Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila.

PubMed

Ghatak, Sandeep; Blom, Jochen; Das, Samir; Sanjukta, Rajkumari; Puro, Kekungu; Mawlong, Michael; Shakuntala, Ingudam; Sen, Arnab; Goesmann, Alexander; Kumar, Ashok; Ngachan, S V

2016-07-01

Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.

Cytoprotective effect of seaweeds with high antioxidant activity from the Peniche coast (Portugal).

PubMed

Pinteus, Susete; Silva, Joana; Alves, Celso; Horta, André; Fino, Nádia; Rodrigues, Ana Inês; Mendes, Susana; Pedrosa, Rui

2017-03-01

Screening of antioxidant potential of dichloromethane and methanolic extracts of twenty-seven seaweeds from the Peniche coast was performed by: total phenolic contents (TPC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity and oxygen radical absorbance capacity (ORAC). Seaweeds revealing the highest antioxidant activity were screened for cytoprotective potential in MCF-7 cells, including the mitochondrial membrane potential analysis and the caspase-9 activity. High correlation was found between TPC of seaweed extracts and their scavenging capacity on DPPH and peroxyl radicals. The highest antioxidant activity was displayed by the methanolic fraction of brown seaweeds belonging to Fucales, however Ulva compressa presented the highest cytoprotective effect by blunting the apoptosis process. These results suggest that high antioxidant activity may not be directly related with high cytoprotective potential. Thus, seaweeds reveal to be a promising source of compounds with potential against oxidative stress. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome-wide association analysis of bacterial cold water disease resistance in rainbow trout reveals the potential of a hybrid approach between genomic selection and marker assisted selection

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) simultaneously incorporates dense SNP marker genotypes with phenotypic data from related animals to predict animal-specific genomic breeding value (GEBV), which circumvents the need to measure the disease phenotype in potential breeders. Marker assisted selection (MAS) involv...

Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde.

PubMed

Semedo-Aguiar, Ana P; Pereira-Leal, Jose B; Leite, Ricardo B

2018-05-05

The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde. Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs. Faveta potentially toxic and bloom-forming Microcystis sp., dominated our samples, while a Cryptomonas green algae and Gammaproteobacteria dominated Saquinho and Poilão reservoirs. We reconstructed and assembled the Microcystis genome, extracted from the metagenome of bulk DNA from Faveta water. Phylogenetic analysis of Microcystis cf. aeruginosa CV01’s genome revealed its close relationship with other Microcystis genomes, as well as clustering with other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This survey reinforces the need to better understand the country’s microbial ecology as a whole of water reservoirs on the rise.

Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde

PubMed Central

Pereira-Leal, Jose B.

2018-01-01

The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde. Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs. Faveta potentially toxic and bloom-forming Microcystis sp., dominated our samples, while a Cryptomonas green algae and Gammaproteobacteria dominated Saquinho and Poilão reservoirs. We reconstructed and assembled the Microcystis genome, extracted from the metagenome of bulk DNA from Faveta water. Phylogenetic analysis of Microcystis cf. aeruginosa CV01’s genome revealed its close relationship with other Microcystis genomes, as well as clustering with other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This survey reinforces the need to better understand the country’s microbial ecology as a whole of water reservoirs on the rise. PMID:29734762

Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma.

PubMed

Lamy, Philippe; Nordentoft, Iver; Birkenkamp-Demtröder, Karin; Thomsen, Mathilde Borg Houlberg; Villesen, Palle; Vang, Søren; Hedegaard, Jakob; Borre, Michael; Jensen, Jørgen Bjerggaard; Høyer, Søren; Pedersen, Jakob Skou; Ørntoft, Torben F; Dyrskjøt, Lars

