia. PMID:29065156

Automated Forensic Animal Family Identification by Nested PCR and Melt Curve Analysis on an Off-the-Shelf Thermocycler Augmented with a Centrifugal Microfluidic Disk Segment.

PubMed

Keller, Mark; Naue, Jana; Zengerle, Roland; von Stetten, Felix; Schmidt, Ulrike

2015-01-01

Nested PCR remains a labor-intensive and error-prone biomolecular analysis. Laboratory workflow automation by precise control of minute liquid volumes in centrifugal microfluidic Lab-on-a-Chip systems holds great potential for such applications. However, the majority of these systems require costly custom-made processing devices. Our idea is to augment a standard laboratory device, here a centrifugal real-time PCR thermocycler, with inbuilt liquid handling capabilities for automation. We have developed a microfluidic disk segment enabling an automated nested real-time PCR assay for identification of common European animal groups adapted to forensic standards. For the first time we utilize a novel combination of fluidic elements, including pre-storage of reagents, to automate the assay at constant rotational frequency of an off-the-shelf thermocycler. It provides a universal duplex pre-amplification of short fragments of the mitochondrial 12S rRNA and cytochrome b genes, animal-group-specific main-amplifications, and melting curve analysis for differentiation. The system was characterized with respect to assay sensitivity, specificity, risk of cross-contamination, and detection of minor components in mixtures. 92.2% of the performed tests were recognized as fluidically failure-free sample handling and used for evaluation. Altogether, augmentation of the standard real-time thermocycler with a self-contained centrifugal microfluidic disk segment resulted in an accelerated and automated analysis reducing hands-on time, and circumventing the risk of contamination associated with regular nested PCR protocols.

RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs

PubMed Central

Yuan, Guozhong; Klämbt, Christian; Bachellerie, Jean-Pierre; Brosius, Jürgen; Hüttenhofer, Alexander

2003-01-01

By generating a specialised cDNA library from four different developmental stages of Drosophila melanogaster, we have identified 66 candidates for small non-messenger RNAs (snmRNAs) and have confirmed their expression by northern blot analysis. Thirteen of them were expressed at certain stages of D.melanogaster development, only. Thirty-five species belong to the class of small nucleolar RNAs (snoRNAs), divided into 15 members from the C/D subclass and 20 members from the H/ACA subclass, which mostly guide 2′-O-methylation and pseudouridylation, respectively, of rRNA and snRNAs. These also include two outstanding C/D snoRNAs, U3 and U14, both functioning as pre-rRNA chaperones. Surprisingly, the sequence of the Drosophila U14 snoRNA reflects a major change of function of this snoRNA in Diptera relative to yeast and vertebrates. Among the 22 snmRNAs lacking known sequence and structure motifs, five were located in intergenic regions, two in introns, five in untranslated regions of mRNAs, eight were derived from open reading frames, and two were transcribed opposite to an intron. Interestingly, detection of two RNA species from this group implies that certain snmRNA species are processed from alternatively spliced pre-mRNAs. Surprisingly, a few snmRNA sequences could not be found on the published D.melanogaster genome, which might suggest that more snmRNA genes (as well as mRNAs) are hidden in unsequenced regions of the genome. PMID:12736298

[On-line monitoring of biomass in 1,3-propanediol fermentation by Fourier-transformed near-infrared spectra analysis].

PubMed

Wang, Lu; Liu, Tao; Chen, Yang; Sun, Yaqin; Xiu, Zhilong

2017-01-25

Biomass is an important parameter reflecting the fermentation dynamics. Real-time monitoring of biomass can be used to control and optimize a fermentation process. To overcome the deficiencies of measurement delay and manual errors from offline measurement, we designed an experimental platform for online monitoring the biomass during a 1,3-propanediol fermentation process, based on using the fourier-transformed near-infrared (FT-NIR) spectra analysis. By pre-processing the real-time sampled spectra and analyzing the sensitive spectra bands, a partial least-squares algorithm was proposed to establish a dynamic prediction model for the biomass change during a 1,3-propanediol fermentation process. The fermentation processes with substrate glycerol concentrations of 60 g/L and 40 g/L were used as the external validation experiments. The root mean square error of prediction (RMSEP) obtained by analyzing experimental data was 0.341 6 and 0.274 3, respectively. These results showed that the established model gave good prediction and could be effectively used for on-line monitoring the biomass during a 1,3-propanediol fermentation process.

Adolescent mice are less sensitive to the effects of acute nicotine on context pre-exposure than adults.

PubMed

Kutlu, Munir Gunes; Braak, David C; Tumolo, Jessica M; Gould, Thomas J

2016-07-01

Adolescence is a critical developmental period associated with both increased vulnerability to substance abuse and maturation of certain brain regions important for learning and memory such as the hippocampus. In this study, we employed a hippocampus-dependent learning context pre-exposure facilitation effect (CPFE) paradigm in order to test the effects of acute nicotine on contextual processing during adolescence (post-natal day (PND) 38) and adulthood (PND 53). In Experiment 1, adolescent or adult C57BL6/J mice received either saline or one of three nicotine doses (0.09, 0.18, and 0.36mg/kg) prior to contextual pre-exposure and testing. Our results demonstrated that both adolescent and adult mice showed CPFE in the saline groups. However, adolescent mice only showed acute nicotine enhancement of CPFE with the highest nicotine dose whereas adult mice showed the enhancing effects of acute nicotine with all three doses. In Experiment 2, to determine if the lack of nicotine's effects on CPFE shown by adolescent mice is specific to the age when they are tested, mice were either given contextual pre-exposure during adolescence or adulthood and received immediate shock and testing during adulthood after a 15day delay. We found that both adolescent and adult mice showed CPFE in the saline groups when tested during adulthood. However, like Experiment 1, mice that received contextual pre-exposure during adolescence did not show acute nicotine enhancement except at the highest dose (0.36mg/kg) whereas both low (0.09mg/kg) and high (0.36mg/kg) doses enhanced CPFE in adult mice. Finally, we showed that the enhanced freezing response found with 0.36mg/kg nicotine in the 15-day experiment may be a result of decreased locomotor activity as mice that received this dose of nicotine traveled shorter distances in an open field paradigm. Overall, our results indicate that while adolescent mice showed normal contextual processing when tested both during adolescence and adulthood, they are less sensitive to the enhancing effects of nicotine on contextual processing. Copyright © 2016 Elsevier B.V. All rights reserved.

RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis

PubMed Central

Réty, Stéphane; Lebaron, Simon; Deschamps, Patrick; Bareille, Joseph; Jombart, Julie; Robert-Paganin, Julien; Delbos, Lila; Chardon, Florian; Zhang, Elodie; Charenton, Clément; Tollervey, David; Leulliot, Nicolas

2014-01-01

During biogenesis of the 40S and 60S ribosomal subunits, the pre-40S particles are exported to the cytoplasm prior to final cleavage of the 20S pre-rRNA to mature 18S rRNA. Amongst the factors involved in this maturation step, Fap7 is unusual, as it both interacts with ribosomal protein Rps14 and harbors adenylate kinase activity, a function not usually associated with ribonucleoprotein assembly. Human hFap7 also regulates Cajal body assembly and cell cycle progression via the p53–MDM2 pathway. This work presents the functional and structural characterization of the Fap7–Rps14 complex. We report that Fap7 association blocks the RNA binding surface of Rps14 and, conversely, Rps14 binding inhibits adenylate kinase activity of Fap7. In addition, the affinity of Fap7 for Rps14 is higher with bound ADP, whereas ATP hydrolysis dissociates the complex. These results suggest that Fap7 chaperones Rps14 assembly into pre-40S particles via RNA mimicry in an ATP-dependent manner. Incorporation of Rps14 by Fap7 leads to a structural rearrangement of the platform domain necessary for the pre-rRNA to acquire a cleavage competent conformation. PMID:24823650

Solar treatment (H2O2, TiO2-P25 and GO-TiO2 photocatalysis, photo-Fenton) of organic micropollutants, human pathogen indicators, antibiotic resistant bacteria and related genes in urban wastewater.

PubMed

Moreira, Nuno F F; Narciso-da-Rocha, Carlos; Polo-López, M Inmaculada; Pastrana-Martínez, Luisa M; Faria, Joaquim L; Manaia, Célia M; Fernández-Ibáñez, Pilar; Nunes, Olga C; Silva, Adrián M T

2018-05-15

Solar-driven advanced oxidation processes were studied in a pilot-scale photoreactor, as tertiary treatments of effluents from an urban wastewater treatment plant. Solar-H 2 O 2 , heterogeneous photocatalysis (with and/or without the addition of H 2 O 2 and employing three different photocatalysts) and the photo-Fenton process were investigated. Chemical (sulfamethoxazole, carbamazepine, and diclofenac) and biological contaminants (faecal contamination indicators, their antibiotic resistant counterparts, 16S rRNA and antibiotic resistance genes), as well as the whole bacterial community, were characterized. Heterogeneous photocatalysis using TiO 2 -P25 and assisted with H 2 O 2 (P25/H 2 O 2 ) was the most efficient process on the degradation of the chemical organic micropollutants, attaining levels below the limits of quantification in less than 4 h of treatment (corresponding to Q UV  < 40 kJ L -1 ). This performance was followed by the same process without H 2 O 2 , using TiO 2 -P25 or a composite material based on graphene oxide and TiO 2 . Regarding the biological indicators, total faecal coliforms and enterococci and their antibiotic resistant (tetracycline and ciprofloxacin) counterparts were reduced to values close, or beneath, the detection limit (1 CFU 100 mL -1 ) for all treatments employing H 2 O 2 , even upon storage of the treated wastewater for 3-days. Moreover, P25/H 2 O 2 and solar-H 2 O 2 were the most efficient processes in the reduction of the abundance (gene copy number per volume of wastewater) of the analysed genes. However, this reduction was transient for 16S rRNA, intI1 and sul1 genes, since after 3-days storage of the treated wastewater their abundance increased to values close to pre-treatment levels. Similar behaviour was observed for the genes qnrS (using TiO 2 -P25), bla CTX-M and bla TEM (using TiO 2 -P25 and TiO 2 -P25/H 2 O 2 ). Interestingly, higher proportions of sequence reads affiliated to the phylum Proteobacteria (Beta- and Gammaproteobacteria) were found after 3-days storage of treated wastewater than before its treatment. Members of the genera Pseudomonas, Rheinheimera and Methylotenera were among those with overgrowth. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microstructure development in Kolmogorov, Johnson-Mehl, and Avrami nucleation and growth kinetics

NASA Astrophysics Data System (ADS)

Pineda, Eloi; Crespo, Daniel

1999-08-01

A statistical model with the ability to evaluate the microstructure developed in nucleation and growth kinetics is built in the framework of the Kolmogorov, Johnson-Mehl, and Avrami theory. A populational approach is used to compute the observed grain-size distribution. The impingement process which delays grain growth is analyzed, and the effective growth rate of each population is estimated considering the previous grain history. The proposed model is integrated for a wide range of nucleation and growth protocols, including constant nucleation, pre-existing nuclei, and intermittent nucleation with interface or diffusion-controlled grain growth. The results are compared with Monte Carlo simulations, giving quantitative agreement even in cases where previous models fail.

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life.

PubMed

Wampach, Linda; Heintz-Buschart, Anna; Hogan, Angela; Muller, Emilie E L; Narayanasamy, Shaman; Laczny, Cedric C; Hugerth, Luisa W; Bindl, Lutz; Bottu, Jean; Andersson, Anders F; de Beaufort, Carine; Wilmes, Paul

2017-01-01

Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus , and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides . Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

PubMed Central

Wampach, Linda; Heintz-Buschart, Anna; Hogan, Angela; Muller, Emilie E. L.; Narayanasamy, Shaman; Laczny, Cedric C.; Hugerth, Luisa W.; Bindl, Lutz; Bottu, Jean; Andersson, Anders F.; de Beaufort, Carine; Wilmes, Paul

2017-01-01

Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract. PMID:28512451

The wandering mood: psychological and neural determinants of rest-related negative affect.

PubMed

Gruberger, Michal; Maron-Katz, Adi; Sharon, Haggai; Hendler, Talma; Ben-Simon, Eti

2013-01-01

Rest related negative affect (RRNA) has gained scientific interest in the past decade. However, it is mostly studied within the context of mind-wandering (MW), and the relevance of other psychological and neural aspects of the resting state to its' occurrence has never been studied. Several indications associate RRNA with internally directed attention, yet the nature of this relation remains largely unknown. Moreover, the role of neural networks associated with rest related phenomenology - the default mode (DMN), executive (EXE), and salience (SAL) networks, has not been studied in this context. To this end, we explored two 5 (baseline) and 15-minute resting-state simultaneous fMRI-EEG scans of 29 participants. As vigilance has been shown to affect attention, and thus its availability for inward allocation, EEG-based vigilance levels were computed for each participant. Questionnaires for affective assessment were administered before and after scans, and retrospective reports of MW were additionally collected. Results revealed increased negative affect following rest, but only among participants who retained high vigilance levels. Among low-vigilance participants, changes in negative affect were negligible, despite reports of MW occurrence in both groups. In addition, in the high-vigilance group only, a significant increase in functional connectivity (FC) levels was found between the DMN-related ventral anterior cingulate cortex (ACC), associated with emotional processing, and the EXE-related dorsal ACC, associated with monitoring of self and other's behavior. These heightened FC levels further correlated with reported negative affect among this group. Taken together, these results demonstrate that, rather than an unavoidable outcome of the resting state, RRNA depends on internal allocation of attention at rest. Results are discussed in terms of two rest-related possible scenarios which defer in mental and neural processing, and subsequently, in the occurrence of RRNA.

Toxicity phenotype does not correlate with phylogeny of Cylindrospermopsis raciborskii strains.

PubMed

Stucken, Karina; Murillo, Alejandro A; Soto-Liebe, Katia; Fuentes-Valdés, Juan J; Méndez, Marco A; Vásquez, Mónica

2009-02-01

Cylindrospermopsis raciborskii is a species of freshwater, bloom-forming cyanobacterium. C. raciborskii produces toxins, including cylindrospermopsin (hepatotoxin) and saxitoxin (neurotoxin), although non toxin-producing strains are also observed. In spite of differences in toxicity, C. raciborskii strains comprise a monophyletic group, based upon 16S rRNA gene sequence identities (greater than 99%). We performed phylogenetic analyses; 16S rRNA gene and 16S-23S rRNA gene internally transcribed spacer (ITS-1) sequence comparisons, and genomic DNA restriction fragment length polymorphism (RFLP), resolved by pulsed-field gel electrophoresis (PFGE), of strains of C. raciborskii, obtained mainly from the Australian phylogeographic cluster. Our results showed no correlation between toxic phenotype and phylogenetic association in the Australian strains. Analyses of the 16S rRNA gene and the respective ITS-1 sequences (long L, and short S) showed an independent evolution of each ribosomal operon. The genes putatively involved in the cylindrospermopsin biosynthetic pathway were present in one locus and only in the hepatotoxic strains, demonstrating a common genomic organization for these genes and the absence of mutated or inactivated biosynthetic genes in the non toxic strains. In summary, our results support the hypothesis that the genes involved in toxicity may have been transferred as an island by processes of gene lateral transfer, rather than convergent evolution.

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly.

PubMed

Falahati, Hanieh; Pelham-Webb, Bobbie; Blythe, Shelby; Wieschaus, Eric

2016-02-08

Membrane-less organelles are intracellular compartments specialized to carry out specific cellular functions. There is growing evidence supporting the possibility that such organelles form as a new phase, separating from cytoplasm or nucleoplasm. However, a main challenge to such phase separation models is that the initial assembly, or nucleation, of the new phase is typically a highly stochastic process and does not allow for the spatiotemporal precision observed in biological systems. Here, we investigate the initial assembly of the nucleolus, a membrane-less organelle involved in different cellular functions including ribosomal biogenesis. We demonstrate that the nucleolus formation is precisely timed in D. melanogaster embryos and follows the transcription of rRNA. We provide evidence that transcription of rRNA is necessary for overcoming the highly stochastic nucleation step in the formation of the nucleolus, through a seeding mechanism. In the absence of rDNA, the nucleolar proteins studied are able to form high-concentration assemblies. However, unlike the nucleolus, these assemblies are highly variable in number, location, and time at which they form. In addition, quantitative study of the changes in the nucleoplasmic concentration and distribution of these nucleolar proteins in the wild-type embryos is consistent with the role of rRNA in seeding the nucleolus formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bacterial diversity at different stages of the composting process

PubMed Central

2010-01-01

Background Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. Results Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. Conclusions Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants. PMID:20350306

Applying Systems Engineering Reduces Radiology Transport Cycle Times in the Emergency Department.

PubMed

White, Benjamin A; Yun, Brian J; Lev, Michael H; Raja, Ali S

2017-04-01

Emergency department (ED) crowding is widespread, and can result in care delays, medical errors, increased costs, and decreased patient satisfaction. Simultaneously, while capacity constraints on EDs are worsening, contributing factors such as patient volume and inpatient bed capacity are often outside the influence of ED administrators. Therefore, systems engineering approaches that improve throughput and reduce waste may hold the most readily available gains. Decreasing radiology turnaround times improves ED patient throughput and decreases patient waiting time. We sought to investigate the impact of systems engineering science targeting ED radiology transport delays and determine the most effective techniques. This prospective, before-and-after analysis of radiology process flow improvements in an academic hospital ED was exempt from institutional review board review as a quality improvement initiative. We hypothesized that reorganization of radiology transport would improve radiology cycle time and reduce waste. The intervention included systems engineering science-based reorganization of ED radiology transport processes, largely using Lean methodologies, and adding no resources. The primary outcome was average transport time between study order and complete time. All patients presenting between 8/2013-3/2016 and requiring plain film imaging were included. We analyzed electronic medical record data using Microsoft Excel and SAS version 9.4, and we used a two-sample t-test to compare data from the pre- and post-intervention periods. Following the intervention, average transport time decreased significantly and sustainably. Average radiology transport time was 28.7 ± 4.2 minutes during the three months pre-intervention. It was reduced by 15% in the first three months (4.4 minutes [95% confidence interval [CI] 1.5-7.3]; to 24.3 ± 3.3 min, P=0.021), 19% in the following six months (5.4 minutes, 95% CI [2.7-8.2]; to 23.3 ± 3.5 min, P=0.003), and 26% one year following the intervention (7.4 minutes, 95% CI [4.8-9.9]; to 21.3 ± 3.1 min, P=0.0001). This result was achieved without any additional resources, and demonstrated a continual trend towards improvement. This innovation demonstrates the value of systems engineering science to increase efficiency in ED radiology processes. In this study, reorganization of the ED radiology transport process using systems engineering science significantly increased process efficiency without additional resource use.

Applying Systems Engineering Reduces Radiology Transport Cycle Times in the Emergency Department

PubMed Central

White, Benjamin A.; Yun, Brian J.; Lev, Michael H.; Raja, Ali S.

2017-01-01

Introduction Emergency department (ED) crowding is widespread, and can result in care delays, medical errors, increased costs, and decreased patient satisfaction. Simultaneously, while capacity constraints on EDs are worsening, contributing factors such as patient volume and inpatient bed capacity are often outside the influence of ED administrators. Therefore, systems engineering approaches that improve throughput and reduce waste may hold the most readily available gains. Decreasing radiology turnaround times improves ED patient throughput and decreases patient waiting time. We sought to investigate the impact of systems engineering science targeting ED radiology transport delays and determine the most effective techniques. Methods This prospective, before-and-after analysis of radiology process flow improvements in an academic hospital ED was exempt from institutional review board review as a quality improvement initiative. We hypothesized that reorganization of radiology transport would improve radiology cycle time and reduce waste. The intervention included systems engineering science-based reorganization of ED radiology transport processes, largely using Lean methodologies, and adding no resources. The primary outcome was average transport time between study order and complete time. All patients presenting between 8/2013–3/2016 and requiring plain film imaging were included. We analyzed electronic medical record data using Microsoft Excel and SAS version 9.4, and we used a two-sample t-test to compare data from the pre- and post-intervention periods. Results Following the intervention, average transport time decreased significantly and sustainably. Average radiology transport time was 28.7 ± 4.2 minutes during the three months pre-intervention. It was reduced by 15% in the first three months (4.4 minutes [95% confidence interval [CI] 1.5–7.3]; to 24.3 ± 3.3 min, P=0.021), 19% in the following six months (5.4 minutes, 95% CI [2.7–8.2]; to 23.3 ± 3.5 min, P=0.003), and 26% one year following the intervention (7.4 minutes, 95% CI [4.8–9.9]; to 21.3 ± 3.1 min, P=0.0001). This result was achieved without any additional resources, and demonstrated a continual trend towards improvement. This innovation demonstrates the value of systems engineering science to increase efficiency in ED radiology processes. Conclusion In this study, reorganization of the ED radiology transport process using systems engineering science significantly increased process efficiency without additional resource use. PMID:28435492

Sleep Problems in Infants Decrease following Massage Therapy.

ERIC Educational Resources Information Center

Field, Tiffany; Hernandez-Reif, Maria

2001-01-01

Examined the effectiveness of pre-bedtime massages for infants and toddlers with sleep onset problems. Found that, compared to bedtime stories, massages produced fewer sleep delays and a shortened latency to sleep onset. (Author/DLH)

Hypo-responsiveness of interleukin-8 production in human embryonic epithelial intestine 407 cells independent of NF-{kappa}B pathway: New lessons from endotoxin and ribotoxic deoxynivalenol

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

Moon, Yuseok; Yang, Hyun; Park, Seung-Hwan

Mucosal epithelium senses external toxic insults and transmits the danger signals into the epithelial cells in order to activate a broad range of inflammatory responses. However, pre-exposure to the commensal endotoxins can induce inflammatory tolerance and maintain the homeostasis without excessive immune responses. We recently reported that ribotoxin deoxynivalenol (DON) and its derivatives elicited the pro-inflammatory response as the mucosal insults in human epithelial cells. Taking the knowledge into consideration, we tested the hypothesis that endotoxin pre-exposure can attenuate ribotoxin-induced epithelial interleukin-8 (IL-8) production via a tolerance mechanism. Pre-exposure to endotoxin repressed IL-8 release and its gene expression. However, inflammatorymore » tolerance was not mediated by the attenuated NF-{kappa}B activation which has been generally recognized as the major mediator of LPS-mediated toll-like receptor (TLR) signaling pathway. Instead, pre-exposure to endotoxin was observed to trigger the delayed induction of peroxisome proliferator-activated receptor gamma (PPAR-{gamma}) which contributed to the diminished IL-8 production in the human epithelial cells. Moreover, endogenous PPAR-{gamma} agonist suppressed toxicant-mediated interleukin-8 production and IL-8 mRNA stability. Taken together, endotoxin induced hypo-production of pro-inflammatory cytokine IL-8 in the human epithelial cells, which was associated with the delayed activation of PPAR-{gamma} expression by pre-existing endotoxin.« less

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

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

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial darkmore » matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.« less

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

DOE PAGES

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.; ...

2016-09-29

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial darkmore » matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.« less

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples.

PubMed

Barb, Jennifer J; Oler, Andrew J; Kim, Hyung-Suk; Chalmers, Natalia; Wallen, Gwenyth R; Cashion, Ann; Munson, Peter J; Ames, Nancy J

2016-01-01

There is much speculation on which hypervariable region provides the highest bacterial specificity in 16S rRNA sequencing. The optimum solution to prevent bias and to obtain a comprehensive view of complex bacterial communities would be to sequence the entire 16S rRNA gene; however, this is not possible with second generation standard library design and short-read next-generation sequencing technology. This paper examines a new process using seven hypervariable or V regions of the 16S rRNA (six amplicons: V2, V3, V4, V6-7, V8, and V9) processed simultaneously on the Ion Torrent Personal Genome Machine (Life Technologies, Grand Island, NY). Four mock samples were amplified using the 16S Ion Metagenomics Kit™ (Life Technologies) and their sequencing data is subjected to a novel analytical pipeline. Results are presented at family and genus level. The Kullback-Leibler divergence (DKL), a measure of the departure of the computed from the nominal bacterial distribution in the mock samples, was used to infer which region performed best at the family and genus levels. Three different hypervariable regions, V2, V4, and V6-7, produced the lowest divergence compared to the known mock sample. The V9 region gave the highest (worst) average DKL while the V4 gave the lowest (best) average DKL. In addition to having a high DKL, the V9 region in both the forward and reverse directions performed the worst finding only 17% and 53% of the known family level and 12% and 47% of the genus level bacteria, while results from the forward and reverse V4 region identified all 17 family level bacteria. The results of our analysis have shown that our sequencing methods using 6 hypervariable regions of the 16S rRNA and subsequent analysis is valid. This method also allowed for the assessment of how well each of the variable regions might perform simultaneously. Our findings will provide the basis for future work intended to assess microbial abundance at different time points throughout a clinical protocol.

Identification of nucleolus-associated chromatin domains reveals the role of the nucleolus in the 3D organisation of the A. thaliana genome

PubMed Central

Pontvianne, Frédéric; Carpentier, Marie-Christine; Durut, Nathalie; Pavlištová, Veronika; Jaške, Karin; Schořová, Šárka; Parrinello, Hugues; Rohmer, Marine; Pikaard, Craig S; Fojtová, Miloslava; Fajkus, Jiří; Saez-Vasquez, Julio

2017-01-01

The nucleolus is the site of ribosomal RNA (rRNA) gene transcription, rRNA processing and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli by Fluorescence Activated Cell Sorting (FACS) and identified Nucleolus-Associated Chromatin Domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein, NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions and mostly inactive protein-coding genes. However, NADs also include active ribosomal RNA genes, and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance. PMID:27477271

The nucleolus—guardian of cellular homeostasis and genome integrity.

PubMed

Grummt, Ingrid

2013-12-01

All organisms sense and respond to conditions that stress their homeostasis by downregulating the synthesis of rRNA and ribosome biogenesis, thus designating the nucleolus as the central hub in coordinating the cellular stress response. One of the most intriguing roles of the nucleolus, long regarded as a mere ribosome-producing factory, is its participation in monitoring cellular stress signals and transmitting them to the RNA polymerase I (Pol I) transcription machinery. As rRNA synthesis is a most energy-consuming process, switching off transcription of rRNA genes is an effective way of saving the energy required to maintain cellular homeostasis during acute stress. The Pol I transcription machinery is the key convergence point that collects and integrates a vast array of information from cellular signaling cascades to regulate ribosome production which, in turn, guides cell growth and proliferation. This review focuses on the mechanisms that link cell physiology to rDNA silencing, a prerequisite for nucleolar integrity and cell survival.

The rRNA evolution and procaryotic phylogeny

NASA Technical Reports Server (NTRS)

Fox, G. E.

1986-01-01

Studies of ribosomal RNA primary structure allow reconstruction of phylogenetic trees for prokaryotic organisms. Such studies reveal major dichotomy among the bacteria that separates them into eubacteria and archaebacteria. Both groupings are further segmented into several major divisions. The results obtained from 5S rRNA sequences are essentially the same as those obtained with the 16S rRNA data. In the case of Gram negative bacteria the ribosomal RNA sequencing results can also be directly compared with hybridization studies and cytochrome c sequencing studies. There is again excellent agreement among the several methods. It seems likely then that the overall picture of microbial phylogeny that is emerging from the RNA sequence studies is a good approximation of the true history of these organisms. The RNA data allow examination of the evolutionary process in a semi-quantitative way. The secondary structures of these RNAs are largely established. As a result it is possible to recognize examples of local structural evolution. Evolutionary pathways accounting for these events can be proposed and their probability can be assessed.

Diversity of Metabolically Active Bacteria in Water-Flooded High-Temperature Heavy Oil Reservoir

PubMed Central

Nazina, Tamara N.; Shestakova, Natalya M.; Semenova, Ekaterina M.; Korshunova, Alena V.; Kostrukova, Nadezda K.; Tourova, Tatiana P.; Min, Liu; Feng, Qingxian; Poltaraus, Andrey B.

2017-01-01

The goal of this work was to study the overall genomic diversity of microorganisms of the Dagang high-temperature oilfield (PRC) and to characterize the metabolically active fraction of these populations. At this water-flooded oilfield, the microbial community of formation water from the near-bottom zone of an injection well where the most active microbial processes of oil degradation occur was investigated using molecular, cultural, radiotracer, and physicochemical techniques. The samples of microbial DNA and RNA from back-flushed water were used to obtain the clone libraries for the 16S rRNA gene and cDNA of 16S rRNA, respectively. The DNA-derived clone libraries were found to contain bacterial and archaeal 16S rRNA genes and the alkB genes encoding alkane monooxygenases similar to those encoded by alkB-geo1 and alkB-geo6 of geobacilli. The 16S rRNA genes of methanogens (Methanomethylovorans, Methanoculleus, Methanolinea, Methanothrix, and Methanocalculus) were predominant in the DNA-derived library of Archaea cloned sequences; among the bacterial sequences, the 16S rRNA genes of members of the genus Geobacillus were the most numerous. The RNA-derived library contained only bacterial cDNA of the 16S rRNA sequences belonging to metabolically active aerobic organotrophic bacteria (Tepidimonas, Pseudomonas, Acinetobacter), as well as of denitrifying (Azoarcus, Tepidiphilus, Calditerrivibrio), fermenting (Bellilinea), iron-reducing (Geobacter), and sulfate- and sulfur-reducing bacteria (Desulfomicrobium, Desulfuromonas). The presence of the microorganisms of the main functional groups revealed by molecular techniques was confirmed by the results of cultural, radioisotope, and geochemical research. Functioning of the mesophilic and thermophilic branches was shown for the microbial food chain of the near-bottom zone of the injection well, which included the microorganisms of the carbon, sulfur, iron, and nitrogen cycles. PMID:28487680

Loss-to-follow-up and delay to treatment initiation in Pakistan's national tuberculosis control programme.

PubMed

Ali, Syed Mustafa; Naureen, Farah; Noor, Arif; Fatima, Irum; Viney, Kerri; Ishaq, Muhammad; Anjum, Naveed; Rashid, Aamna; Haider, Ghulam Rasool; Khan, Muhammad Aamir; Aamir, Javariya

2018-03-09

Researchers and policy-makers have identified loss to follow-up as a major programmatic problem. Therefore, the objective of this study is to quantify TB related pre-treatment loss to follow up and treatment delay in private sector health care facilities in Pakistan. This was a retrospective, descriptive cohort study using routinely collected programmatic data from TB referral, diagnosis and treatment registers. Data from 48 private healthcare facilities were collected using an online questionnaire prepared in ODK Collect, for the period October 2015 to March 2016. Data were analysed using SPSS. We calculated the: (1) number and proportion of patients who were lost to follow-up during the diagnostic period, (2) number and proportion of patients with pre-treatment loss to follow-up, and (3) the number of days between diagnosis and initiation of treatment. One thousand five hundred ninety-six persons with presumptive TB were referred to the laboratory. Of these, 96% (n = 1538) submitted an on-the-spot sputum sample. Of the 1538 people, 1462 (95%) people subsequently visited the laboratory to submit the early morning (i.e. the second) sample. Hence, loss to follow-up during the diagnostic process was 8% overall (n = 134). Of the 1462 people who submitted both sputum samples, 243 (17%) were diagnosed with sputum smear-positive pulmonary TB and 231 were registered for anti-TB treatment, hence, loss in the pre-treatment phase was 4.9% (n = 12). 152 persons with TB (66%) initiated TB treatment either on the day of TB diagnosis or the next day. A further 79 persons with TB (34%) commenced TB treatment within a mean time of 7 days (range 2 to 64 days). Concentrated efforts should be made by the National TB Control Programme to retain TB patients and innovative methods such as text reminders and behavior change communication may need to be used and tested.

Emergency surgery pre-operative delays - realities and economic impacts.

PubMed

O'Leary, D P; Beecher, S; McLaughlin, R

2014-12-01

A key principle of acute surgical service provision is the establishment of a distinct patient flow process and an emergency theatre. Time-to-theatre (TTT) is a key performance indicator of theatre efficiency. The combined impacts of an aging population, increasing demands and complexity associated with centralisation of emergency and oncology services has placed pressure on emergency theatre access. We examined our institution's experience with running a designated emergency theatre for acute surgical patients. A retrospective review of an electronic prospectively maintained database was performed between 1/1/12 and 31/12/13. A cost analysis was conducted to assess the economic impact of delayed TTT, with every 24hr delay incurring the cost of an additional overnight bed. Delays and the economic effects were assessed only after the first 24 h as an in-patient had elapsed. In total, 7041 procedures were performed. Overall mean TTT was 26 h, 2 min. There were significant differences between different age groups, with those aged under 16 year and over 65 having mean TTT at 6 h, 34 min (95% C.I. 0.51-2.15, p < 0.001) and 23 h, 41 min (95% C.I. 19.6-23.9, p < 0.001) respectively. 2421 (34%) waited greater than 24 h for emergency procedures. The >65 years age group had a mean TTT of 23 h, 41 min which was significantly longer than the overall mean TTT Vascular and urological emergencies are significantly disadvantaged in competition with other services for a shared emergency theatre. The economic impact of delayed TTT was calculated at €7,116,000, or €9880/day of additional costs generated from delayed TTT over a 24 month period. One third of patients waited longer than 24 h for emergency surgery, with the elderly disproportionately represented in this group. Aside from the clinical risks of delayed and out of hours surgery, such practices incur significant additional costs. New strategies must be devised to ensure efficient access to emergency theatres, investment in such services is likely to be financially and clinically beneficial. Copyright © 2014 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

Texture analysis of common renal masses in multiple MR sequences for prediction of pathology

NASA Astrophysics Data System (ADS)

Hoang, Uyen N.; Malayeri, Ashkan A.; Lay, Nathan S.; Summers, Ronald M.; Yao, Jianhua

2017-03-01

This pilot study performs texture analysis on multiple magnetic resonance (MR) images of common renal masses for differentiation of renal cell carcinoma (RCC). Bounding boxes are drawn around each mass on one axial slice in T1 delayed sequence to use for feature extraction and classification. All sequences (T1 delayed, venous, arterial, pre-contrast phases, T2, and T2 fat saturated sequences) are co-registered and texture features are extracted from each sequence simultaneously. Random forest is used to construct models to classify lesions on 96 normal regions, 87 clear cell RCCs, 8 papillary RCCs, and 21 renal oncocytomas; ground truths are verified through pathology reports. The highest performance is seen in random forest model when data from all sequences are used in conjunction, achieving an overall classification accuracy of 83.7%. When using data from one single sequence, the overall accuracies achieved for T1 delayed, venous, arterial, and pre-contrast phase, T2, and T2 fat saturated were 79.1%, 70.5%, 56.2%, 61.0%, 60.0%, and 44.8%, respectively. This demonstrates promising results of utilizing intensity information from multiple MR sequences for accurate classification of renal masses.

Fungal community and cellulose-degrading genes in the composting process of Chinese medicinal herbal residues.

PubMed

Tian, Xueping; Yang, Tao; He, Jingzhong; Chu, Qian; Jia, Xiaojun; Huang, Jun

2017-10-01

The fungal community and the population of 16S rRNA, 18S rRNA and cellulose-degrading genes during the 30-day composting process of Chinese medicinal herbal residues were investigated using Illumina MiSeq and quantitative real-time PCR. An obvious succession of fungal communities occurred during the composting process. Unidentified fungi predominated in the raw materials. As composting progressed, Ascomycota became the most dominant phylum, with Aspergillus being the most dominant genus, and Aspergillus fumigatus making up 99.65% of that genus. Because of the inoculation of cellulolytic fungi in the mature stage, the cellulose degradation rate in inoculation groups was faster and the relative abundances of Aspergillus and the glycoside hydrolase family 7 genes were significantly higher than those in the control groups. These indicated that the fungal inoculants facilitated the degradation of cellulose, increased cellulolytic fungi and optimized the community structure. Copyright © 2017. Published by Elsevier Ltd.

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

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

Xu, Ling; Naylor, Dan; Dong, Zhaobin

Here, drought stress is a major obstacle to crop productivity, and the severity and frequency of drought are expected to increase in the coming century. Certain root-associated bacteria have been shown to mitigate the negative effects of drought stress on plant growth, and manipulation of the crop microbiome is an emerging strategy for overcoming drought stress in agricultural systems, yet the effect of drought on the development of the root microbiome is poorly understood. Through 16S rRNA amplicon and metatranscriptome sequencing, as well as root metabolomics, we demonstrate that drought delays the development of the early sorghum root microbiome andmore » causes increased abundance and activity of monoderm bacteria, which lack an outer cell membrane and contain thick cell walls. Our data suggest that altered plant metabolism and increased activity of bacterial ATP-binding cassette (ABC) transporter genes are correlated with these shifts in community composition. Finally, inoculation experiments with monoderm isolates indicate that increased colonization of the root during drought can positively impact plant growth. Collectively, these results demonstrate the role that drought plays in restructuring the root microbiome and highlight the importance of temporal sampling when studying plant-associated microbiomes.« less

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria.

PubMed

Xu, Ling; Naylor, Dan; Dong, Zhaobin; Simmons, Tuesday; Pierroz, Grady; Hixson, Kim K; Kim, Young-Mo; Zink, Erika M; Engbrecht, Kristin M; Wang, Yi; Gao, Cheng; DeGraaf, Stephanie; Madera, Mary A; Sievert, Julie A; Hollingsworth, Joy; Birdseye, Devon; Scheller, Henrik V; Hutmacher, Robert; Dahlberg, Jeffery; Jansson, Christer; Taylor, John W; Lemaux, Peggy G; Coleman-Derr, Devin

2018-05-01

Drought stress is a major obstacle to crop productivity, and the severity and frequency of drought are expected to increase in the coming century. Certain root-associated bacteria have been shown to mitigate the negative effects of drought stress on plant growth, and manipulation of the crop microbiome is an emerging strategy for overcoming drought stress in agricultural systems, yet the effect of drought on the development of the root microbiome is poorly understood. Through 16S rRNA amplicon and metatranscriptome sequencing, as well as root metabolomics, we demonstrate that drought delays the development of the early sorghum root microbiome and causes increased abundance and activity of monoderm bacteria, which lack an outer cell membrane and contain thick cell walls. Our data suggest that altered plant metabolism and increased activity of bacterial ATP-binding cassette (ABC) transporter genes are correlated with these shifts in community composition. Finally, inoculation experiments with monoderm isolates indicate that increased colonization of the root during drought can positively impact plant growth. Collectively, these results demonstrate the role that drought plays in restructuring the root microbiome and highlight the importance of temporal sampling when studying plant-associated microbiomes. Copyright © 2018 the Author(s). Published by PNAS.