2016-10-01

Greater knowledge concerning tumor heterogeneity and clonality is needed to determine the impact of targeted treatment in the setting of bladder cancer. In this study, we performed whole-exome, transcriptome, and deep-focused sequencing of metachronous tumors from 29 patients initially diagnosed with early-stage bladder tumors (14 with nonprogressive disease and 15 with progressive disease). Tumors from patients with progressive disease showed a higher variance of the intrapatient mutational spectrum and a higher frequency of APOBEC-related mutations. Allele-specific expression was also higher in these patients, particularly in tumor suppressor genes. Phylogenetic analysis revealed a common origin of the metachronous tumors, with a higher proportion of clonal mutations in the ancestral branch; however, 19 potential therapeutic targets were identified as both ancestral and tumor-specific alterations. Few subclones were present based on PyClone analysis. Our results illuminate tumor evolution and identify candidate therapeutic targets in bladder cancer. Cancer Res; 76(19); 5894-906. ©2016 AACR. ©2016 American Association for Cancer Research.

Fashioning the Subject: The Rhetorical Accomplishment of Assessment Tasks

ERIC Educational Resources Information Center

Nicoll, Katherine

2007-01-01

This paper explores the potential of a poststructuralist and rhetorical analysis in appreciating more fully the discursive work of assessment tasks as mechanisms of power/knowledge within discourses of professional development. It is argued that such analysis may reveal detail in the way in which assessments work as material elements within a body…

Symbolic Competence in Multilingual Interactions in a University Setting: A Complexity Analysis

ERIC Educational Resources Information Center

Gu, Michelle

2017-01-01

This paper, drawing on the notion of symbolic competence and insights from complexity theory, investigates the multilingual practices of university students in group discussions. The data analysis reveals that the protagonists' language uses index the various ways in which their rehearsal of potential identities, language ideologies, histories,…

[ECOLOGICAL AND GEOGRAPHIC ANALYSIS OF THE SPREAD OF MITES OF THE FAMILY TROMBICULIDAE IN MONGOLIA].

PubMed

Karimova, T Yu; Kudryashova, N I; Lushchekina, A A; Neronov, V M

2016-01-01

The paper gives data on the fauna of chigger mites (Thrombiculinae), the ectoparasites of small mammals in Mongolia. The ecological and geographic analysis could reveal the major abiotic and biotic determinants of the spread of the chigger mites and make a map of their potential area.

Findings from an Organizational Network Analysis to Support Local Public Health Management

PubMed Central

Caldwell, Michael; Rockoff, Maxine L.; Gebbie, Kristine; Carley, Kathleen M.; Bakken, Suzanne

2008-01-01

We assessed the feasibility of using organizational network analysis in a local public health organization. The research setting was an urban/suburban county health department with 156 employees. The goal of the research was to study communication and information flow in the department and to assess the technique for public health management. Network data were derived from survey questionnaires. Computational analysis was performed with the Organizational Risk Analyzer. Analysis revealed centralized communication, limited interdependencies, potential knowledge loss through retirement, and possible informational silos. The findings suggested opportunities for more cross program coordination but also suggested the presences of potentially efficient communication paths and potentially beneficial social connectedness. Managers found the findings useful to support decision making. Public health organizations must be effective in an increasingly complex environment. Network analysis can help build public health capacity for complex system management. PMID:18481183

Polychlorinated Biphenyl (PCB)-Degrading Potential of Microbes Present in a Cryoconite of Jamtalferner Glacier

PubMed Central

Weiland-Bräuer, Nancy; Fischer, Martin A.; Schramm, Karl-Werner; Schmitz, Ruth A.

2017-01-01

Aiming to comprehensively survey the potential pollution of an alpine cryoconite (Jamtalferner glacier, Austria), and its bacterial community structure along with its biodegrading potential, first chemical analyses of persistent organic pollutants, explicitly polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) as well as polycyclic aromatic hydrocarbons (PAHs), revealed a significant contamination. In total, 18 PCB congeners were detected by high resolution gas chromatography/mass spectrometry with a mean concentration of 0.8 ng/g dry weight; 16 PAHs with an average concentration of 1,400 ng/g; and 26 out of 29 OCPs with a mean concentration of 2.4 ng/g. Second, the microbial composition was studied using 16S amplicon sequencing. The analysis revealed high abundances of Proteobacteria (66%), the majority representing α-Proteobacteria (87%); as well as Cyanobacteria (32%), however high diversity was due to 11 low abundant phyla comprising 75 genera. Biodegrading potential of cryoconite bacteria was further analyzed using enrichment cultures (microcosms) with PCB mixture Aroclor 1242. 16S rDNA analysis taxonomically classified 37 different biofilm-forming and PCB-degrading bacteria, represented by Pseudomonas, Shigella, Subtercola, Chitinophaga, and Janthinobacterium species. Overall, the combination of culture-dependent and culture-independent methods identified degrading bacteria that can be potential candidates to develop novel bioremediation strategies. PMID:28663747

Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing

PubMed Central

Lu, Xin; Zhang, Xu-Xiang; Wang, Zhu; Huang, Kailong; Wang, Yuan; Liang, Weigang; Tan, Yunfei; Liu, Bo; Tang, Junying

2015-01-01

This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence. PMID:25938416

Bioactivity Assessment of Indian Origin-Mangrove Actinobacteria against Candida albicans.

PubMed

Pavan Kumar, J G S; Gomathi, Ajitha; Gothandam, K M; Vasconcelos, Vitor

2018-02-12

Actinobacteria is found to have a potent metabolic activity against pathogens. The present study reveals the assessment of potent antifungal secondary metabolites from actinobacteria isolated from Indian marine mangrove sediments. The samples were collected from the coastal regions of Muthupet, Andaman and the Nicobar Islands. Identification was carried out using 16S rRNA analysis and biosynthetic genes (Polyketide synthase type I/II and Non-ribosomal peptide synthase) were screened. Actinobacteria were assayed for their antifungal activity against 16 clinical Candida albicans and the compound analysis was performed using gas chromatography-mass spectrometry GC-MS. The 31 actinobacterial strains were isolated and 16S rRNA gene sequencing revealed that this ecosystem is rich on actinobacteria, with Streptomyces as the predominant genus. The PCR based screening of biosynthetic genes revealed the presence of PKS-I in six strains, PKS-II in four strains and NRPS in 11 strains. The isolated actinobacteria VITGAP240 and VITGAP241 (two isolates) were found to have a potential antifungal activity against all the tested C. albicans . GC-MS results revealed that the actinobacterial compounds were belonging to heterocyclic, polyketides and peptides. Overall, the strains possess a wide spectrum of antifungal properties which affords the production of significant bioactive metabolites as potential antibiotics.

Bioactivity Assessment of Indian Origin—Mangrove Actinobacteria against Candida albicans

PubMed Central

Pavan Kumar, J. G. S.; Gomathi, Ajitha; Vasconcelos, Vitor

2018-01-01

Actinobacteria is found to have a potent metabolic activity against pathogens. The present study reveals the assessment of potent antifungal secondary metabolites from actinobacteria isolated from Indian marine mangrove sediments. The samples were collected from the coastal regions of Muthupet, Andaman and the Nicobar Islands. Identification was carried out using 16S rRNA analysis and biosynthetic genes (Polyketide synthase type I/II and Non-ribosomal peptide synthase) were screened. Actinobacteria were assayed for their antifungal activity against 16 clinical Candida albicans and the compound analysis was performed using gas chromatography-mass spectrometry GC-MS. The 31 actinobacterial strains were isolated and 16S rRNA gene sequencing revealed that this ecosystem is rich on actinobacteria, with Streptomyces as the predominant genus. The PCR based screening of biosynthetic genes revealed the presence of PKS-I in six strains, PKS-II in four strains and NRPS in 11 strains. The isolated actinobacteria VITGAP240 and VITGAP241 (two isolates) were found to have a potential antifungal activity against all the tested C. albicans. GC-MS results revealed that the actinobacterial compounds were belonging to heterocyclic, polyketides and peptides. Overall, the strains possess a wide spectrum of antifungal properties which affords the production of significant bioactive metabolites as potential antibiotics. PMID:29439535

The challenge of informed consent and return of results in translational genomics: empirical analysis and recommendations.