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

DOE PAGES

Xu, Ling; Naylor, Dan; Dong, Zhaobin; ...

2018-04-16

Here, drought stress is a major obstacle to crop productivity, and the severity and frequency of drought are expected to increase in the coming century. Certain root-associated bacteria have been shown to mitigate the negative effects of drought stress on plant growth, and manipulation of the crop microbiome is an emerging strategy for overcoming drought stress in agricultural systems, yet the effect of drought on the development of the root microbiome is poorly understood. Through 16S rRNA amplicon and metatranscriptome sequencing, as well as root metabolomics, we demonstrate that drought delays the development of the early sorghum root microbiome andmore » causes increased abundance and activity of monoderm bacteria, which lack an outer cell membrane and contain thick cell walls. Our data suggest that altered plant metabolism and increased activity of bacterial ATP-binding cassette (ABC) transporter genes are correlated with these shifts in community composition. Finally, inoculation experiments with monoderm isolates indicate that increased colonization of the root during drought can positively impact plant growth. Collectively, these results demonstrate the role that drought plays in restructuring the root microbiome and highlight the importance of temporal sampling when studying plant-associated microbiomes.« less

Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays

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

Thanh, Vo Hong, E-mail: vo@cosbi.eu; Priami, Corrado, E-mail: priami@cosbi.eu; Department of Mathematics, University of Trento

2014-10-07

We propose a new exact stochastic rejection-based simulation algorithm for biochemical reactions and extend it to systems with delays. Our algorithm accelerates the simulation by pre-computing reaction propensity bounds to select the next reaction to perform. Exploiting such bounds, we are able to avoid recomputing propensities every time a (delayed) reaction is initiated or finished, as is typically necessary in standard approaches. Propensity updates in our approach are still performed, but only infrequently and limited for a small number of reactions, saving computation time and without sacrificing exactness. We evaluate the performance improvement of our algorithm by experimenting with concretemore » biological models.« less

Systematic Analysis of γ-Aminobutyric Acid (GABA) Metabolism and Function in the Social Amoeba Dictyostelium discoideum*

PubMed Central

Wu, Yuantai; Janetopoulos, Chris

2013-01-01

While GABA has been suggested to regulate spore encapsulation in the social amoeba Dictyostelium discoideum, the metabolic profile and other potential functions of GABA during development remain unclear. In this study, we investigated the homeostasis of GABA metabolism by disrupting genes related to GABA metabolism and signaling. Extracellular levels of GABA are tightly regulated during early development, and GABA is generated by the glutamate decarboxylase, GadB, during growth and in early development. However, overexpression of the prespore-specific homologue, GadA, in the presence of GadB reduces production of extracellular GABA. Perturbation of extracellular GABA levels delays the process of aggregation. Cytosolic GABA is degraded by the GABA transaminase, GabT, in the mitochondria. Disruption of a putative vesicular GABA transporter (vGAT) homologue DdvGAT reduces secreted GABA. We identified the GABAB receptor-like family member GrlB as the major GABA receptor during early development, and either disruption or overexpression of GrlB delays aggregation. This delay is likely the result of an abolished pre-starvation response and late expression of several “early” developmental genes. Distinct genes are employed for GABA generation during sporulation. During sporulation, GadA alone is required for generating GABA and DdvGAT is likely responsible for GABA secretion. GrlE but not GrlB is the GABA receptor during late development. PMID:23548898

The Effects of HZE Particles, γ and X-ray Radiation on the Survival and Genetic Integrity of Halobacterium salinarum NRC-1, Halococcus hamelinensis, and Halococcus morrhuae

NASA Astrophysics Data System (ADS)

Leuko, Stefan; Rettberg, Petra

2017-02-01

Three halophilic archaea, Halobacterium salinarum NRC-1, Halococcus hamelinensis, and Halococcus morrhuae, have been exposed to different regimes of simulated outer space ionizing radiation. Strains were exposed to high-energy heavy ion (HZE) particles, namely iron and argon ions, as well as to γ radiation (60Co) and X-rays, and the survival and the genetic integrity of the 16S rRNA gene were evaluated. Exposure to 1 kGy of argon or iron ions at the Heavy Ion Medical Accelerator in Chiba (HIMAC) facility at the National Institute for Radiological Sciences (NIRS) in Japan did not lead to a detectable loss in viability; only after exposure to 2 kGy of iron ions a decline in survival was observed. Furthermore, a delay in growth was manifested following exposure to 2 kGy iron ions. DNA integrity of the 16S rRNA was not compromised up to 1 kGy, with the exception of Hcc. hamelinensis following exposure to argon particles. All three strains showed a high resistance toward X-rays (exposed at the DLR in Cologne, Germany), where Hcc. hamelinensis and Hcc. morrhuae displayed better survival compared to Hbt. salinarum NRC-1. In all three organisms the DNA damage increased in a dose-dependent manner. To determine a biological endpoint for survival following exposure to γ radiation, strains were exposed to up to 112 kGy at the Beta-Gamma-Service GmbH (BGS) in Germany. Although all strains were incubated for up to 4 months, only Hcc. hamelinensis and Hcc. morrhuae recovered from 6 kGy of γ radiation. In comparison, Hbt. salinarum NRC-1 did not recover. The 16S rRNA gene integrity stayed remarkably well preserved up to 48 kGy for both halococci. This research presents novel data on the survival and genetic stability of three halophilic archaea following exposure to simulated outer space radiation.

Molecular characterization of 5S ribosomal RNA genes and transcripts in the protozoan parasite Leishmania major.

PubMed

Moreno-Campos, Rodrigo; Florencio-Martínez, Luis E; Nepomuceno-Mejía, Tomás; Rojas-Sánchez, Saúl; Vélez-Ramírez, Daniel E; Padilla-Mejía, Norma E; Figueroa-Angulo, Elisa; Manning-Cela, Rebeca; Martínez-Calvillo, Santiago

2016-12-01

Eukaryotic 5S rRNA, synthesized by RNA polymerase III (Pol III), is an essential component of the large ribosomal subunit. Most organisms contain hundreds of 5S rRNA genes organized into tandem arrays. However, the genome of the protozoan parasite Leishmania major contains only 11 copies of the 5S rRNA gene, which are interspersed and associated with other Pol III-transcribed genes. Here we report that, in general, the number and order of the 5S rRNA genes is conserved between different species of Leishmania. While in most organisms 5S rRNA genes are normally associated with the nucleolus, combined fluorescent in situ hybridization and indirect immunofluorescence experiments showed that 5S rRNA genes are mainly located at the nuclear periphery in L. major. Similarly, the tandemly repeated 5S rRNA genes in Trypanosoma cruzi are dispersed throughout the nucleus. In contrast, 5S rRNA transcripts in L. major were localized within the nucleolus, and scattered throughout the cytoplasm, where mature ribosomes are located. Unlike other rRNA species, stable antisense RNA complementary to 5S rRNA is not detected in L. major.

Decreasing delays in urgent and expedited surgery in a university teaching hospital through audit and communication between peri-operative and surgical directorates.

PubMed

Cosgrove, J F; Gaughan, M; Snowden, C P; Lees, T

2008-06-01

National Confidential Enquiry into Patient Outcome and Death guidelines for urgent surgery recommend a fully staffed emergency operating theatre and restriction of 'after-midnight' operating to immediate life-, limb- or organ-threatening conditions. Audit performed in our institution demonstrated significant decreases in waiting times for urgent surgery and an increased seniority of medical care associated with overnight pre-operative assessment of patients by anaesthetic trainees. Nevertheless, urgent cases continued to be delayed unnecessarily. A classification of delays was developed from existing guidelines and their incidence was audited. The results were disseminated to involved directorates. A repeat of the audit demonstrated a significant decrease in delays (p = 0.001), a significant increase in the availability of surgeons (p = 0.001) and a significant decrease in the median waiting time for urgent surgery compared to the first audit cycle and a previous standard (p < 0.01). We conclude that auditing delays and disseminating the results of the audit significantly decreases delays and median waiting times for urgent surgery because of improved surgical availability.

The dopamine antagonist cis-flupenthixol blocks the expression of the conditioned positive but not the negative effects of cocaine in rats

PubMed Central

Wenzel, Jennifer M.; Su, Zu-In; Shelton, Kerisa; Dominguez, Hiram M.; von Furstenberg, Victoria A.; Ettenberg, Aaron

2013-01-01

Human cocaine users report that the initial “high” produced by cocaine administration is followed by an anxiogenic “crash”. Given that cocaine has such robust and opposing properties, it is likely that both the positive and negative effects of cocaine contribute to an individual’s motivation to administer the drug. Despite this likelihood, the neurobiology underlying cocaine’s dual processes remains unclear. While much literature supports a role for dopamine (DA) in cocaine reward, it is uncertain if DA also contributes to the drug’s negative effects. Our laboratory has extensively utilized a modified conditioned place test to explore cocaine’s opponent processes. In this paradigm rats develop conditioned place preferences (CPPs) for an environment paired with the immediate/positive effects of cocaine, and conditioned place aversions (CPAs) for an environment paired with the delayed/negative effects present 15-min after i.v. injection. In the current study rats were conditioned to associate an environment with either the immediate or delayed effects of i.v. cocaine (1 mg/kg/0.1 ml) three hours after i.p. pre-treatment with either the DA D1/D2 receptor antagonist cis-flupenthixol (0.5 mg/kg/ml) or saline vehicle. As expected, vehicle-treated control animals developed the normal pattern of CPPs for cocaine’s immediate effects or CPAs for the delayed effects of cocaine. However, while DA receptor antagonism prevented the expression of cocaine CPPs it did not alter the expression of cocaine-induced CPAs. These data confirm a role for DA transmission in cocaine reward but suggest that different neural pathways mediate the drug’s negative/anxiogenic properties. PMID:24012795

The increasing threat to stratospheric ozone from dichloromethane.

PubMed

Hossaini, Ryan; Chipperfield, Martyn P; Montzka, Stephen A; Leeson, Amber A; Dhomse, Sandip S; Pyle, John A

2017-06-27

It is well established that anthropogenic chlorine-containing chemicals contribute to ozone layer depletion. The successful implementation of the Montreal Protocol has led to reductions in the atmospheric concentration of many ozone-depleting gases, such as chlorofluorocarbons. As a consequence, stratospheric chlorine levels are declining and ozone is projected to return to levels observed pre-1980 later this century. However, recent observations show the atmospheric concentration of dichloromethane-an ozone-depleting gas not controlled by the Montreal Protocol-is increasing rapidly. Using atmospheric model simulations, we show that although currently modest, the impact of dichloromethane on ozone has increased markedly in recent years and if these increases continue into the future, the return of Antarctic ozone to pre-1980 levels could be substantially delayed. Sustained growth in dichloromethane would therefore offset some of the gains achieved by the Montreal Protocol, further delaying recovery of Earth's ozone layer.

The increasing threat to stratospheric ozone from dichloromethane

NASA Astrophysics Data System (ADS)

Hossaini, Ryan; Chipperfield, Martyn P.; Montzka, Stephen A.; Leeson, Amber A.; Dhomse, Sandip S.; Pyle, John A.

2017-06-01

It is well established that anthropogenic chlorine-containing chemicals contribute to ozone layer depletion. The successful implementation of the Montreal Protocol has led to reductions in the atmospheric concentration of many ozone-depleting gases, such as chlorofluorocarbons. As a consequence, stratospheric chlorine levels are declining and ozone is projected to return to levels observed pre-1980 later this century. However, recent observations show the atmospheric concentration of dichloromethane--an ozone-depleting gas not controlled by the Montreal Protocol--is increasing rapidly. Using atmospheric model simulations, we show that although currently modest, the impact of dichloromethane on ozone has increased markedly in recent years and if these increases continue into the future, the return of Antarctic ozone to pre-1980 levels could be substantially delayed. Sustained growth in dichloromethane would therefore offset some of the gains achieved by the Montreal Protocol, further delaying recovery of Earth's ozone layer.

An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

PubMed

Shiao, Yih-Horng; Lupascu, Sorin T; Gu, Yuhan D; Kasprzak, Wojciech; Hwang, Christopher J; Fields, Janet R; Leighty, Robert M; Quiñones, Octavio; Shapiro, Bruce A; Alvord, W Gregory; Anderson, Lucy M

2009-10-19

Ribosomal RNA (rRNA) is a central regulator of cell growth and may control cancer development. A cis noncoding rRNA (nc-rRNA) upstream from the 45S rRNA transcription start site has recently been implicated in control of rRNA transcription in mouse fibroblasts. We investigated whether a similar nc-rRNA might be expressed in human cancer epithelial cells, and related to any genomic characteristics. Using quantitative rRNA measurement, we demonstrated that a nc-rRNA is transcribed in human lung epithelial and lung cancer cells, starting from approximately -1000 nucleotides upstream of the rRNA transcription start site (+1) and extending at least to +203. This nc-rRNA was significantly more abundant in the majority of lung cancer cell lines, relative to a nontransformed lung epithelial cell line. Its abundance correlated negatively with total 45S rRNA in 12 of 13 cell lines (P = 0.014). During sequence analysis from -388 to +306, we observed diverse, frequent intercopy single nucleotide polymorphisms (SNPs) in rRNA, with a frequency greater than predicted by chance at 12 sites. A SNP at +139 (U/C) in the 5' leader sequence varied among the cell lines and correlated negatively with level of the nc-rRNA (P = 0.014). Modelling of the secondary structure of the rRNA 5'-leader sequence indicated a small increase in structural stability due to the +139 U/C SNP and a minor shift in local configuration occurrences. The results demonstrate occurrence of a sense nc-rRNA in human lung epithelial and cancer cells, and imply a role in regulation of the rRNA gene, which may be affected by a +139 SNP in the 5' leader sequence of the primary rRNA transcript.

Discriminating neurological from psychiatric hypersomnia using the forced awakening test.

PubMed

Peter-Derex, L; Perrin, F; Petitjean, T; Garcia-Larrea, L; Bastuji, H

2013-06-01

Sleep inertia refers to the inability to attain full alertness following awakening from sleep and is a major component of hypersomnia. As event-related potentials (ERPs) are correlated to the degree of consciousness, they allow exploring information processing in transitional states of vigilance. Their modifications during forced awakening (FA) context have been shown to reflect sleep inertia. To assess the diagnostic value of a FA test using an oddball stimulation protocol during a nap in a representative sample of patients with excessive daytime sleepiness (EDS). One hundred and seventy three patients [30 narcolepsy, 62 idiopathic hypersomnia, 33 sleep apnoea syndrome, and 48 other (mainly psychiatric) hypersomnia] performed an auditory target detection stimulation task during pre-, post-nap wakefulness, and during two successive intra-nap FA while the EEG was simultaneously recorded. Both the accuracy of target detection and the ERPs were evaluated. ERPs during forced awakening test were considered to reflect sleep inertia if they presented with a P300 delay and/or sleep negativities (N350/N550). Pre-nap behavior and ERPs were normal in all patients. Behavioral results were significantly worse during FA than during wakefulness for all groups of patients. P300 latencies were significantly delayed on FA conditions in each group of patients except the psychiatric group. Sensitivity and specificity for detection of sleep inertia were 64% and 94%, respectively, with predictive values of 96% (positive) and 50% (negative). Our results suggest that the FA test could be helpful as a diagnostic procedure for discriminating neurological from psychiatric hypersomnia. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Standardized Reporting System Use During Handoffs Reduces Patient Length of Stay in the Emergency Department.

PubMed

Dahlquist, Robert T; Reyner, Karina; Robinson, Richard D; Farzad, Ali; Laureano-Phillips, Jessica; Garrett, John S; Young, Joseph M; Zenarosa, Nestor R; Wang, Hao

2018-05-01

Emergency department (ED) shift handoffs are potential sources of delay in care. We aimed to determine the impact that using standardized reporting tool and process may have on throughput metrics for patients undergoing a transition of care at shift change. We performed a prospective, pre- and post-intervention quality improvement study from September 1 to November 30, 2015. A handoff procedure intervention, including a mandatory workshop and personnel training on a standard reporting system template, was implemented. The primary endpoint was patient length of stay (LOS). A comparative analysis of differences between patient LOS and various handoff communication methods were assessed pre- and post-intervention. Communication methods were entered a multivariable logistic regression model independently as risk factors for patient LOS. The final analysis included 1,006 patients, with 327 comprising the pre-intervention and 679 comprising the post-intervention populations. Bedside rounding occurred 45% of the time without a standard reporting during pre-intervention and increased to 85% of the time with the use of a standard reporting system in the post-intervention period (P < 0.001). Provider time (provider-initiated care to patient care completed) in the pre-intervention period averaged 297 min, but decreased to 265 min in the post-intervention period (P < 0.001). After adjusting for other communication methods, the use of a standard reporting system during handoff was associated with shortened ED LOS (OR = 0.60, 95% CI 0.40 - 0.90, P < 0.05). Standard reporting system use during emergency physician handoffs at shift change improves ED throughput efficiency and is associated with shorter ED LOS.

Evaluation of focused ultrasound algorithms: Issues for reducing pre-focal heating and treatment time.

PubMed

Yiannakou, Marinos; Trimikliniotis, Michael; Yiallouras, Christos; Damianou, Christakis

2016-02-01

Due to the heating in the pre-focal field the delay between successive movements in high intensity focused ultrasound (HIFU) are sometimes as long as 60s, resulting to treatment time in the order of 2-3h. Because there is generally a requirement to reduce treatment time, we were motivated to explore alternative transducer motion algorithms in order to reduce pre-focal heating and treatment time. A 1 MHz single element transducer with 4 cm diameter and 10 cm focal length was used. A simulation model was developed that estimates the temperature, thermal dose and lesion development in the pre-focal field. The simulated temperature history that was combined with the motion algorithms produced thermal maps in the pre-focal region. Polyacrylimde gel phantom was used to evaluate the induced pre-focal heating for each motion algorithm used, and also was used to assess the accuracy of the simulation model. Three out of the six algorithms having successive steps close to each other, exhibited severe heating in the pre-focal field. Minimal heating was produced with the algorithms having successive steps apart from each other (square, square spiral and random). The last three algorithms were improved further (with small cost in time), thus eliminating completely the pre-focal heating and reducing substantially the treatment time as compared to traditional algorithms. Out of the six algorithms, 3 were successful in eliminating the pre-focal heating completely. Because these 3 algorithms required no delay between successive movements (except in the last part of the motion), the treatment time was reduced by 93%. Therefore, it will be possible in the future, to achieve treatment time of focused ultrasound therapies shorter than 30 min. The rate of ablated volume achieved with one of the proposed algorithms was 71 cm(3)/h. The intention of this pilot study was to demonstrate that the navigation algorithms play the most important role in reducing pre-focal heating. By evaluating in the future, all commercially available geometries, it will be possible to reduce the treatment time, for thermal ablation protocols intended for oncological targets. Copyright © 2015 Elsevier B.V. All rights reserved.

Delayed high school start times later than 8:30am and impact on graduation rates and attendance rates.