PubMed

Henderson, Gail E; Wolf, Susan M; Kuczynski, Kristine J; Joffe, Steven; Sharp, Richard R; Parsons, D Williams; Knoppers, Bartha M; Yu, Joon-Ho; Appelbaum, Paul S

2014-01-01

As exome and genome sequencing move into clinical application, questions surround how to elicit consent and handle potential return of individual genomic results. This study analyzes nine consent forms used in NIH-funded sequencing studies. Content analysis reveals considerable heterogeneity, including in defining results that may be returned, identifying potential benefits and risks of return, protecting privacy, addressing placement of results in the medical record, and data-sharing. In response to lack of consensus, we offer recommendations. © 2014 American Society of Law, Medicine & Ethics, Inc.

Global Warming Wars: Rhetorical and Discourse Analytic Approaches to ExxonMobil's Corporate Public Discourse.

ERIC Educational Resources Information Center

Livesey, Sharon M.

2002-01-01

Analyzes texts published by ExxonMobil on the issue of climate change, employing both rhetorical analysis and discourse analysis to show their uses and potential value in business communication research. Shows how both reveal the socially constructed nature "reality" and the social effects of language, but are never the less distinct in…

International publication trends in the Journal of Applied Behavior Analysis: 2000-2014.

PubMed

Martin, Neil T; Nosik, Melissa R; Carr, James E

2016-06-01

Dymond, Clarke, Dunlap, and Steiner's (2000) analysis of international publication trends in the Journal of Applied Behavior Analysis (JABA) from 1970 to 1999 revealed low numbers of publications from outside North America, leading the authors to express concern about the lack of international involvement in applied behavior analysis. They suggested that a future review would be necessary to evaluate any changes in international authorship in the journal. As a follow-up, we analyzed non-U.S. publication trends in the most recent 15 years of JABA and found similar results. We discuss potential reasons for the relative paucity of international authors and suggest potential strategies for increasing non-U.S. contributions to the advancement of behavior analysis. © 2015 Society for the Experimental Analysis of Behavior.

Mechanisms of astrocytic K(+) clearance and swelling under high extracellular K(+) concentrations.

PubMed

Murakami, Shingo; Kurachi, Yoshihisa

2016-03-01

In response to the elevation of extracellular K(+) concentration ([K(+)]out), astrocytes clear excessive K(+) to maintain conditions necessary for neural activity. K(+) clearance in astrocytes occurs via two processes: K(+) uptake and K(+) spatial buffering. High [K(+)]out also induces swelling in astrocytes, leading to edema and cell death in the brain. Despite the importance of astrocytic K(+) clearance and swelling, the underlying mechanisms remain unclear. Here, we report results from a simulation analysis of astrocytic K(+) clearance and swelling. Astrocyte models were constructed by incorporating various mechanisms such as intra/extracellular ion concentrations of Na(+), K(+), and Cl(-), cell volume, and models of Na,K-ATPase, Na-K-Cl cotransporter (NKCC), K-Cl cotransporter, inwardly-rectifying K(+) (KIR) channel, passive Cl(-) current, and aquaporin channel. The simulated response of astrocyte models under the uniform distribution of high [K(+)]out revealed significant contributions of NKCC and Na,K-ATPase to increases of intracellular K(+) and Cl(-) concentrations, and swelling. Moreover, we found that, under the non-uniform distribution of high [K(+)]out, KIR channels localized at synaptic clefts absorbed excess K(+) by depolarizing the equivalent potential of K(+) (E K) above membrane potential, while K(+) released through perivascular KIR channels was enhanced by hyperpolarizing E K and depolarizing membrane potential. Further analysis of simulated drug effects revealed that astrocyte swelling was modulated by blocking each of the ion channels and transporters. Our simulation analysis revealed controversial mechanisms of astrocytic K(+) clearance and swelling resulting from complex interactions among ion channels and transporters.

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles* #

PubMed Central

Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen

2016-01-01

Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles.

PubMed

Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-Yu; Zhang, Xiao-Mei; Song, Da-Feng; Zhang, Chen

2016-08-01

In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.

In vitro and in vivo antibiofilm potential of 2,4-Di-tert-butylphenol from seaweed surface associated bacterium Bacillus subtilis against group A streptococcus.

PubMed

Viszwapriya, Dharmaprakash; Prithika, Udayakumar; Deebika, Sundaresan; Balamurugan, Krishnaswamy; Pandian, Shunmugiah Karutha

2016-10-01

Biofilm formation of Group A Streptococcus (GAS) is recognized as an important virulent determinant. The present study reports the antibiofilm potential of seaweed (Gracilaria gracilis) surface associated Bacillus subtilis against GAS. Purification revealed 2,4-Di-tert-butyl-phenol (DTBP) as the active principle. DTBP exhibited a dose dependent antibiofilm activity against GAS (SF370 & six different clinical M serotypes). Microscopic analysis revealed changes in cell surface architecture and reduced thickness upon DTBP treatment. Results of extracellular polymeric substance quantification, microbial adhesion to hydrocarbon assay and fourier transform infrared spectroscopic analysis suggested that DTBP probably interferes with the initial adhesion stage of biofilm formation cascade. Reduction in hyaluronic acid synthesis goes in unison with blood survival assay wherein, increased susceptibility to phagocytosis was observed. In vivo studies using Caenorhabditis elegans manifested the reduction in adherence and virulence, which prompts further investigation of the potential of DTBP for the treatment of GAS infections. Copyright © 2016 Elsevier GmbH. All rights reserved.

Qualitative analysis of certain generalized classes of quadratic oscillator systems

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

Bagchi, Bijan, E-mail: bbagchi123@gmail.com; Ghosh, Samiran, E-mail: sran-g@yahoo.com; Pal, Barnali, E-mail: barrna.roo@gmail.com

2016-02-15

We carry out a systematic qualitative analysis of the two quadratic schemes of generalized oscillators recently proposed by Quesne [J. Math. Phys. 56, 012903 (2015)]. By performing a local analysis of the governing potentials, we demonstrate that while the first potential admits a pair of equilibrium points one of which is typically a center for both signs of the coupling strength λ, the other points to a centre for λ < 0 but a saddle λ > 0. On the other hand, the second potential reveals only a center for both the signs of λ from a linear stability analysis.more » We carry out our study by extending Quesne’s scheme to include the effects of a linear dissipative term. An important outcome is that we run into a remarkable transition to chaos in the presence of a periodic force term fcosωt.« less

Quinone 1 e – and 2 e – /2 H + Reduction Potentials: Identification and Analysis of Deviations from Systematic Scaling Relationships

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

Huynh, Mioy T.; Anson, Colin W.; Cavell, Andrew C.

Quinones participate in diverse electron transfer and proton-coupled electron transfer processes in chemistry and biology. An experimental study of common quinones reveals a non-linear correlation between the 1 e – and 2 e –/2 H + reduction potentials. This unexpected observation prompted a computational study of 128 different quinones, probing their 1 e – reduction potentials, pKa values, and 2 e –/2 H + reduction potentials. The density functional theory calculations reveal an approximately linear correlation between these three properties and an effective Hammett constant associated with the quinone substituent(s). However, deviations from this linear scaling relationship are evident formore » quinones that feature halogen substituents, charged substituents, intramolecular hydrogen bonding in the hydroquinone, and/or sterically bulky substituents. These results, particularly the different substituent effects on the 1 e – versus 2 e – /2 H + reduction potentials, have important implications for designing quinones with tailored redox properties.« less

Neurophysiological modification of CA1 pyramidal neurons in a transgenic mouse expressing a truncated form of disrupted-in-schizophrenia 1