PubMed

McKeever, Pamela Malaspina; Clark, Linda

2017-04-01

The first purpose of this study was to investigate changes in high school graduation rates with a delayed school start time of later than 8:30am. The second aim of the study was to analyze the association between a delayed high school start time later than 8:30am and attendance rates. In the current study, a pre-post design using a repeated-measures analysis of variance was used to examine changes in attendance and graduation rates 2 years after a delayed start was implemented. Public high schools from 8 school districts (n=29 high schools) located throughout 7 different states. Schools were identified using previous research from the Children's National Medical Center's Division of Sleep Medicine Research Team. A total membership of more than 30,000 high school students enrolled in the 29 schools identified by the Children's National Medical Center's Research Team. A pre-post design was used for a within-subject design, controlling for any school-to-school difference in the calculation of the response variable. This is the recommended technique for a study that may include data with potential measurement error. Findings from this study linked a start time of later than 8:30am to improved attendance rates and graduation rates. Attendance rates and graduation rates significantly improved in schools with delayed start times of 8:30am or later. School officials need to take special notice that this investigation also raises questions about whether later start times are a mechanism for closing the achievement gap due to improved graduation rates. Copyright © 2017 National Sleep Foundation. Published by Elsevier Inc. All rights reserved.

The Tradeoff between Travel Time from Home to Hospital and Door to Balloon Time in Determining Mortality among STEMI Patients Undergoing PCI.

PubMed

Di Domenicantonio, Riccardo; Cappai, Giovanna; Sciattella, Paolo; Belleudi, Valeria; Di Martino, Mirko; Agabiti, Nera; Mataloni, Francesca; Ricci, Roberto; Perucci, Carlo Alberto; Davoli, Marina; Fusco, Danilo

2016-01-01

In ST-segment elevation myocardial infarction (STEMI), even in presence of short door to balloon time (DTBT), timely reperfusion with percutaneous coronary intervention (PCI) is hampered by pre-hospital delays. Travel time (TT) constitutes a relevant part of these delays and may contribute to worse outcomes. To evaluate the relationship between TT from home to hospital and DTBT on 30-day mortality after PCI among patients with STEMI. We enrolled a cohort of 3,608 STEMI patients with a DTBT within 120 minutes who underwent PCI between years 2009 and 2013 in Lazio Region (Italy). We calculated the minimum travel time from residential address to emergency department where the first medical contact occurred. We defined system delay as the sum of travel time and DTBT time. Logistic regression models, including clinical and demographic characteristics were used to estimate the effect of TT and DTBT on mortality. Among patients with 0-90 minutes of system delay, TT above the median value is positively associated with mortality (OR = 2.46; P = 0.009). Survival benefit associated with DTBT below the median results only among patients with TT below the median (OR for DTBT below the median = 0.39; P = 0.013), (OR for interaction between TT and DTBT = 2.36; p = 0.076). TT affects survival after PCI for STEMI, even in the presence of health care systems compliant with current guidelines. Results emphasize the importance of health system initiatives to reduce pre-hospital delay. Utilization of TT can contribute to a better estimate of patient mortality risk in the evaluation of quality of care.

Thrombolysis in Acute Ischemic Stroke: A Simulation Study to Improve Pre- and in-Hospital Delays in Community Hospitals

PubMed Central

Lahr, Maarten M. H.; van der Zee, Durk-Jouke; Vroomen, Patrick C. A. J.; Luijckx, Gert-Jan; Buskens, Erik

2013-01-01

Background Various studies demonstrate better patient outcome and higher thrombolysis rates achieved by centralized stroke care compared to decentralized care, i.e. community hospitals. It remains largely unclear how to improve thrombolysis rate in decentralized care. The aim of this simulation study was to assess the impact of previously identified success factors in a central model on thrombolysis rates and patient outcome when implemented for a decentral model. Methods Based on a prospectively collected dataset of 1084 ischemic stroke patients, simulation was used to replicate current practice and estimate the effect of re-organizing decentralized stroke care to resemble a centralized model. Factors simulated included symptom onset call to help, emergency medical services transportation, and in-hospital diagnostic workup delays. Primary outcome was proportion of patients treated with thrombolysis; secondary endpoints were good functional outcome at 90 days, Onset-Treatment-Time (OTT), and OTT intervals, respectively. Results Combining all factors might increase thrombolysis rate by 7.9%, of which 6.6% ascribed to pre-hospital and 1.3% to in-hospital factors. Good functional outcome increased by 11.4%, 8.7% ascribed to pre-hospital and 2.7% to in-hospital factors. The OTT decreased 17 minutes, 7 minutes ascribed to pre-hospital and 10 minutes to in-hospital factors. An increase was observed in the proportion thrombolyzed within 1.5 hours; increasing by 14.1%, of which 5.6% ascribed to pre-hospital and 8.5% to in-hospital factors. Conclusions Simulation technique may target opportunities for improving thrombolysis rates in acute stroke. Pre-hospital factors proved to be the most promising for improving thrombolysis rates in an implementation study. PMID:24260151

The impact of manual defibrillation technique on no-flow time during simulated cardiopulmonary resuscitation.

PubMed

Perkins, Gavin D; Davies, Robin P; Soar, Jasmeet; Thickett, David R

2007-04-01

Rapid defibrillation is the most effective strategy for establishing return of spontaneous circulation following cardiac arrest due to ventricular fibrillation. The aim of this study is to measure the delay due to of charging the defibrillator during chest compression in an attempt to reduce the duration of the pre-shock pause in between cessation of chest compressions and shock delivery as advocated by the American Heart Association (AHA) guidelines compared to charging the defibrillator immediately following rhythm analysis without resuming chest compressions as recommended by the European Resuscitation Council (ERC). This was a randomised controlled cross over trial comparing pre-shock pause times when defibrillation was performed on a manikin according to the AHA and ERC guidelines using paddles and hands free defibrillation systems. The pre-shock pause between cessation of chest compression and shock delivery was significantly different between techniques (Friedman test, P<0.0001). ERC paddles technique had the greatest pre-shock pause (7.4 s [6.7-11.2]) followed by ERC hands free (7.0 s [6.5-8.5]) and AHA paddles (1.6 s [1.1-2.3]). AHA hands free took the least amount of time (1.5 s [0.8-1.5]). Extrapolating these data to older defibrillators with longer charge times saw pre-shock pause intervals of 9 s (Codemaster XL) and 12 s (Lifepak 20) with the ERC approach. This study demonstrated clinically significant delays to defibrillation by analysing and charging the defibrillator without performing concurrent chest compressions. In a simulated scenario, charging the defibrillator whilst performing chest compressions was perceived as safe and significantly reduced the pre-shock pause between cessation of chest compression and shock delivery.

Capacity for ethical and regulatory review of herbal trials in developing countries: a case study of Moringa oleifera research in HIV-infected patients.

PubMed

Monera-Penduka, Tsitsi G; Maponga, Charles C; Morse, Gene D; Nhachi, Charles F B

2017-01-01

Lack of regulatory capacity limits the conduct of ethical and rigorous trials of herbal medicines in developing countries. Sharing ethical and regulatory experiences of successful herbal trials may accelerate the field while assuring human subjects protection. The methods and timelines for the ethical and regulatory review processes for the first drug regulatory authority approved herbal trial in Zimbabwe are described in this report. The national drug regulatory authority and ethics committee were engaged for pre-submission discussions. Six applications were submitted. Application procedures and communications with the various regulatory and ethics review boards were reviewed. Key issues raised and timelines for communications were summarized. There was no special framework for the approval of herbal trials. One local institutional review committee granted an exemption. Key issues raised for revision were around pre-clinical efficacy and safety data, standardization and quality assurance of the intervention as well as consenting procedures. Approval timelines ranged between eight and 72 weeks. In the absence of a defined framework for review of herbal trials, approval processes can be delayed. Dialogue between researchers and regulators is important for successful and efficient protocol approval for herbal trials in developing countries. The study was registered prospectively on August 3, 2011 with clinicaltrials.gov (NCT01410058).

LIGHT EXPOSURE AMONG ADOLESCENTS WITH DELAYED SLEEP PHASE DISORDER: A PROSPECTIVE COHORT STUDY

PubMed Central

Auger, R. Robert; Burgess, Helen J.; Dierkhising, Ross A.; Sharma, Ruchi G.; Slocumb, Nancy L.

2012-01-01

Our study objective was to compare light exposure and sleep parameters between adolescents with delayed sleep phase disorder (n=16, 15.3 ± 1.8 years) and unaffected controls (n=22, 13.7 ± 2.4 years) using a prospective cohort design. Participants wore wrist actigraphs with photosensors for 14 days. Mean hourly lux levels from 20:00-05:00 h and 05:00-14:00 h were examined, in addition to the 9-hour intervals prior to sleep onset and after sleep offset. Sleep parameters were compared separately, and were also included as covariates within models that analyzed associations with specified light intervals. Additional covariates included group and school night status. Adolescent subjects with delayed sleep phase disorder received more evening (p<0.02, 22:00-02:00 h) and less morning light (p<0.05, 08:00-09:00 h and 10:00-12:00 h) than controls, but had less pre-sleep exposure with adjustments for the time of sleep onset (p<0.03, fifth-seventh hours prior to onset hour). No differences were identified with respect to the sleep offset interval. Increased total sleep time and later sleep offset times were associated with decreased evening (p<0.001 and p=0.02, respectively) and morning (p=0.01 and p<0.001, respectively) exposure, and later sleep onset times were associated with increased evening exposure (p<0.001). Increased total sleep time also correlated with increased exposure during the 9 hours before sleep-onset (p=0.01), and a later sleep onset time corresponded with decreased exposure during the same interval (p<0.001). Outcomes persisted regardless of school night status. In conclusion, light exposure interpretation requires adjustments for sleep timing among adolescents with delayed sleep phase disorder. Pre- and post-sleep exposure do not appear to contribute directly to phase delays. Sensitivity to morning light may be reduced among adolescents with delayed sleep phase disorder. PMID:22080736

Effect of pre-fixation delay and freezing on mink testicular endpoints for environmental research.

PubMed

Spörndly-Nees, Ellinor; Ekstedt, Elisabeth; Magnusson, Ulf; Fakhrzadeh, Azadeh; Luengo Hendriks, Cris L; Holm, Lena

2015-01-01

There is growing interest in using wild animals to monitor the real-life cocktail effect of environmental chemicals on male reproduction. However, practical difficulties, such as long distances to the laboratory, generally prolong the time between euthanisation and specimen handling. For instance, tissue fixation is often performed on frozen material or on material where deterioration has started, which may affect tissue morphology. This study examined the effect of pre-fixation delay and freezing on mink testicular endpoints in order to determine robust endpoints in suboptimally handled specimens. Sexually mature farmed mink (n=30) selected at culling were divided into six groups and subjected to different time intervals between euthanisation and fixation or freezing: 0 hours (fixed immediately post mortem), 6 hours, 18 hours, 30 hours, 42 hours, or frozen 6 hours post mortem and thawed overnight. Unaffected endpoints when pre-fixation storage was extended to 30 hours included: area and diameter of the seminiferous tubules, length and weight of the testes, and acrosomes marked with Gata-4. Epithelial height, Sertoli cells marked with Gata-4 and cell morphology were affected endpoints after 6 hours of storage. Freezing the tissue prior to fixation severely altered cell morphology and reduced testicular weight, tubular diameter and area. Morphological changes seen after 6 hours included shredded germ cells and excess cytoplasm in seminiferous tubular lumen, chromatin rearrangements and increased germ cell death. Extended delay before fixation and freezing affected many endpoints in the mink testicular tissue. Some of these endpoints may mimic chemically induced effects, which is important to consider when evaluating specimens from wild animals for environmental toxicity.

Pyruvate incubation enhances glycogen stores and sustains neuronal function during subsequent glucose deprivation.

PubMed

Shetty, Pavan K; Sadgrove, Matthew P; Galeffi, Francesca; Turner, Dennis A

2012-01-01

The use of energy substrates, such as lactate and pyruvate, has been shown to improve synaptic function when administered during glucose deprivation. In the present study, we investigated whether prolonged incubation with monocarboxylate (pyruvate or lactate) prior rather than during glucose deprivation can also sustain synaptic and metabolic function. Pyruvate pre-incubation(3-4h) significantly prolonged (>25 min) the tolerance of rat hippocampal slices to delayed glucose deprivation compared to control and lactate pre-incubated slices, as revealed by field excitatory post synaptic potentials (fEPSPs); pre-incubation with pyruvate also reduced the marked decrease in NAD(P)H fluorescence resulting from glucose deprivation. Moreover, pyruvate exposure led to the enhancement of glycogen stores with time, compared to glucose alone (12 μmol/g tissue at 4h vs. 3.5 μmol/g tissue). Prolonged resistance to glucose deprivation following exogenous pyruvate incubation was prevented by glycogenolysis inhibitors, suggesting that enhanced glycogen mediates the delay in synaptic activity failure. The application of an adenosine A1 receptor antagonist enhanced glycogen utilization and prolonged the time to synaptic failure, further confirming this hypothesis of the importance of glycogen. Moreover, tissue levels of ATP were also significantly maintained during glucose deprivation in pyruvate pretreated slices compared to control and lactate. In summary, these experiments indicate that pyruvate exposure prior to glucose deprivation significantly increased the energy buffering capacity of hippocampal slices, particularly by enhancing internal glycogen stores, delaying synaptic failure during glucose deprivation by maintaining ATP levels, and minimizing the decrease in the levels of NAD(P)H. Copyright © 2011 Elsevier Inc. All rights reserved.

The influence of prepulse level on the 3p-3s XUV laser output from Ne-like ions of Zn, Cu and Ni

NASA Astrophysics Data System (ADS)

MacPhee, A. G.; Lewis, C. L. S.; Warwick, P. J.; Weaver, I.; Jaeglé, P.; Carillon, A.; Jamelot, G.; Klisnick, A.; Rus, B.; Zeitoun, Ph.; Nantel, M.; Goedkindt, P.; Sebban, S.; Tallents, G. J.; Demir, A.; Holden, M.; Krishnan, J.

1997-02-01

We have studied the effect of prepulses in enhancing the efficiency of generating ASE beams in soft X-ray laser plasma amplifiers based on pumping Ne-like ions. Slab targets were irradiated with a weak prepulse followed by a main plasma heating pulse of nanosecond duration. Time-integrated: time and spectrally resolved and time and angularly resolved lasing emissions on the 3p-3s ( J = 0-1) XUV lasing lines of Ne-like Ni, Cu and Zn at wavelengths 232 Å, 221 Å and 212 Å respectively have been monitored. Measurements were made for pre-pulse/main-pulse intensity ratios from 10 -5-10 -1 and for pump delay times of 2 ns and 4.5 ns. Zinc is shown to exhibit a peak in output intensity at ˜ 2 × 10 -3 pre-pulse fraction for a 4.5 ns pump delay, with a main pulse pump intensity of ˜ 1.3 × 10 13W cm -2 on a 20 mm target. The Zn lasing emission had a duration of ˜ 240 ps and this was insensitive to prepulse fraction. The J = 0-1 XUV laser output for nickel and copper increased monotonically with prepulse fraction, with copper targets showing least sensitivity to either prepulse level or prepulse to main pulse delay. Under the conditions of the study, the pre-pulse level was observed to have no significant influence on the output intensity of the 3p-3s ( J = 2-1) lines of any of the elements investigated.

Apparatus and Method for Compensating for Process, Voltage, and Temperature Variation of the Time Delay of a Digital Delay Line

NASA Technical Reports Server (NTRS)

Seefeldt, James (Inventor); Feng, Xiaoxin (Inventor); Roper, Weston (Inventor)

2013-01-01

A process, voltage, and temperature (PVT) compensation circuit and a method of continuously generating a delay measure are provided. The compensation circuit includes two delay lines, each delay line providing a delay output. The two delay lines may each include a number of delay elements, which in turn may include one or more current-starved inverters. The number of delay lines may differ between the two delay lines. The delay outputs are provided to a combining circuit that determines an offset pulse based on the two delay outputs and then averages the voltage of the offset pulse to determine a delay measure. The delay measure may be one or more currents or voltages indicating an amount of PVT compensation to apply to input or output signals of an application circuit, such as a memory-bus driver, dynamic random access memory (DRAM), a synchronous DRAM, a processor or other clocked circuit.

Benefit-cost evaluation of a highway-railroad intermodal control system (ICS)

DOT National Transportation Integrated Search

2004-06-01

Improved train location information and vehicle detection combined with grade crossing controls, traveler information, and traffic management can improve safety and reduce delay for both passengers and vehicles. In addition, the possibility of pre-em...

[Evaluation of therapeutic strategies for myocardial infarction: the ESTIM Midi-Pyrénées survey].

PubMed

Charpentier, S; Celse, D; Cambou, J P; Lauque, D; Carrie, D; Galinier, M; Baïxas, C; Ducassé, J L; Puel, J

2005-11-01

The aim of the ESTIM Midi-Pyrénées survey was to monitor the management of acute coronary syndrome with ST segment elevation by cardiologists and emergency departments in the Midi-Pyrénées region. Over a period of 2 years between June 2001 and June 2003, 1287 patients presenting with acute coronary syndrome within the first 24 hours were recruited prospectively. The initial management of these patients was undertaken either by a mobile medical team in the pre-hospital phase, or in a hospital emergency department, non-interventional cardiology department or an interventional cardiology department in 51.8%, 28.8%, 9.6% et 9.9% of cases respectively. Depending on these four modes of initial management, the median time for initial management was 1h30, 2h45, 4h30 et 4h respectively. Emergency coronary reperfusion was proposed in 89.6% of cases. Of the patients in whom reperfusion was attempted within the first 12 hours, 33.7% underwent pre-hospital thrombolysis (median delay of 1h48), 35.8% underwent thrombolysis in hospital (median delay 3h), and 30.4% underwent primary angioplasty (median delay 4h40). Thrombolysis was followed by angioplasty in 80% of cases. A combined approach with thrombolysis and angioplasty was applied in 41% of patients. At one month the rate of major cardiac events, death, and/or subsequent myocardial infarction was 12%. Multivariate analysis revealed that the only significant adverse prognostic features were: not offering reperfusion [Odds ratio (OR) 4, confidence interval (CI) 2.3-3.7] and age [OR 3.8, CI 2.3-6.2]. The method of reperfusion did not influence the subsequent outcome in this regional survey. pre-hospital management allows early revascularisation. In our region there was no significant prognostic difference between pre-hospital thrombolysis and primary angioplasty. It shows that the logistic and therapeutic potentials of prehospital care are not being sufficiently exploited.

77 FR 47705 - Open Meeting of the Taxpayer Advocacy Panel Return Processing Delays Project Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-09

... Return Processing Delays Project Committee AGENCY: Internal Revenue Service (IRS), Treasury. ACTION... Project Committee will be conducted. The Taxpayer Advocacy Panel is soliciting public comments, ideas, and... Processing Delays Project Committee will be held Tuesday, September 04, 2012, at 9:30 a.m. Pacific Time via...

77 FR 2611 - Open Meeting of the Taxpayer Advocacy Panel Return Processing Delays Project Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-18

... Return Processing Delays Project Committee AGENCY: Internal Revenue Service (IRS) Treasury. ACTION... Project Committee will be conducted. The Taxpayer Advocacy Panel is soliciting public comments, ideas, and... Processing Delays Project Committee will be held Tuesday, February 7, 2012, at 9:30 a.m. Pacific Time via...

Examining Plasmodium falciparum and P. vivax clearance subsequent to antimalarial drug treatment in the Myanmar-China border area based on quantitative real-time polymerase chain reaction.

PubMed

Lo, Eugenia; Nguyen, Jennifer; Oo, Winny; Hemming-Schroeder, Elizabeth; Zhou, Guofa; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

2016-04-16

Recent emergence of artemisinin-resistant P. falciparum has posed a serious hindrance to the elimination of malaria in the Greater Mekong Subregion. Parasite clearance time, a measure of change in peripheral parasitaemia in a sequence of samples taken after treatment, can be used to reflect the susceptibility of parasites or the efficiency of antimalarials. The association of genetic polymorphisms and artemisinin resistance has been documented. This study aims to examine clearance time of P. falciparum and P. vivax parasitemia as well as putative gene mutations associated with residual or recurred parasitemia in Myanmar. A total of 63 P. falciparum and 130 P. vivax samples collected from two internally-displaced populations and one surrounding village were examined for parasitemia changes. At least four samples were taken from each patient, at the first day of diagnosis up to 3 months following the initial treatment. The amount of parasite gene copy number was estimated using quantitative real-time PCR based on a species-specific region of the 18S rRNA gene. For samples that showed residual or recurred parasitemia after treatment, microsatellites were used to identify the 'post-treatment' parasite genotype and compared such with the 'pre-treatment' genotype. Mutations in genes pfcrt, pfmdr1, pfatp6, pfmrp1 and pfK13 that are potentially associated with ACT resistance were examined to identify if mutation is a factor for residual or persistent parasitemia. Over 30% of the P. falciprium infections showed delayed clearance of parasitemia after 2-3 days of treatment and 9.5% showed recurred parasitemia. Mutations in codon 876 of the pfmrp1 corroborated significance association with slow clearance time. However, no association was observed in the variation in pfmdr1 gene copy number as well as mutations of various codonsinpfatp6, pfcrt, and pfK13 with clearance time. For P. vivax, over 95% of the infections indicated cleared parasitemia at days 2-3 of treatment. Four samples were found to be re-infected with new parasite strains based on microsatellite genotypes after initial treatment. The appearance of P.falciparum infected samples showing delayed clearance or recurred parasitemia after treatment raises concerns on current treatment and ACT drug resistance.

An Integrative Literature Review of Organisational Factors Associated with Admission and Discharge Delays in Critical Care

PubMed Central

Peltonen, Laura-Maria; McCallum, Louise; Siirala, Eriikka; Haataja, Marjaana; Lundgrén-Laine, Heljä; Salanterä, Sanna; Lin, Frances

2015-01-01

The literature shows that delayed admission to the intensive care unit (ICU) and discharge delays from the ICU are associated with increased adverse events and higher costs. Identifying factors related to delays will provide information to practice improvements, which contribute to better patient outcomes. The aim of this integrative review was to explore the incidence of patients' admission and discharge delays in critical care and to identify organisational factors associated with these delays. Seven studies were included. The major findings are as follows: (1) explanatory research about discharge delays is scarce and one study on admission delays was found, (2) delays are a common problem mostly due to organisational factors, occurring in 38% of admissions and 22–67% of discharges, and (3) redesigning care processes by improving information management and coordination between units and interdisciplinary teams could reduce discharge delays. In conclusion, patient outcomes can be improved through efficient and safe care processes. More exploratory research is needed to identify factors that contribute to admission and discharge delays to provide evidence for clinical practice improvements. Shortening delays requires an interdisciplinary and multifaceted approach to the whole patient flow process. Conclusions should be made with caution due to the limited number of articles included in this review. PMID:26558286

Detection of rabbit and hare processed material in compound feeds by TaqMan real-time PCR.

PubMed

Pegels, N; López-Calleja, I; García, T; Martín, R; González, I

2013-01-01

Food and feed traceability has become a priority for governments due to consumer demand for comprehensive and integrated safety policies. In the present work, a TaqMan real-time PCR assay targeting the mitochondrial 12S rRNA gene was developed for specific detection of rabbit and hare material in animal feeds and pet foods. The technique is based on the use of three species-specific primer/probe detection systems targeting three 12S rRNA gene fragments: one from rabbit species, another one from hare species and a third fragment common to rabbit and hare (62, 102 and 75 bp length, respectively). A nuclear 18S rRNA PCR system, detecting a 77-bp amplicon, was used as positive amplification control. Assay performance and sensitivity were assessed through the analysis of a batch of laboratory-scale feeds treated at 133°C at 3 bar for 20 min to reproduce feed processing conditions dictated by European regulations. Successful detection of highly degraded rabbit and hare material was achieved at the lowest target concentration assayed (0.1%). Furthermore, the method was applied to 96 processed commercial pet food products to determine whether correct labelling had been used at the market level. The reported real-time PCR technique detected the presence of rabbit tissues in 80 of the 96 samples analysed (83.3%), indicating a possible labelling fraud in some pet foods. The real-time PCR method reported may be a useful tool for traceability purposes within the framework of feed control.

Chemistry and haematology sample rejection and clinical impact in a tertiary laboratory in Cape Town.

PubMed

Jacobsz, Lourens A; Zemlin, Annalise E; Roos, Mark J; Erasmus, Rajiv T

2011-10-14

Recent publications report that up to 70% of total laboratory errors occur in the pre-analytical phase. Identification of specific problems highlights pre-analytic processes susceptible to errors. The rejection of unsuitable samples can lead to delayed turnaround time and affect patient care. A retrospective audit was conducted investigating the rejection rate of routine blood specimens received at chemistry and haematology laboratories over a 2-week period. The reasons for rejection and potential clinical impact of these rejections were investigated. Thirty patient files were randomly selected and examined to assess the impact of these rejections on clinical care. A total of 32,910 specimens were received during the study period, of which 481 were rejected, giving a rejection rate of 1.46%. The main reasons for rejection were inappropriate clotting (30%) and inadequate sample volume (22%). Only 51.7% of rejected samples were repeated and the average time for a repeat sample to reach the laboratory was about 5 days (121 h). Of the repeated samples, 5.1% had results within critical values. Examination of patient folders showed that in 40% of cases the rejection of samples had an impact on patient care. The evaluation of pre-analytical processes in the laboratory, with regard to sample rejection, allowed one to identify problem areas where improvement is necessary. Rejected samples due to factors out of the laboratory's control had a definite impact on patient care and can thus affect customer satisfaction. Clinicians should be aware of these factors to prevent such rejections.

Working Memory Load Affects Processing Time in Spoken Word Recognition: Evidence from Eye-Movements

PubMed Central

Hadar, Britt; Skrzypek, Joshua E.; Wingfield, Arthur; Ben-David, Boaz M.

2016-01-01

In daily life, speech perception is usually accompanied by other tasks that tap into working memory capacity. However, the role of working memory on speech processing is not clear. The goal of this study was to examine how working memory load affects the timeline for spoken word recognition in ideal listening conditions. We used the “visual world” eye-tracking paradigm. The task consisted of spoken instructions referring to one of four objects depicted on a computer monitor (e.g., “point at the candle”). Half of the trials presented a phonological competitor to the target word that either overlapped in the initial syllable (onset) or at the last syllable (offset). Eye movements captured listeners' ability to differentiate the target noun from its depicted phonological competitor (e.g., candy or sandal). We manipulated working memory load by using a digit pre-load task, where participants had to retain either one (low-load) or four (high-load) spoken digits for the duration of a spoken word recognition trial. The data show that the high-load condition delayed real-time target discrimination. Specifically, a four-digit load was sufficient to delay the point of discrimination between the spoken target word and its phonological competitor. Our results emphasize the important role working memory plays in speech perception, even when performed by young adults in ideal listening conditions. PMID:27242424

Pre-cementation of deep shaft

NASA Astrophysics Data System (ADS)

Heinz, W. F.

1988-12-01

Pre-cementation or pre-grouting of deep shafts in South Africa is an established technique to improve safety and reduce water ingress during shaft sinking. The recent completion of several pre-cementation projects for shafts deeper than 1000m has once again highlighted the effectiveness of pre-grouting of shafts utilizing deep slimline boreholes and incorporating wireline technique for drilling and conventional deep borehole grouting techniques for pre-cementation. Pre-cementation of deep shaft will: (i) Increase the safety of shaft sinking operation (ii) Minimize water and gas inflow during shaft sinking (iii) Minimize the time lost due to additional grouting operations during sinking of the shaft and hence minimize costly delays and standing time of shaft sinking crews and equipment. (iv) Provide detailed information of the geology of the proposed shaft site. Informations on anomalies, dykes, faults as well as reef (gold bearing conglomerates) intersections can be obtained from the evaluation of cores of the pre-cementation boreholes. (v) Provide improved rock strength for excavations in the immediate vicinity of the shaft area. The paper describes pre-cementation techniques recently applied successfully from surface and some conclusions drawn for further considerations.

Post-deployment usability evaluation of a radiology workstation.

PubMed

Jorritsma, Wiard; Cnossen, Fokie; Dierckx, Rudi A; Oudkerk, Matthijs; Van Ooijen, Peter M A

2016-01-01

To determine the number, nature and severity of usability issues radiologists encounter while using a commercially available radiology workstation in clinical practice, and to assess how well the results of a pre-deployment usability evaluation of this workstation generalize to clinical practice. The usability evaluation consisted of semi-structured interviews and observations of twelve users using the workstation during their daily work. Usability issues and positive usability findings were documented. Each issue was given a severity rating and its root cause was determined. Results were compared to the results of a pre-deployment usability evaluation of the same workstation. Ninety-two usability issues were identified, ranging from issues that cause minor frustration or delay, to issues that cause significant delays, prevent users from completing tasks, or even pose a potential threat to patient safety. The results of the pre-deployment usability evaluation had limited generalizability to clinical practice. This study showed that radiologists encountered a large number and a wide variety of usability issues when using a commercially available radiology workstation in clinical practice. This underlines the need for effective usability engineering in radiology. Given the limitations of pre-deployment usability evaluation in radiology, which were confirmed by our finding that the results of a pre-deployment usability evaluation of this workstation had limited generalizability to clinical practice, it is vital that radiology workstation vendors devote significant resources to usability engineering efforts before deployment of their workstation, and to continue these efforts after the workstation is deployed in a hospital. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Towards the ecology of hyperthermophiles: biotopes, new isolation strategies and novel metabolic properties.

PubMed

Huber, R; Huber, H; Stetter, K O

2000-12-01

Ecological studies have shown that water-containing terrestrial, subterranean and submarine high-temperature environments harbor a great diversity of hyperthermophilic prokaryotes, growing fastest at temperatures of 80 degrees C or above. The investigations included cultivation, isolation and detailed analysis of these hyperthermophiles as well as in situ 16S rRNA gene sequence analysis and in situ hybridization studies. For a safe and fast isolation of novel hyperthermophiles from mixed cultures, a new, plating-independent isolation technique was developed, based on the use of a laser microscope ('optical tweezers'). This method, combined with 16S rRNA gene sequence analysis and whole-cell hybridization using fluorescently labelled oligonucleotide probes, even allows the recovery of pure cultures of phylogenetically predicted organisms harboring novel 16S rRNA gene sequences. In their natural habitats, hyperthermophiles form complex food webs, consisting of primary producers and consumers of organic material. Their metabolic potential includes various types of aerobic and anaerobic respiration and different modes of fermentation. In hydrothermal and geothermal environments, hyperthermophiles have important ecological functions in biogeochemical processes. Members of the Sulfolobales are able to mobilize heavy metals from sulfidic ores like pyrite or chalcopyrite. Biomineralization processes of hyperthermophiles include the formation of magnetite from iron or the precipitation of arsenate as realgar, a reaction performed by a novel hyperthermophile that was isolated from Pisciarelli Solfatara, Naples, Italy.

Frailty and sarcopenia - newly emerging and high impact complications of diabetes.

PubMed

Sinclair, Alan J; Abdelhafiz, Ahmed H; Rodríguez-Mañas, Leocadio

2017-09-01

Diabetes increases the risk of physical dysfunction and disability. Diabetes-related complications and coexisting morbidities partially explain the deterioration in physical function. The decline in muscle mass, strength and function associated with diabetes leads to sarcopenia, frailty and eventually disability. Frailty acts as a mediator in the pathogenesis of disability in older people with diabetes and its measurement in routine daily practice is recommended. Frailty is a dynamic process which progresses from a robust condition to a pre-frail stage then frailty and eventually disability. Therefore, a multimodal intervention which includes adequate nutrition, exercise training, good glycaemic control and the use of appropriate hypoglycemic medications may help delay or prevent the progression to disability. Copyright © 2017 Elsevier Inc. All rights reserved.

Studies of the quenching phenomenon in delayed contact hypersensitivity reactions.

PubMed

Basketter, D A; Allenby, C F

1991-09-01

Studies in guinea pig and man have shown that eugenol can quench non-specifically contact urticarial responses, whereas limonene seems largely ineffective. In a comprehensive series of studies, there was little evidence of quenching of delayed contact hypersensitivity reactions to cinnamic aldehyde or citral, including in 'pre-quenched' material supplied by a perfume/flavour company, and in a similar mixture prepared in this laboratory, in the guinea pig model. In addition, there was no evidence of the quenching by eugenol of allergic reactions to cinnamic aldehyde in a panel of human subjects with a proven history of cinnamic-aldehyde-induced allergic contact dermatitis. Overall, the results lend little credibility to earlier literature reports of quenching phenomena in delayed contact hypersensitivity responses.

Decreased Expression of Stable RNA Can Alleviate the Lethality Associated with RNase E Deficiency in Escherichia coli.

PubMed

Himabindu, P; Anupama, K

2017-04-15

The endoribonuclease RNase E participates in mRNA degradation, rRNA processing, and tRNA maturation in Escherichia coli , but the precise reasons for its essentiality are unclear and much debated. The enzyme is most active on RNA substrates with a 5'-terminal monophosphate, which is sensed by a domain in the enzyme that includes residue R169; E. coli also possesses a 5'-pyrophosphohydrolase, RppH, that catalyzes conversion of 5'-terminal triphosphate to 5'-terminal monophosphate on RNAs. Although the C-terminal half (CTH), beyond residue approximately 500, of RNase E is dispensable for viability, deletion of the CTH is lethal when combined with an R169Q mutation or with deletion of rppH In this work, we show that both these lethalities can be rescued in derivatives in which four or five of the seven rrn operons in the genome have been deleted. We hypothesize that the reduced stable RNA levels under these conditions minimize the need of RNase E to process them, thereby allowing for its diversion for mRNA degradation. In support of this hypothesis, we have found that other conditions that are known to reduce stable RNA levels also suppress one or both lethalities: (i) alterations in relA and spoT , which are expected to lead to increased basal ppGpp levels; (ii) stringent rpoB mutations, which mimic high intracellular ppGpp levels; and (iii) overexpression of DksA. Lethality suppression by these perturbations was RNase R dependent. Our work therefore suggests that its actions on the various substrates (mRNA, rRNA, and tRNA) jointly contribute to the essentiality of RNase E in E. coli IMPORTANCE The endoribonuclease RNase E is essential for viability in many Gram-negative bacteria, including Escherichia coli Different explanations have been offered for its essentiality, including its roles in global mRNA degradation or in the processing of several tRNA and rRNA species. Our work suggests that, rather than its role in the processing of any one particular substrate, its distributed functions on all the different substrates (mRNA, rRNA, and tRNA) are responsible for the essentiality of RNase E in E. coli . Copyright © 2017 American Society for Microbiology.

Delay discounting as emotional processing: an electrophysiological study.

PubMed

Blackburn, Marianna; Mason, Liam; Hoeksma, Marco; Zandstra, Elizabeth H; El-Deredy, Wael

2012-01-01

Both theoretical models and functional imaging studies implicate the involvement of emotions within the delay discounting process. However, defining this role has been difficult to establish with neuroimaging techniques given the automaticity of emotional responses. To address this, the current study examined electrophysiological correlates involved in the detection and evaluation of immediate and delayed monetary outcomes. Our results showed that modulation of both early and later ERP components previously associated with affective stimuli processing are sensitive to the signalling of delayed rewards. Together with behavioural reaction times that favoured immediacy, we demonstrated, for the first time, that time delays modify the incentive value of monetary rewards via mechanisms of emotional bias and selective visual attention. Furthermore, our data are consistent with the hypothesis that delayed and thus intangible rewards are perceived less saliently, and rely on emotion as a common currency within decision making. This study provides a new approach to delay discounting and highlights a potential novel route through which delay discounting may be investigated.

Linear-phase delay filters for ultra-low-power signal processing in neural recording implants.

PubMed

Gosselin, Benoit; Sawan, Mohamad; Kerherve, Eric

2010-06-01

We present the design and implementation of linear-phase delay filters for ultra-low-power signal processing in neural recording implants. We use these filters as low-distortion delay elements along with an automatic biopotential detector to perform integral waveform extraction and efficient power management. The presented delay elements are realized employing continuous-time OTA-C filters featuring 9th-order equiripple transfer functions with constant group delay. Such analog delay enables processing neural waveforms with reduced overhead compared to a digital delay since it does not requires sampling and digitization. It uses an allpass transfer function for achieving wider constant-delay bandwidth than all-pole does. Two filters realizations are compared for implementing the delay element: the Cascaded structure and the Inverse follow-the-leader feedback filter. Their respective strengths and drawbacks are assessed by modeling parasitics and non-idealities of OTAs, and by transistor-level simulations. A budget of 200 nA is used in both filters. Experimental measurements with the chosen filter topology are presented and discussed.

Tandem repeats of the 5' non-transcribed spacer of Tetrahymena rDNA function as high copy number autonomous replicons in the macronucleus but do not prevent rRNA gene dosage regulation.

PubMed Central

Pan, W J; Blackburn, E H

1995-01-01

The rRNA genes in the somatic macronucleus of Tetrahymena thermophila are normally on 21 kb linear palindromic molecules (rDNA). We examined the effect on rRNA gene dosage of transforming T.thermophila macronuclei with plasmid constructs containing a pair of tandemly repeated rDNA replication origin regions unlinked to the rRNA gene. A significant proportion of the plasmid sequences were maintained as high copy circular molecules, eventually consisting solely of tandem arrays of origin regions. As reported previously for cells transformed by a construct in which the same tandem rDNA origins were linked to the rRNA gene [Yu, G.-L. and Blackburn, E. H. (1990) Mol. Cell. Biol., 10, 2070-2080], origin sequences recombined to form linear molecules bearing several tandem repeats of the origin region, as well as rRNA genes. The total number of rDNA origin sequences eventually exceeded rRNA gene copies by approximately 20- to 40-fold and the number of circular replicons carrying only rDNA origin sequences exceeded rRNA gene copies by 2- to 3-fold. However, the rRNA gene dosage was unchanged. Hence, simply monitoring the total number of rDNA origin regions is not sufficient to regulate rRNA gene copy number. Images PMID:7784211

Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

PubMed

Beauparlant, Marc A; Drouin, Guy

2014-02-01

Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

Emergency medical services and congestion : urban sprawl and pre-hospital emergency care time.

DOT National Transportation Integrated Search

2009-01-01

This research measured the association between urban sprawl and emergency medical service (EMS) response time. The purpose was to test the hypothesis that features of the built environment increase the probability of delayed ambulance arrival. Using ...

Anxiety, depression and PTSD in asylum-seekers: assocations with pre-migration trauma and post-migration stressors.