PubMed Central

Booth, Clair A; Brown, Jonathan T; Randall, Andrew D

2014-01-01

A t(1;11) balanced chromosomal translocation transects the Disc1 gene in a large Scottish family and produces genome-wide linkage to schizophrenia and recurrent major depressive disorder. This study describes our in vitro investigations into neurophysiological function in hippocampal area CA1 of a transgenic mouse (DISC1tr) that expresses a truncated version of DISC1 designed to reproduce aspects of the genetic situation in the Scottish t(1;11) pedigree. We employed both patch-clamp and extracellular recording methods in vitro to compare intrinsic properties and synaptic function and plasticity between DISC1tr animals and wild-type littermates. Patch-clamp analysis of CA1 pyramidal neurons (CA1-PNs) revealed no genotype dependence in multiple subthreshold parameters, including resting potential, input resistance, hyperpolarization-activated ‘sag’ and resonance properties. Suprathreshold stimuli revealed no alteration to action potential (AP) waveform, although the initial rate of AP production was higher in DISC1tr mice. No difference was observed in afterhyperpolarizing potentials following trains of 5–25 APs at 50 Hz. Patch-clamp analysis of synaptic responses in the Schaffer collateral commissural (SC) pathway indicated no genotype-dependence of paired pulse facilitation, excitatory postsynaptic potential summation or AMPA/NMDA ratio. Extracellular recordings also revealed an absence of changes to SC synaptic responses and indicated input–output and short-term plasticity were also unaltered in the temporoammonic (TA) input. However, in DISC1tr mice theta burst-induced long-term potentiation was enhanced in the SC pathway but completely lost in the TA pathway. These data demonstrate that expressing a truncated form of DISC1 affects intrinsic properties of CA1-PNs and produces pathway-specific effects on long-term synaptic plasticity. PMID:24712988

Towards a Fuzzy Bayesian Network Based Approach for Safety Risk Analysis of Tunnel-Induced Pipeline Damage.

PubMed

Zhang, Limao; Wu, Xianguo; Qin, Yawei; Skibniewski, Miroslaw J; Liu, Wenli

2016-02-01

Tunneling excavation is bound to produce significant disturbances to surrounding environments, and the tunnel-induced damage to adjacent underground buried pipelines is of considerable importance for geotechnical practice. A fuzzy Bayesian networks (FBNs) based approach for safety risk analysis is developed in this article with detailed step-by-step procedures, consisting of risk mechanism analysis, the FBN model establishment, fuzzification, FBN-based inference, defuzzification, and decision making. In accordance with the failure mechanism analysis, a tunnel-induced pipeline damage model is proposed to reveal the cause-effect relationships between the pipeline damage and its influential variables. In terms of the fuzzification process, an expert confidence indicator is proposed to reveal the reliability of the data when determining the fuzzy probability of occurrence of basic events, with both the judgment ability level and the subjectivity reliability level taken into account. By means of the fuzzy Bayesian inference, the approach proposed in this article is capable of calculating the probability distribution of potential safety risks and identifying the most likely potential causes of accidents under both prior knowledge and given evidence circumstances. A case concerning the safety analysis of underground buried pipelines adjacent to the construction of the Wuhan Yangtze River Tunnel is presented. The results demonstrate the feasibility of the proposed FBN approach and its application potential. The proposed approach can be used as a decision tool to provide support for safety assurance and management in tunnel construction, and thus increase the likelihood of a successful project in a complex project environment. © 2015 Society for Risk Analysis.

Integrative analysis of gut microbiota composition, host colonic gene expression and intraluminal metabolites in aging C57BL/6J mice.

PubMed

van der Lugt, Benthe; Rusli, Fenni; Lute, Carolien; Lamprakis, Andreas; Salazar, Ethel; Boekschoten, Mark V; Hooiveld, Guido J; Müller, Michael; Vervoort, Jacques; Kersten, Sander; Belzer, Clara; Kok, Dieuwertje E G; Steegenga, Wilma T