PubMed

Silove, D; Sinnerbrink, I; Field, A; Manicavasagar, V; Steel, Z

1997-04-01

Research into the mental health of refugees has burgeoned in recent times, but there is a dearth of studies focusing specifically on the factors associated with psychiatric distress in asylum-seekers who have not been accorded residency status. Forty consecutive asylum-seekers attending a community resource centre in Sydney, Australia, were interviewed using structured instruments and questionnaires. Anxiety scores were associated with female gender, poverty, and conflict with immigration officials, while loneliness and boredom were linked with both anxiety and depression. Thirty subjects (79%) had experienced a traumatic event such as witnessing killings, being assaulted, or suffering torture and captivity, and 14 subjects (37%) met full criteria for PTSD. A diagnosis of PTSD was associated with greater exposure to pre-migration trauma, delays in processing refugee applications, difficulties in dealing with immigration officials, obstacles to employment, racial discrimination, and loneliness and boredom. Although based on correlational data derived from'a convenient' sample, our findings raise the possibility that current procedures for dealing with asylum-seekers may contribute to high levels of stress and psychiatric symptoms in those who have been previously traumatised.

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

PubMed

Ferme, D; Banjac, M; Calsamiglia, S; Busquet, M; Kamel, C; Avgustin, G

2004-01-01

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

Comparative Response of Platelet fV and Plasma fV to Activated Protein C and Relevance to a Model of Acute Traumatic Coagulopathy

DTIC Science & Technology

2014-06-12

inducing concen tration. To test this hypothesis, we investigated the concentration of aPC required to induce significant delays in clot time, decrease...instructions and mixed with 50 ml plasma ( pre incubated at 37 uC). The Mean Normal PT is listed as 13.5 s for this device, and INR is calculated by...and pair wise comparison Bonferroni posttests . Results Nanomolar aPC Is Required to Prolong PT/INR PT measurements in fVdp are delayed compared to

Use of a 3-Telsa magnet to perform delayed gadolinium-enhanced magnetic resonance imaging of the distal interphalangeal joint of horses with and without naturally occurring osteoarthritis.

PubMed

Bischofberger, Andrea S; Fürst, Anton E; Torgerson, Paul R; Carstens, Ann; Hilbe, Monika; Kircher, Patrick

2018-03-01

OBJECTIVE To characterize delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) features of healthy hyaline cartilage of the distal interphalangeal joint (DIPJ) of horses, to determine whether dGEMRIC can be used to differentiate various stages of naturally occurring osteoarthritis of the DIPJ, and to correlate relaxation times determined by dGEMRIC with the glycosaminoglycan concentration, water content, and macroscopic and histologic findings of hyaline cartilage of DIPJs with and without osteoarthritis. SAMPLE 1 cadaveric forelimb DIPJ from each of 12 adult warmblood horses. PROCEDURES T1-weighted cartilage relaxation times were obtained for predetermined sites of the DIPJ before (T1 preGd ) and after (T1 postGd ) intra-articular gadolinium administration. Corresponding cartilage sites underwent macroscopic, histologic, and immunohistochemical evaluation, and cartilage glycosaminoglycan concentration and water content were determined. Median T1 preGd and T1 postGd were correlated with macroscopic, histologic, and biochemical data. Mixed generalized linear models were created to evaluate the effects of cartilage site, articular surface, and macroscopic and histologic scores on relaxation times. RESULTS 122 cartilage specimens were analyzed. Median T1 postGd was lower than the median T1 preGd for normal and diseased cartilage. Both T1 preGd and T1 postGd were correlated with macroscopic and histologic scores, whereby T1 preGd increased and T1 postGd decreased as osteoarthritis progressed. There was topographic variation of T1 preGd and T1 postGd within the DIPJ. Cartilage glycosaminoglycan concentration and water content were significantly correlated with T1 preGd and macroscopic and histologic scores but were not correlated with T1 postGd . CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that dGEMRIC relaxation times varied for DIPJs with various degrees of osteoarthritis. These findings may help facilitate early detection of osteoarthritis.

Transcriptome analysis provides insights into the delayed sticky disease symptoms in Carica papaya.

PubMed

Madroñero, Johana; Rodrigues, Silas P; Antunes, Tathiana F S; Abreu, Paolla M V; Ventura, José A; Fernandes, A Alberto R; Fernandes, Patricia Machado Bueno

2018-03-21

Global gene expression analysis indicates host stress responses, mainly those mediated by SA, associated to the tolerance to sticky disease symptoms at pre-flowering stage in Carica papaya. Carica papaya plants develop the papaya sticky disease (PSD) as a result of the combined infection of papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2), or PMeV complex. PSD symptoms appear only after C. papaya flowers. To understand the mechanisms involved in this phenomenon, the global gene expression patterns of PMeV complex-infected C. papaya at pre-and post-flowering stages were assessed by RNA-Seq. The result was 633 and 88 differentially expressed genes at pre- and post-flowering stages, respectively. At pre-flowering stage, genes related to stress and transport were up-regulated while metabolism-related genes were down-regulated. It was observed that induction of several salicylic acid (SA)-activated genes, including PR1, PR2, PR5, WRKY transcription factors, ROS and callose genes, suggesting SA signaling involvement in the delayed symptoms. In fact, pre-flowering C. papaya treated with exogenous SA showed a tendency to decrease the PMeV and PMeV2 loads when compared to control plants. However, pre-flowering C. papaya also accumulated transcripts encoding a NPR1-inhibitor (NPR1-I/NIM1-I) candidate, genes coding for UDP-glucosyltransferases (UGTs) and several genes involved with ethylene pathway, known to be negative regulators of SA signaling. At post-flowering, when PSD symptoms appeared, the down-regulation of PR-1 encoding gene and the induction of BSMT1 and JA metabolism-related genes were observed. Hence, SA signaling likely operates at the pre-flowering stage of PMeV complex-infected C. papaya inhibiting the development of PSD symptoms, but the induction of its negative regulators prevents the full-scale and long-lasting tolerance.

Phylogenetic analyses of bacteria associated with the processing of iru and ogiri condiments.

PubMed

Ademola, Oluwatoyin M; Adeyemi, Taiwo E; Ezeokoli, Obinna T; Ayeni, Kolawole I; Obadina, Adewale O; Somorin, Yinka M; Omemu, Adebukola M; Adeleke, Rasheed A; Nwangburuka, Cyril C; Oluwafemi, Flora; Oyewole, Olusola B; Ezekiel, Chibundu N

2018-06-27

Analysis of the bacterial community dynamics during the production of traditional fermented condiments is important for food safety assessment, quality control and development of starter culture technology. In this study, bacteria isolated during the processing of iru and ogiri, two commonly consumed condiments in Nigeria, were characterised based on phylogenetic analyses of the bacterial 16S rRNA gene. A total of 227 isolates were obtained and clustered into 12 operational taxonomic units (OTUs) based on 97% 16S rRNA gene similarity. The OTUs spanned three phyla (Firmicutes, Actinobacteria and Proteobacteria), and nine genera: Acinetobacter, Aerococcus, Bacillus, Enterococcus, Enterobacter, Lysinibacillus, Micrococcus, Proteus and Staphylococcus. OTUs closely related to species of Bacillus dominated the processing stages of both condiments. Although no single OTU occurred throughout iru processing stages, an OTU (mostly related to B. safensis) dominated the ogiri processing stages indicating potentials for the development of starter culture. However, other isolates such as those of Enterococcus spp. and Lysinibacillus spp. may be potential starters for iru fermentation. Presumptive foodborne pathogens were also detected at some stages of the condiments' processing, possibly due to poor hygienic practices. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

RNA processing in Neurospora crassa mitochondria: use of transfer RNA sequences as signals.

PubMed Central

Breitenberger, C A; Browning, K S; Alzner-DeWeerd, B; RajBhandary, U L

1985-01-01

We have used RNA gel transfer hybridization, S1 nuclease mapping and primer extension to analyze transcripts derived from several genes in Neurospora crassa mitochondria. The transcripts studied include those for cytochrome oxidase subunit III, 17S rRNA and an unidentified open reading frame. In all three cases, initial transcripts are long, include tRNA sequences, and are subsequently processed to generate the mature RNAs. We find that endpoints of the most abundant transcripts generally coincide with those of tRNA sequences. We therefore conclude that tRNA sequences in long transcripts act as primary signals for RNA processing in N. crassa mitochondria. The situation is somewhat analogous to that observed in mammalian mitochondrial systems. The difference, however, is that in mammalian mitochondria, noncoding spacers between tRNA, rRNA and protein genes are very short and in many cases non-existent, allowing no room for intergenic RNA processing signals whereas, in N. crassa mtDNA, intergenic non-coding sequences are usually several hundred nucleotides long and contain highly conserved GC-rich palindromic sequences. Since these GC-rich palindromic sequences are retained in the processed mature RNAs, we conclude that they do not serve as signals for RNA processing. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. PMID:2990893

Optimal timing of pulse onset for language mapping with navigated repetitive transcranial magnetic stimulation.

PubMed

Krieg, Sandro M; Tarapore, Phiroz E; Picht, Thomas; Tanigawa, Noriko; Houde, John; Sollmann, Nico; Meyer, Bernhard; Vajkoczy, Peter; Berger, Mitchel S; Ringel, Florian; Nagarajan, Srikantan

2014-10-15

Within the primary motor cortex, navigated transcranial magnetic stimulation (nTMS) has been shown to yield maps strongly correlated with those generated by direct cortical stimulation (DCS). However, the stimulation parameters for repetitive nTMS (rTMS)-based language mapping are still being refined. For this purpose, the present study compares two rTMS protocols, which differ in the timing of pulse train onset relative to picture presentation onset during object naming. Results were the correlated with DCS language mapping during awake surgery. Thirty-two patients with left-sided perisylvian tumors were examined by rTMS prior to awake surgery. Twenty patients underwent rTMS pulse trains starting at 300 ms after picture presentation onset (delayed TMS), whereas another 12 patients received rTMS pulse trains starting at the picture presentation onset (ONSET TMS). These rTMS results were then evaluated for correlation with intraoperative DCS results as gold standard in terms of differential consistencies in receiver operating characteristics (ROC) statistics. Logistic regression analysis by protocols and brain regions were conducted. Within and around Broca's area, there was no difference in sensitivity (onset TMS: 100%, delayed TMS: 100%), negative predictive value (NPV) (onset TMS: 100%, delayed TMS: 100%), and positive predictive value (PPV) (onset TMS: 55%, delayed TMS: 54%) between the two protocols compared to DCS. However, specificity differed significantly (onset TMS: 67%, delayed TMS: 28%). In contrast, for posterior language regions, such as supramarginal gyrus, angular gyrus, and posterior superior temporal gyrus, early pulse train onset stimulation showed greater specificity (onset TMS: 92%, delayed TMS: 20%), NPV (onset TMS: 92%, delayed TMS: 57%) and PPV (onset TMS: 75%, delayed TMS: 30%) with comparable sensitivity (onset TMS: 75%, delayed TMS: 70%). Logistic regression analysis also confirmed the greater fit of the predictions by rTMS that had the pulse train onset coincident with the picture presentation onset when compared to the delayed stimulation. Analyses of differential disruption patterns of mapped cortical regions were further able to distinguish clusters of cortical regions standardly associated with semantic and pre-vocalization phonological networks proposed in various models of word production. Repetitive nTMS predictions by both protocols correlate well with DCS outcomes especially in Broca's region, particularly with regard to TMS negative predictions. With this study, we have demonstrated that rTMS stimulation onset coincident with picture presentation onset improves the accuracy of preoperative language maps, particularly within posterior language areas. Moreover, immediate and delayed pulse train onsets may have complementary disruption patterns that could differentially capture cortical regions causally necessary for semantic and pre-vocalization phonological networks. Published by Elsevier Inc.

Learning monopolies with delayed feedback on price expectations

NASA Astrophysics Data System (ADS)

Matsumoto, Akio; Szidarovszky, Ferenc

2015-11-01

We call the intercept of the price function with the vertical axis the maximum price and the slope of the price function the marginal price. In this paper it is assumed that a monopolistic firm has full information about the marginal price and its own cost function but is uncertain on the maximum price. However, by repeated interaction with the market, the obtained price observations give a basis for an adaptive learning process of the maximum price. It is also assumed that the price observations have fixed delays, so the learning process can be described by a delayed differential equation. In the cases of one or two delays, the asymptotic behavior of the resulting dynamic process is examined, stability conditions are derived. Three main results are demonstrated in the two delay learning processes. First, it is possible to stabilize the equilibrium which is unstable in the one delay model. Second, complex dynamics involving chaos, which is impossible in the one delay model, can emerge. Third, alternations of stability and instability (i.e., stability switches) occur repeatedly.

Hardware Verification of Laser Noise Cancellation and Gravitational Wave Extraction using Time-Delay Interferometry

NASA Astrophysics Data System (ADS)

Mitryk, Shawn; Mueller, Guido

The Laser Interferometer Space Antenna (LISA) is a space-based modified Michelson interfer-ometer designed to measure gravitational radiation in the frequency range from 30 uHz to 1 Hz. The interferometer measurement system (IMS) utilizes one-way laser phase measurements to cancel the laser phase noise, reconstruct the proof-mass motion, and extract the gravitational wave (GW) induced laser phase modulations in post-processing using a technique called time-delay interferometry (TDI). Unfortunately, there exist few hard-ware verification experiments of the IMS. The University of Florida LISA Interferometry Simulator (UFLIS) is designed to perform hardware-in-the-loop simulations of the LISA interferometry system, modeling the characteris-tics of the LISA mission as accurately as possible. This depends, first, on replicating the laser pre-stabilization by locking the laser phase to an ultra-stable Zerodur cavity length reference using the PDH locking method. Phase measurements of LISA-like photodetector beat-notes are taken using the UF-phasemeter (PM) which can measure the laser BN frequency to within an accuracy of 0.22 uHz. The inter-space craft (SC) laser links including the time-delay due to the 5 Gm light travel time along the LISA arms, the laser Doppler shifts due to differential SC motion, and the GW induced laser phase modulations are simulated electronically using the electronic phase delay (EPD) unit. The EPD unit replicates the laser field propagation between SC by measuring a photodetector beat-note frequency with the UF-phasemeter and storing the information in memory. After the requested delay time, the frequency information is added to a Doppler offset and a GW-like frequency modulation. The signal is then regenerated with the inter-SC laser phase affects applied. Utilizing these components, I will present the first complete TDI simulations performed using the UFLIS. The LISA model is presented along-side the simulation, comparing the generation and measurement of LISA-like signals. Phasemeter measurements are used in post-processing and combined in the linear combinations defined by TDI, thus, canceling the laser phase and phase-lock loop noise to extract the applied GW modulation buried under the noise. Nine order of magnitude common mode laser noise cancellation is achieved at a frequency of 1 mHz and the GW signal is clearly visible after the laser and PLL noise cancellation.

Mesobiotus philippinicus sp. nov., the first limnoterrestrial tardigrade from the Philippines.

PubMed

Mapalo, Marc A; Stec, Daniel; Mirano-Bascos, Denise; Michalczyk, Łukasz

2016-06-20

The limnoterrestrial tardigrade fauna of the Philippines is completely unknown. In this paper, we describe the first ever limnoterrestrial water bear species from this southeast Asian country, Mesobiotus philippinicus sp. nov., found in a moss sample collected in Quezon City. Apart from morphometrics and imaging in light microscopy, we also analysed the new species under scanning electron microscope and sequenced four DNA markers differing in mutation rates, three nuclear (18S rRNA, 28S rRNA, and ITS-2) and one mitochondrial (COI). This allowed not only a detailed description but also provided barcodes to aid future species identification. The new species belongs to the harmsworthi group and is most similar to M. diffusus (Binda & Pilato, 1987), M. pseudocoronatus (Pilato et al., 2006), M. montanus (Murray, 1910) and M. mottai (Binda & Pilato, 1994), but differs from these species by whorled egg processes and dimensions of some morphometric traits. The 28S rRNA, ITS-2 and COI sequences presented in this paper are the first published DNA sequences for the genus Mesobiotus.

Effects of acute and chronic caffeine on risk-taking behavior in children and adolescents.

PubMed

Temple, Jennifer L; Ziegler, Amanda M; Graczyk, Adam M; Crandall, Amanda

2017-05-01

Consumption of caffeinated beverages is associated with increased risk-taking behavior. The purpose of this study was to determine if acute caffeine administration influences risk-taking behavior in a dose-dependent manner. Participants were pre- (ages 8-9) and post-pubertal (ages 15-17) children who visited the laboratory three times and consumed a beverage containing 0, 1, or 2 mg/kg of caffeine. Thirty minutes later, participants completed the balloon analogue risk task (BART), the Iowa gambling task (IGT), and a delay discounting task. The number of balloons exploded on the BART task was significantly increased after 2 mg/kg of caffeine in moderate caffeine consumers, but was decreased after 2 mg/kg of caffeine in high caffeine consumers. There were no main effects of caffeine dose on the delay discounting task or on the IGT. Post-pubertal participants showed reduced delay discounting compared with pre-pubertal participants. Finally, average daily caffeine use was significantly, positively correlated with scores on a risk-taking questionnaire. These data suggest that caffeine dose-dependently influences decision making and risk taking. More research is needed to determine the mechanism of this difference as well as the extent to which sex and pubertal phase influence these relationships.

Ciguatoxin reduces regenerative capacity of axotomized peripheral neurons and delays functional recovery in pre-exposed mice after peripheral nerve injury.

PubMed

Au, Ngan Pan Bennett; Kumar, Gajendra; Asthana, Pallavi; Tin, Chung; Mak, Yim Ling; Chan, Leo Lai; Lam, Paul Kwan Sing; Ma, Chi Him Eddie

2016-05-27

Ciguatera fish poisoning (CFP) results from consumption of tropical reef fish containing ciguatoxins (CTXs). Pacific (P)-CTX-1 is among the most potent known CTXs and the predominant source of CFP in the endemic region responsible for the majority of neurological symptoms in patients. Chronic and persistent neurological symptoms occur in some CFP patients, which often result in incomplete functional recovery for years. However, the direct effects of exposure to CTXs remain largely unknown. In present study, we exposed mice to CTX purified from ciguatera fish sourced from the Pacific region. P-CTX-1 was detected in peripheral nerves within hours and persisted for two months after exposure. P-CTX-1 inhibited axonal regrowth from axotomized peripheral neurons in culture. P-CTX-1 exposure reduced motor function in mice within the first two weeks of exposure before returning to baseline levels. These pre-exposed animals exhibited delayed sensory and motor functional recovery, and irreversible motor deficits after peripheral nerve injury in which formation of functional synapses was impaired. These findings are consistent with reduced muscle function, as assessed by electromyography recordings. Our study provides strong evidence that the persistence of P-CTX-1 in peripheral nerves reduces the intrinsic growth capacity of peripheral neurons, resulting in delayed functional recovery after injury.

Automated Forensic Animal Family Identification by Nested PCR and Melt Curve Analysis on an Off-the-Shelf Thermocycler Augmented with a Centrifugal Microfluidic Disk Segment

PubMed Central

Zengerle, Roland; von Stetten, Felix; Schmidt, Ulrike

2015-01-01

Nested PCR remains a labor-intensive and error-prone biomolecular analysis. Laboratory workflow automation by precise control of minute liquid volumes in centrifugal microfluidic Lab-on-a-Chip systems holds great potential for such applications. However, the majority of these systems require costly custom-made processing devices. Our idea is to augment a standard laboratory device, here a centrifugal real-time PCR thermocycler, with inbuilt liquid handling capabilities for automation. We have developed a microfluidic disk segment enabling an automated nested real-time PCR assay for identification of common European animal groups adapted to forensic standards. For the first time we utilize a novel combination of fluidic elements, including pre-storage of reagents, to automate the assay at constant rotational frequency of an off-the-shelf thermocycler. It provides a universal duplex pre-amplification of short fragments of the mitochondrial 12S rRNA and cytochrome b genes, animal-group-specific main-amplifications, and melting curve analysis for differentiation. The system was characterized with respect to assay sensitivity, specificity, risk of cross-contamination, and detection of minor components in mixtures. 92.2% of the performed tests were recognized as fluidically failure-free sample handling and used for evaluation. Altogether, augmentation of the standard real-time thermocycler with a self-contained centrifugal microfluidic disk segment resulted in an accelerated and automated analysis reducing hands-on time, and circumventing the risk of contamination associated with regular nested PCR protocols. PMID:26147196

Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18

PubMed Central

Smirnov, Alexandre; Entelis, Nina; Martin, Robert P.; Tarassov, Ivan

2011-01-01

5S rRNA is an essential component of ribosomes of all living organisms, the only known exceptions being mitochondrial ribosomes of fungi, animals, and some protists. An intriguing situation distinguishes mammalian cells: Although the mitochondrial genome contains no 5S rRNA genes, abundant import of the nuclear DNA-encoded 5S rRNA into mitochondria was reported. Neither the detailed mechanism of this pathway nor its rationale was clarified to date. In this study, we describe an elegant molecular conveyor composed of a previously identified human 5S rRNA import factor, rhodanese, and mitochondrial ribosomal protein L18, thanks to which 5S rRNA molecules can be specifically withdrawn from the cytosolic pool and redirected to mitochondria, bypassing the classic nucleolar reimport pathway. Inside mitochondria, the cytosolic 5S rRNA is shown to be associated with mitochondrial ribosomes. PMID:21685364

5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general

NASA Technical Reports Server (NTRS)

Van den Eynde, H.; De Baere, R.; Shah, H. N.; Gharbia, S. E.; Fox, G. E.; Michalik, J.; Van de Peer, Y.; De Wachter, R.

1989-01-01

The 5S ribosomal ribonucleic acid (rRNA) sequences were determined for Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides capillosus, Bacteroides veroralis, Porphyromonas gingivalis, Anaerorhabdus furcosus, Fusobacterium nucleatum, Fusobacterium mortiferum, and Fusobacterium varium. A dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5S rRNA sequences, showed differences as well as similarities with respect to results derived from 16S rRNA analyses. In the 5S rRNA dendrogram, Bacteroides clustered together with Cytophaga and Fusobacterium, as in 16S rRNA analyses. Intraphylum relationships deduced from 5S rRNAs suggested that Bacteroides is specifically related to Cytophaga rather than to Fusobacterium, as was suggested by 16S rRNA analyses. Previous taxonomic considerations concerning the genus Bacteroides, based on biochemical and physiological data, were confirmed by the 5S rRNA sequence analysis.

Door-to-balloon delays before primary angioplasty in the Regional Acute Myocardial Infarction Registry of Brittany. An analysis of the Observatoire Régional Breton sur l'Infarctus du myocarde (ORBI).

PubMed

Leurent, Guillaume; Fougerou, Claire; Pennec, Pierre-Yves; Filippi, Emmanuelle; Moquet, Benoît; Druelles, Philippe; Hacot, Jean-Philippe; Rialan, Antoine; Rouault, Gilles; Gervais, Renaud; Bedossa, Marc; Boulmier, Dominique; Boulanger, Bertrand; Hamon, Christian; Treuil, Josiane; Coudert, Isabelle; Courcoux, Hubert; Le Breton, Hervé

2009-11-01

Minimizing delays to coronary reperfusion is critical in the management of acute myocardial infarction (AMI). To determine delays in in-hospital management and factors associated with delays of over 45min. We analysed data from the Observatoire Régional Breton sur l'Infarctus, a registry of AMI patients admitted within 24h of symptom onset (July 2007 to December 2008) to an interventional cardiology centre in Brittany. Prehospital delay was defined as time between first responder arrival at the patient and patient arrival at an interventional cardiovascular centre. In-hospital delay was defined as time between admission to the interventional cardiovascular centre and first balloon inflation. Patients were grouped according to duration of in-hospital delay (>45 vs

Identification of an Alternative rRNA Post-transcriptional Maturation of 26S rRNA in the Kingdom Fungi.

PubMed

Navarro-Ródenas, Alfonso; Carra, Andrea; Morte, Asunción

2018-01-01

Despite of the integrity of their RNA, some desert truffles present a non-canonical profile of rRNA where 3.3 kb is absent, 1.8 kb is clear and a band of 1.6 kb is observed. A similar rRNA profile was identified in organisms belonging to different life kingdoms, with the exception of the Kingdom Fungi, as a result of a split LSU rRNA called hidden gap . rRNA profiles of desert truffles were analyzed to verify the presence of the non-canonical profile. The RNA of desert truffles and yeast were blotted and hybridized with probes complementary to LSU extremes. RACE of LSU rRNA was carried out to determine the LSU rRNA breakage point. LSU rRNA of desert truffles presents a post-transcriptional cleavage of five nucleotides that generates a hidden gap located in domain D7. LSU splits into two molecules of 1.6 and 1.8 kb. Similar to other organisms, a UAAU tract, downstream of the breakage point, was identified. Phylogenetic comparison suggests that during fungi evolution mutations were introduced in the hypervariable D7 domain, resulting in a sequence that is specifically post-transcriptionally cleaved in some desert truffles.

AGOR 28

DTIC Science & Technology

2016-01-30

start delay will not be necessary. Still waiting for confirmation. • Ballast Tank Coatings – Monitoring GDR’s for coating issues on Armstrong. WTA...for pre delivery ballast tank inspection on Ride is in the works. • Anchor Windlass – Port and Starboard Anchor Windlasses were tested during sea

Use of retarders with cement treated soils : final report.

DOT National Transportation Integrated Search

1970-01-01

The purpose of this study was to investigate various set retarding admixtures for possible use as an economical method of allowing long delay periods between the mixing of cement, soil and water and remixing. Three types of retarders were used in pre...

A multiplex real-time PCR assay, based on invA and pagC genes, for the detection and quantification of Salmonella enterica from cattle lymph nodes.

PubMed

Bai, Jianfa; Trinetta, Valentina; Shi, Xiaorong; Noll, Lance W; Magossi, Gabriela; Zheng, Wanglong; Porter, Elizabeth P; Cernicchiaro, Natalia; Renter, David G; Nagaraja, Tiruvoor G

2018-05-01

Cattle lymph nodes can harbor Salmonella and potentially contaminate beef products. We have developed and validated a new real-time PCR (qPCR) assay for the detection and quantification of Salmonella enterica in cattle lymph nodes. The assay targets both the invA and pagC genes, the most conserved molecular targets in Salmonella enterica. An 18S rRNA gene assay that amplifies from cattle and other animal species was also included as an internal control. Available DNA sequences for invA, pagC and 18S rRNA genes were used for primer and probe selections. Three Salmonella serotypes, S. Typhimurium, S. Anatum, and S. Montevideo, were used to assess the assay's analytical sensitivity. Correlation coefficients of standard curves generated for each target and for all three serotypes were >99% and qPCR amplification efficiencies were between 93% and 110%. Assay sensitivity was also determined using standard curve data generated from Salmonella-negative cattle lymph nodes spiked with 10-fold dilutions of the three Salmonella serotypes. Assay specificity was determined using Salmonella culture method, and qPCR testing on 36 Salmonella strains representing 33 serotypes, 38 Salmonella strains of unknown serotypes, 252 E. coli strains representing 40 serogroups, and 31 other bacterial strains representing 18 different species. A collection of 647 cattle lymph node samples from steers procured from the Midwest region of the US were tested by the qPCR, and compared to culture-method of detection. Salmonella prevalence by qPCR for pre-enriched and enriched lymph nodes was 19.8% (128/647) and 94.9% (614/647), respectively. A majority of qPCR positive pre-enriched samples (105/128) were at concentrations between 10 4 and 10 5  CFU/mL. Culture method detected Salmonella in 7.7% (50/647) and 80.7% (522/647) of pre- and post-enriched samples, respectively; 96.0% (48/50) of pre-enriched and 99.4% (519/522) of post-enriched culture-positive samples were also positive by qPCR. More samples tested positive by qPCR than by culture method, indicating that the real-time PCR assay was more sensitive. Our data indicate that this triplex qPCR can be used to accurately detect and quantify Salmonella enterica strains from cattle lymph node samples. The assay may serve as a useful tool to monitor the prevalence of Salmonella in beef production systems. Copyright © 2018 Elsevier B.V. All rights reserved.

Amino acid-dependent signaling via S6K1 and MYC is essential for regulation of rDNA transcription

PubMed Central

Kang, Jian; Kusnadi, Eric P.; Ogden, Allison J.; Hicks, Rodney J.; Bammert, Lukas; Kutay, Ulrike; Hung, Sandy; Sanij, Elaine; Hannan, Ross D.; Hannan, Katherine M.; Pearson, Richard B.

2016-01-01

Dysregulation of RNA polymerase I (Pol I)-dependent ribosomal DNA (rDNA) transcription is a consistent feature of malignant transformation that can be targeted to treat cancer. Understanding how rDNA transcription is coupled to the availability of growth factors and nutrients will provide insight into how ribosome biogenesis is maintained in a tumour environment characterised by limiting nutrients. We demonstrate that modulation of rDNA transcription initiation, elongation and rRNA processing is an immediate, co-regulated response to altered amino acid abundance, dependent on both mTORC1 activation of S6K1 and MYC activity. Growth factors regulate rDNA transcription initiation while amino acids modulate growth factor-dependent rDNA transcription by primarily regulating S6K1-dependent rDNA transcription elongation and processing. Thus, we show for the first time amino acids regulate rRNA synthesis by a distinct, post-initiation mechanism, providing a novel model for integrated control of ribosome biogenesis that has implications for understanding how this process is dysregulated in cancer. PMID:27385002

Sulfur-oxidizing bacteria dominate the microbial diversity shift during the pyrite and low-grade pyrolusite bioleaching process.

PubMed

Han, Yifan; Ma, Xiaomei; Zhao, Wei; Chang, Yunkang; Zhang, Xiaoxia; Wang, Xingbiao; Wang, Jingjing; Huang, Zhiyong

2013-10-01

The microbial ecology of the pyrite-pyrolusite bioleaching system and its interaction with ore has not been well-described. A 16S rRNA gene clone library was created to evaluate changes in the microbial community at different stages of the pyrite-pyrolusite bioleaching process in a shaken flask. The results revealed that the bacterial community was disturbed after 5 days of the reaction. Phylogenetic analysis of 16S rRNA sequences demonstrated that the predominant microorganisms were members of a genus of sulfur-oxidizing bacteria, Thiomonas sp., that subsequently remained dominant during the bioleaching process. Compared with iron-oxidizing bacteria, sulfur-oxidizing bacteria were more favorable to the pyrite-pyrolusite bioleaching system. Decreased pH due to microbial acid production was an important condition for bioleaching efficiency. Iron-oxidizing bacteria competed for pyrite reduction power with Mn(IV) in pyrolusite under specific conditions. These results extend our knowledge of microbial dynamics during pyrite-pyrolusite bioleaching, which is a key issue to improve commercial applications. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Defining the RNA-Protein Interactions in the Trypanosome Preribosomal Complex

PubMed Central

Wang, Lei; Ciganda, Martin

2013-01-01

In eukaryotes, 5S rRNA is transcribed in the nucleoplasm and requires the ribosomal protein L5 to deliver it to the nucleolus for ribosomal assembly. The trypanosome-specific proteins P34 and P37 form a novel preribosomal complex with the eukaryotic conserved L5-5S rRNA complex in the nucleoplasm. Previous results suggested that P34 acts together with L5 to bridge the interaction with 5S rRNA and thus to stabilize 5S rRNA, an important role in the early steps of ribosomal biogenesis. Here, we have delineated the domains of the two protein components, L5 and P34, and regions of the RNA partner, 5S rRNA, that are critical for protein-RNA interactions within the complex. We found that the L18 domain of L5 and the N terminus and RNA recognition motif of P34 bind 5S rRNA. We showed that Trypanosoma brucei L5 binds the β arm of 5S rRNA, while P34 binds loop A/stem V of 5S rRNA. We demonstrated that 5S rRNA is able to enhance the association between the protein components of the complex, L5 and P34. Both loop A/stem V and the β arm of 5S rRNA can separately enhance the protein-protein association, but their effects are neither additive nor synergistic. Domains in the two proteins for protein-protein and protein-RNA interactions overlap or are close to each other. This suggests that 5S rRNA binding might cause conformational changes in L5 and P34 and might also bridge the interactions, thus enhancing binding between the protein partners of this novel complex. PMID:23397568

Relationships between processing delay and microbial load of broiler neck skin samples.

PubMed

Lucianez, A; Holmes, M A; Tucker, A W

2010-01-01

The measurable microbial load on poultry carcasses during processing is determined by a number of factors including farm or origin, processing hygiene, and external temperature. This study investigated associations between carcass microbial load and progressive delays to processing. A total of 30 carcasses were delayed immediately after defeathering and before evisceration in a commercial abattoir in groups of five, and were held at ambient temperature for 1, 2, 3, 4, 6, and 8 h. Delayed carcasses were reintroduced to the processing line, and quantitative assessment of total viable count, coliforms, Staphylococcus aureus, and Pseudomonas spp. was undertaken on neck skin flap samples collected after carcass chilling and then pooled for each group. Sampling was repeated on 5 separate days, and the data were combined. Significant increases in total viable count (P = 0.001) and coliforms (P = 0.004), but not for S. aureus or Pseudomonas loads, were observed across the 8-h period of delay. In line with previous studies, there was significant variation in microbiological data according to sampling day. In conclusion, there is a significant and measurable decline in microbiological status of uneviscerated but defeathered poultry carcasses after an 8-h delay, but the variability of sampling results, reflecting the wide range of factors that impact microbial load, means that it is not possible to determine maximum or minimum acceptable periods of processing delay based on this criterion alone.

Mechanisms for ribotoxin-induced ribosomal RNA cleavage

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

He, Kaiyu; Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824; Zhou, Hui-Ren

The Type B trichothecene deoxynivalenol (DON), a ribotoxic mycotoxin known to contaminate cereal-based foods, induces ribosomal RNA (rRNA) cleavage in the macrophage via p38-directed activation of caspases. Here we employed the RAW 264.7 murine macrophage model to test the hypothesis that this rRNA cleavage pathway is similarly induced by other ribotoxins. Capillary electrophoresis confirmed that the antibiotic anisomycin (≥ 25 ng/ml), the macrocylic trichothecene satratoxin G (SG) (≥ 10 ng/ml) and ribosome-inactivating protein ricin (≥ 300 ng/ml) induced 18s and 28s rRNA fragmentation patterns identical to that observed for DON. Also, as found for DON, inhibition of p38, double-stranded RNA-activatedmore » kinase (PKR) and hematopoietic cell kinase (Hck) suppressed MAPK anisomycin-induced rRNA cleavage, while, in contrast, their inhibition did not affect SG- and ricin-induced rRNA fragmentation. The p53 inhibitor pifithrin-μ and pan caspase inhibitor Z-VAD-FMK suppressed rRNA cleavage induced by anisomycin, SG and ricin, indicating that these ribotoxins shared with DON a conserved downstream pathway. Activation of caspases 8, 9 and 3 concurrently with apoptosis further suggested that rRNA cleavage occurred in parallel with both extrinsic and intrinsic pathways of programmed cell death. When specific inhibitors of cathepsins L and B (lysosomal cysteine cathepsins active at cytosolic neutral pH) were tested, only the former impaired anisomycin-, SG-, ricin- and DON-induced rRNA cleavage. Taken together, the data suggest that (1) all four ribotoxins induced p53-dependent rRNA cleavage via activation of cathepsin L and caspase 3, and (2) activation of p53 by DON and anisomycin involved p38 whereas SG and ricin activated p53 by an alternative mechanism. Highlights: ► Deoxynivalenol (DON) anisomycin, satratoxin G (SG) and ricin are ribotoxins. ► Ribotoxins induce 18s and 28s rRNA cleavage in the RAW 264.7 macrophage model. ► Ribotoxins induce rRNA cleavage via activation of p53, caspases and cathepsins. ► DON- and anisomycin-triggered rRNA cleavage is p38-dependent. ► SG- and ricin-induced rRNA cleavage is p38-independent.« less

Microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion.

PubMed

Lin, Qiang; He, Guihua; Rui, Junpeng; Fang, Xiaoyu; Tao, Yong; Li, Jiabao; Li, Xiangzhen

2016-06-03

Temperature is an important factor determining the performance and stability of the anaerobic digestion process. However, the microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion systems remain further elusive. To address this issue, we investigated the changes in composition, diversity and activities of microbial communities under temperature gradient from 25 to 55 °C using 16S rRNA gene amplicon sequencing approach based on genomic DNA (refer to as "16S rDNA") and total RNA (refer to as "16S rRNA"). Microbial community structure and activities changed dramatically along the temperature gradient, which corresponded to the variations in digestion performance (e.g., daily CH4 production, total biogas production and volatile fatty acids concentration). The ratios of 16S rRNA to 16S rDNA of microbial taxa, as an indicator of the potentially relative activities in situ, and whole activities of microbial community assessed by the similarity between microbial community based on 16S rDNA and rRNA, varied strongly along the temperature gradient, reflecting different metabolic activities. The daily CH4 production increased with temperature from 25 to 50 °C and declined at 55 °C. Among all the examined microbial properties, the whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities showed highest correlations to the performance. The whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities were sensitive indicators for the performance of anaerobic digestion systems under temperature gradient, while beta-diversity could predict functional differences. Microorganism-regulated mechanisms of temperature effects on anaerobic digestion performance were likely realized through increasing alpha-diversity of both microbial communities and potentially relative activities to supply more functional pathways and activities for metabolic network, and increasing the whole activities of microbial community, especially methanogenesis, to improve the strength and efficiency in anaerobic digestion process.

Mechanistic Insight into the Reactivation of BCAII Enzyme from Denatured and Molten Globule States by Eukaryotic Ribosomes and Domain V rRNAs

PubMed Central

Chakraborty, Biprashekhar; Bhakta, Sayan; Sengupta, Jayati

2016-01-01

In all life forms, decoding of messenger-RNA into polypeptide chain is accomplished by the ribosome. Several protein chaperones are known to bind at the exit of ribosomal tunnel to ensure proper folding of the nascent chain by inhibiting their premature folding in the densely crowded environment of the cell. However, accumulating evidence suggests that ribosome may play a chaperone role in protein folding events in vitro. Ribosome-mediated folding of denatured proteins by prokaryotic ribosomes has been studied extensively. The RNA-assisted chaperone activity of the prokaryotic ribosome has been attributed to the domain V, a span of 23S rRNA at the intersubunit side of the large subunit encompassing the Peptidyl Transferase Centre. Evidently, this functional property of ribosome is unrelated to the nascent chain protein folding at the exit of the ribosomal tunnel. Here, we seek to scrutinize whether this unique function is conserved in a primitive kinetoplastid group of eukaryotic species Leishmania donovani where the ribosome structure possesses distinct additional features and appears markedly different compared to other higher eukaryotic ribosomes. Bovine Carbonic Anhydrase II (BCAII) enzyme was considered as the model protein. Our results manifest that domain V of the large subunit rRNA of Leishmania ribosomes preserves chaperone activity suggesting that ribosome-mediated protein folding is, indeed, a conserved phenomenon. Further, we aimed to investigate the mechanism underpinning the ribosome-assisted protein reactivation process. Interestingly, the surface plasmon resonance binding analyses exhibit that rRNA guides productive folding by directly interacting with molten globule-like states of the protein. In contrast, native protein shows no notable affinity to the rRNA. Thus, our study not only confirms conserved, RNA-mediated chaperoning role of ribosome but also provides crucial insight into the mechanism of the process. PMID:27099964

Autonomic Recovery Is Delayed in Chinese Compared with Caucasian following Treadmill Exercise.

PubMed

Sun, Peng; Yan, Huimin; Ranadive, Sushant M; Lane, Abbi D; Kappus, Rebecca M; Bunsawat, Kanokwan; Baynard, Tracy; Hu, Min; Li, Shichang; Fernhall, Bo

2016-01-01

Caucasian populations have a higher prevalence of cardiovascular disease (CVD) when compared with their Chinese counterparts and CVD is associated with autonomic function. It is unknown whether autonomic function during exercise recovery differs between Caucasians and Chinese. The present study investigated autonomic recovery following an acute bout of treadmill exercise in healthy Caucasians and Chinese. Sixty-two participants (30 Caucasian and 32 Chinese, 50% male) performed an acute bout of treadmill exercise at 70% of heart rate reserve. Heart rate variability (HRV) and baroreflex sensitivity (BRS) were obtained during 5-min epochs at pre-exercise, 30-min, and 60-min post-exercise. HRV was assessed using frequency [natural logarithm of high (LnHF) and low frequency (LnLF) powers, normalized high (nHF) and low frequency (nLF) powers, and LF/HF ratio] and time domains [Root mean square of successive differences (RMSSD), natural logarithm of RMSSD (LnRMSSD) and R-R interval (RRI)]. Spontaneous BRS included both up-up and down-down sequences. At pre-exercise, no group differences were observed for any HR, HRV and BRS parameters. During exercise recovery, significant race-by-time interactions were observed for LnHF, nHF, nLF, LF/HF, LnRMSSD, RRI, HR, and BRS (up-up). The declines in LnHF, nHF, RMSSD, RRI and BRS (up-up) and the increases in LF/HF, nLF and HR were blunted in Chinese when compared to Caucasians from pre-exercise to 30-min to 60-min post-exercise. Chinese exhibited delayed autonomic recovery following an acute bout of treadmill exercise. This delayed autonomic recovery may result from greater sympathetic dominance and extended vagal withdrawal in Chinese. Chinese Clinical Trial Register ChiCTR-IPR-15006684.

Autonomic Recovery Is Delayed in Chinese Compared with Caucasian following Treadmill Exercise

PubMed Central

Sun, Peng; Yan, Huimin; Ranadive, Sushant M.; Lane, Abbi D.; Kappus, Rebecca M.; Bunsawat, Kanokwan; Baynard, Tracy; Hu, Min; Li, Shichang; Fernhall, Bo

2016-01-01

Caucasian populations have a higher prevalence of cardiovascular disease (CVD) when compared with their Chinese counterparts and CVD is associated with autonomic function. It is unknown whether autonomic function during exercise recovery differs between Caucasians and Chinese. The present study investigated autonomic recovery following an acute bout of treadmill exercise in healthy Caucasians and Chinese. Sixty-two participants (30 Caucasian and 32 Chinese, 50% male) performed an acute bout of treadmill exercise at 70% of heart rate reserve. Heart rate variability (HRV) and baroreflex sensitivity (BRS) were obtained during 5-min epochs at pre-exercise, 30-min, and 60-min post-exercise. HRV was assessed using frequency [natural logarithm of high (LnHF) and low frequency (LnLF) powers, normalized high (nHF) and low frequency (nLF) powers, and LF/HF ratio] and time domains [Root mean square of successive differences (RMSSD), natural logarithm of RMSSD (LnRMSSD) and R–R interval (RRI)]. Spontaneous BRS included both up-up and down-down sequences. At pre-exercise, no group differences were observed for any HR, HRV and BRS parameters. During exercise recovery, significant race-by-time interactions were observed for LnHF, nHF, nLF, LF/HF, LnRMSSD, RRI, HR, and BRS (up-up). The declines in LnHF, nHF, RMSSD, RRI and BRS (up-up) and the increases in LF/HF, nLF and HR were blunted in Chinese when compared to Caucasians from pre-exercise to 30-min to 60-min post-exercise. Chinese exhibited delayed autonomic recovery following an acute bout of treadmill exercise. This delayed autonomic recovery may result from greater sympathetic dominance and extended vagal withdrawal in Chinese. Trial Registration: Chinese Clinical Trial Register ChiCTR-IPR-15006684 PMID:26784109

Brief Report: Impact of Early Antiretroviral Therapy on the Performance of HIV Rapid Tests and HIV Incidence Assays.

PubMed

Fogel, Jessica M; Piwowar-Manning, Estelle; Debevec, Barbara; Walsky, Tamara; Schlusser, Katherine; Laeyendecker, Oliver; Wilson, Ethan A; McCauley, Marybeth; Gamble, Theresa; Tegha, Gerald; Soko, Dean; Kumwenda, Johnstone; Hosseinipour, Mina C; Chen, Ying Q; Cohen, Myron S; Eshleman, Susan H

2017-08-01

Antiretroviral therapy (ART) can downregulate antibody responses to HIV infection. We evaluated the impact of early vs. delayed ART on the performance of HIV diagnostic and incidence assays. Samples were obtained from 207 participants in the HPTN 052 trial, who were stably suppressed on ART for ≥4 years [Malawi sites; pre-ART CD4 cell count 350-550 cells/mm (early ART arm, N = 180) or <250 cells/mm or an AIDS-defining illness (delayed ART arm, N = 27)]. Samples were tested with 2 HIV rapid tests and 2 HIV incidence assays; selected samples were also tested with two fourth-generation immunoassays and a Western blot (WB) assay. A pre-ART sample was analyzed if the follow-up sample had a false-negative or weakly-reactive rapid test result, or had an incidence assay result indicative of recent infection (false-recent result). Ten (4.8%) samples had a nonreactive or weakly-reactive rapid test result (7/180 early ART arm, 3/27 delayed ART arm, P = 0.13); one sample had nonreactive fourth-generation assay results and 3 had indeterminate WBs. Forty (18.9%) samples had a false-recent incidence assay result; 16 (7.8%) had false-recent results with both incidence assays. Baseline samples had stronger rapid test and WB bands, higher fourth-generation assay signal-to-cutoff values, and fewer HIV incidence assay results indicative of recent infection. False-negative/weakly-reactive HIV rapid tests and false-recent HIV incidence assay results were observed in virally-suppressed individuals, regardless of pre-ART CD4 cell count. Downregulation of the antibody response to HIV infection in the setting of ART may impact population-level surveys of HIV prevalence and incidence.

Effects of Immediate vs. Delayed Massage-like Loading on Skeletal Muscle Viscoelastic Properties Following Eccentric Exercise

PubMed Central

Crawford, Scott K.; Haas, Caroline; Wang, Qian; Zhang, Xiaoli; Zhao, Yi; Best, Thomas M.

2014-01-01

Background This study compared immediate versus delayed massage-like compressive loading on skeletal muscle viscoelastic properties following eccentric exercise. Methods Eighteen rabbits were surgically instrumented with peroneal nerve cuffs for stimulation of the tibialis anterior muscle. Rabbits were randomly assigned to a massage loading protocol applied immediately post exercise (n=6), commencing 48 hours post exercise (n=6), or exercised no-massage control (n=6). Viscoelastic properties were evaluated in vivo by performing a stress-relaxation test pre- and post-exercise and daily pre- and post-massage for four consecutive days of massage loading. A quasi-linear viscoelastic approach modeled the instantaneous elastic response (AG0), fast ( g1p) and slow ( g2p) relaxation coefficients, and the corresponding relaxation time constants τ1 and τ2. Findings Exercise increased AG0 in all groups (P<0.05). After adjusting for the three multiple comparisons, recovery of AG0 was not significant in the immediate (P=0.021) or delayed (P=0.048) groups compared to the control group following four days of massage. However, within-day (pre- to post-massage) analysis revealed a decrease in AG0 in both massage groups. Following exercise, g1p increased and g2p and τ1 decreased for all groups (P<0.05). Exercise had no effect on τ2 (P>0.05). After four days of massage, there was no significant recovery of the relaxation parameters for either massage loading group compared to the control group. Interpretation Our findings suggest that massage loading following eccentric exercise has a greater effect on reducing muscle stiffness, estimated by AG0, within-day rather than affecting recovery over multiple days. Massage loading also has little effect on the relaxation response. PMID:24861827

Effect of the time interval from harvesting to the pre-drying step on natural fumonisin contamination in freshly harvested corn from the State of Parana, Brazil.

PubMed

Da Silva, M; Garcia, G T; Vizoni, E; Kawamura, O; Hirooka, E Y; Ono, E Y S

2008-05-01

Natural mycoflora and fumonisins were analysed in 490 samples of freshly harvested corn (Zea mays L.) (2003 and 2004 crops) collected at three points in the producing chain from the Northern region of Parana State, Brazil, and correlated to the time interval between the harvesting and the pre-drying step. The two crops showed a similar profile concerning the fungal frequency, and Fusarium sp. was the prevalent genera (100%) for the sampling sites from both crops. Fumonisins were detected in all samples from the three points of the producing chain (2003 and 2004 crops). The levels ranged from 0.11 to 15.32 microg g(-1)in field samples, from 0.16 to 15.90 microg g(-1)in reception samples, and from 0.02 to 18.78 microg g(-1)in pre-drying samples (2003 crop). Samples from the 2004 crop showed lower contamination and fumonisin levels ranged from 0.07 to 4.78 microg g(-1)in field samples, from 0.03 to 4.09 microg g(-1)in reception samples, and from 0.11 to 11.21 microg g(-1)in pre-drying samples. The mean fumonisin level increased gradually from < or = 5.0 to 19.0 microg g(-1)as the time interval between the harvesting and the pre-drying step increased from 3.22 to 8.89 h (2003 crop). The same profile was observed for samples from the 2004 crop. Fumonisin levels and the time interval (rho = 0.96) showed positive correlation (p < or = 0.05), indicating that delay in the drying process can increase fumonisin levels.

Standardized Reporting System Use During Handoffs Reduces Patient Length of Stay in the Emergency Department

PubMed Central

Dahlquist, Robert T.; Reyner, Karina; Robinson, Richard D.; Farzad, Ali; Laureano-Phillips, Jessica; Garrett, John S.; Young, Joseph M.; Zenarosa, Nestor R.; Wang, Hao

2018-01-01

Background Emergency department (ED) shift handoffs are potential sources of delay in care. We aimed to determine the impact that using standardized reporting tool and process may have on throughput metrics for patients undergoing a transition of care at shift change. Methods We performed a prospective, pre- and post-intervention quality improvement study from September 1 to November 30, 2015. A handoff procedure intervention, including a mandatory workshop and personnel training on a standard reporting system template, was implemented. The primary endpoint was patient length of stay (LOS). A comparative analysis of differences between patient LOS and various handoff communication methods were assessed pre- and post-intervention. Communication methods were entered a multivariable logistic regression model independently as risk factors for patient LOS. Results The final analysis included 1,006 patients, with 327 comprising the pre-intervention and 679 comprising the post-intervention populations. Bedside rounding occurred 45% of the time without a standard reporting during pre-intervention and increased to 85% of the time with the use of a standard reporting system in the post-intervention period (P < 0.001). Provider time (provider-initiated care to patient care completed) in the pre-intervention period averaged 297 min, but decreased to 265 min in the post-intervention period (P < 0.001). After adjusting for other communication methods, the use of a standard reporting system during handoff was associated with shortened ED LOS (OR = 0.60, 95% CI 0.40 - 0.90, P < 0.05). Conclusions Standard reporting system use during emergency physician handoffs at shift change improves ED throughput efficiency and is associated with shorter ED LOS. PMID:29581808

Analysis of Factors for Incorporating User Preferences in Air Traffic Management: A system Perspective

NASA Technical Reports Server (NTRS)

Sheth, Kapil S.; Gutierrez-Nolasco, Sebastian

2010-01-01

This paper presents an analysis of factors that impact user flight schedules during air traffic congestion. In pre-departure flight planning, users file one route per flight, which often leads to increased delays, inefficient airspace utilization, and exclusion of user flight preferences. In this paper, first the idea of filing alternate routes and providing priorities on each of those routes is introduced. Then, the impact of varying planning interval and system imposed departure delay increment is discussed. The metrics of total delay and equity are used for analyzing the impact of these factors on increased traffic and on different users. The results are shown for four cases, with and without the optional routes and priority assignments. Results demonstrate that adding priorities to optional routes further improves system performance compared to filing one route per flight and using first-come first-served scheme. It was also observed that a two-hour planning interval with a five-minute system imposed departure delay increment results in highest delay reduction. The trend holds for a scenario with increased traffic.

Textural and geochemical constraints on eruptive style of the 79AD eruption at Vesuvius

NASA Astrophysics Data System (ADS)

Balcone-Boissard, Hélène; Boudon, Georges; Villemant, Benoît.

2010-05-01

The 79AD eruption of Vesuvius, also known as the "Pompeii eruption", is the reference for one of the explosive eruptive styles, the plinian-type eruption. The eruption involved H2O-rich phonolitic magmas and is commonly divided into three phases: an initial phreatomagmatic phase, followed by a plinian event which produced a thick pumice fallout deposit and a final phase that was dominated by numerous column-collapse events. During the plinian phase, a first white pumice fallout was produced from a high steady eruptive column, followed by a grey pumice fallout originated by an oscillatory eruptive column with several partial column collapse events. This study focuses on the pumice fallout deposits, sampled in a proximal thick section, at the Terzigno quarry, 6 km southeast of the present crater. In order to constrain the degassing processes and the eruptive dynamics, major element compositions, residual volatile contents (H2O, Cl) and textural characteristics (vesicularity and microcrystallinity) were studied. A previous study that we performed on the pre-eruptive Cl content has shown that Cl may be used as an indicator of magma saturation with Cl-rich fluids and of pre-eruptive pressures. Cl contents measured in melt inclusions show that only the white pumice and the upper part of the grey pumice magma were H2O saturated prior eruption. Large variations in residual volatile contents exist between the different eruptive units and textural features strongly differ between white and grey pumice clasts but also within the grey pumice clasts. The degassing processes were thus highly heterogeneous: the white pumice eruptive units represent a typical closed-system degassing evolution whereas the first grey pumice one, stored in the same pre-eruptive saturation conditions, follows a particular open-system degassing evolution. Here we propose a new model of the 79AD eruption where pre-eruptive conditions (H2O saturation, magma temperature and viscosity) are the critical parameters which determine the diversity of the syn-eruptive degassing processes and hence the eruptive dynamics. We suggest that the oscillatory regime that dominates the grey pumice eruptive phase is linked to the pre-eruptive water undersaturation of most part of the grey magma and to the time delays necessary for H2O exsolution.

Long-term Transfer of Learning from Books and Videos during Toddlerhood

PubMed Central

Brito, Natalie; Barr, Rachel; McIntyre, Paula; Simcock, Gabrielle

2011-01-01

Television viewing and picture book reading are prevalent activities during toddlerhood and research has shown that toddlers can imitate from both books and videos after short delays (Barr & Hayne, 1999; Simcock & DeLoache, 2006). This is the first study to directly compare toddlers’ long-term retention rates for target actions learned from a video or book. Toddlers (N = 158) aged 18- and 24-months saw an experimenter demonstrating how to make a novel 3-step toy rattle via a pre-recorded video or a picture book. The toddlers’ imitation of the target actions was tested after a specific delay (e.g., 2 weeks, 4 weeks) and their performance was compared to that of age-matched controls who did not see a demonstration. The 18-month-olds retained the target actions for 2 weeks, exhibiting forgetting at 4 weeks, whereas the 24-month-olds retained the information for up to 4 weeks, exhibiting forgetting at 8 weeks. Retention rates for books and videos did not differ at either age. These findings demonstrate very impressive retention from a brief 2D media demonstration and they contribute to our overall understanding of long-term memory processes during infancy. PMID:21911223

Changes in biogeochemical cycling following forest defoliation by pine wilt disease in Kiryu experimental catchment in Japan

NASA Astrophysics Data System (ADS)

Tokuchi, Naoko; Ohte, Nobuhito; Hobara, Satoru; Kim, Su-Jin; Masanori, Katsuyama

2004-10-01

Changes in nutrient budgets and hydrological processes due to the natural disturbance of pine wilt disease (PWD) were monitored in a small, forested watershed in Japan. The disturbance caused changes in soil nitrogen transformations. Pre-disturbance, mineralized nitrogen remained in the form of NH4+, whereas in disturbed areas most mineralized nitrogen was nitrified. Stream NO3- concentrations increased following PWD. There was a delay between time of disturbance and the increase of NO3- in ground and stream waters. Stream concentrations of NO3- and cations (Ca2+ + Mg2+) were significantly correlated from 1994 to 1996, whereas the correlation among NO3-, H+, and SO42- was significant only in 1995. Although both cation exchange and SO42- adsorption buffered protons, cation exchange was the dominant and continuous mechanism for acid buffering. SO42- adsorption was variable and highly pH dependent. The disturbance also resulted in slight delayed changes of input-output nutrient balances. The nitrogen contribution to PWD litter inputs was 7.39 kmol ha-1, and nitrogen loss from streamwater was less than 0.5 kmol ha-1 year-1 throughout the observation period. This large discrepancy suggested substantial nitrogen immobilization.

Overcrowding of accident & emergency units: is it a growing concern in Nigeria?

PubMed

Makama, Jerry G; Iribhogbe, Pius; Ameh, Emmanuel A

2015-06-01

The inability of the Nigeria's Accident and Emergency Departments (AED) to meet current demands is growing among the public and health care professionals. The data supporting perceptions of insufficient capacity are limited. Therefore, this study was intended to determine the prevalence, causes, and effects of overcrowding AEDs in Nigeria. This was a cross sectional, descriptive study carried out among AED staff of 3 referral teaching hospitals in Nigeria, using a pre-tested and validated structured questionnaire. The analysis of the 267 AED staff revealed 20-56 years (36.40+5.1 mean) age range. One hundred and twenty eight (47.9%) were males, 139 (52.1%) females. Two hundred and fifty nine (97%) agreed that an AED should have a bed capacity of 21-30. Agreement to AED overcrowding in Nigeria was quite considerable. The frequency of AED overcrowding per week was 4-7 times. The average bed occupancy level was 3.25. Agreed common causes of prolonged AED admissions were to be a high volume of critically ill patients, Delayed transfer of patients to the wards, delay in theatre operation, delay in radiological investigations and exceptionally high proportion of patients requiring admission in AED. Also, long pre-review waiting time and haematological delays were more causes. The average waiting time for victims to be seen was 29.7 minutes. There are many causes of AED overcrowding in this environment. However, improving AED bed management, better organized and diligent discharge planning, and reducing access block should be a priority to reduce AED overcrowding.