2018-05-16

The aging process is associated with diminished colonic health. In this study, we applied an integrative approach to reveal potential interactions between determinants of colonic health in aging C57BL/6J mice. Analysis of gut microbiota composition revealed an enrichment of various potential pathobionts, including Desulfovibrio spp . , and a decline of the health-promoting Akkermansia spp . and Lactobacillus spp. during aging. Intraluminal concentrations of various metabolites varied between ages and we found evidence for an increased gut permeability at higher age. Colonic gene expression analysis suggested that during the early phase of aging (between 6 and 12 months), expression of genes involved in epithelial-to-mesenchymal transition and (re)organization of the extracellular matrix were increased. Differential expression of these genes was strongly correlated with Bifidobacterium spp. During the later phase of aging (between 12 and 28 months), gene expression profiles pointed towards a diminished antimicrobial defense and were correlated with an uncultured Gastranaerophilales spp. This study demonstrates that aging is associated with pronounced changes in gut microbiota composition and colonic gene expression. Furthermore, the strong correlations between specific bacterial genera and host gene expression may imply that orchestrated interactions take place in the vicinity of the colonic wall and potentially mediate colonic health during aging.

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

PubMed

Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

2016-01-04

Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

Co-authorship network analysis in health research: method and potential use.

PubMed

Fonseca, Bruna de Paula Fonseca E; Sampaio, Ricardo Barros; Fonseca, Marcus Vinicius de Araújo; Zicker, Fabio

2016-04-30

Scientific collaboration networks are a hallmark of contemporary academic research. Researchers are no longer independent players, but members of teams that bring together complementary skills and multidisciplinary approaches around common goals. Social network analysis and co-authorship networks are increasingly used as powerful tools to assess collaboration trends and to identify leading scientists and organizations. The analysis reveals the social structure of the networks by identifying actors and their connections. This article reviews the method and potential applications of co-authorship network analysis in health. The basic steps for conducting co-authorship studies in health research are described and common network metrics are presented. The application of the method is exemplified by an overview of the global research network for Chikungunya virus vaccines.

Dielectric barrier discharge-based investigation and analysis of wastewater treatment and pollutant removal.

PubMed

Ramdani, N; Lousdad, A; Tilmatine, A; Nemmich, S

2016-01-01

Current research reveals that the oxidation by ozone is considered as an effective solution and offers irrefutable advantages in wastewater treatment. It is also well known that ozone is used to treat different types of water due to its effectiveness in water purification and for its oxidation potential. This process of ozonation is becoming progressively an alternative technology and is inscribed in a sustainable development perspective in Algeria. In this regards, the present paper investigates the wastewater treatment process by ozone produced by dielectric barrier discharge (DBD) under high potential. Three (DBD) ozone generators of cylindrical form have been used, at a laboratory scale, for treating collected samples from the wastewater treatment plant (WWTP) of the city of Sidi-Bel-Abbes located in the west of Algeria. Our experimental results reveal the efficiency of this type of treatment on the basis of the physicochemical analysis (pH, turbidity, chemical oxygen demand, biological oxygen demand, heavy metals) and microbial analysis downstream of the WWTP, which showed a high rate of elimination of all the parameters.

Proteomic Analysis Reveals Differentially Regulated Protein Acetylation in Human Amyotrophic Lateral Sclerosis Spinal Cord

PubMed Central

Azadzoi, Kazem; Yang, Yun; Fei, Zhou; Dou, Kefeng; Kowall, Neil W.; Choi, Han-Pil; Vieira, Fernando; Yang, Jing-Hua

2013-01-01

Amyotrophic lateral sclerosis (ALS) is a progressive fatal neurodegenerative disease that primarily affects motor neurons in the brain and spinal cord. Histone deacetylase (HDAC) inhibitors have neuroprotective effects potentially useful for the treatment of neurodegenerative diseases including ALS; however, the molecular mechanisms underlying their potential efficacy is not well understood. Here we report that protein acetylation in urea-soluble proteins is differently regulated in post-mortem ALS spinal cord. Two-dimensional electrophoresis (2-DE) analysis reveals several protein clusters with similar molecular weight but different charge status. Liquid chromatography and tandem mass spectrometry (LC-MS/MS) identifies glial fibrillary acidic protein (GFAP) as the dominant component in the protein clusters. Further analysis indicates six heavily acetylated lysine residues at positions 89, 153, 189, 218, 259 and 331 of GFAP. Immunoprecipitation followed by Western blotting confirms that the larger form of GFAP fragments are acetylated and upregulated in ALS spinal cord. Further studies demonstrate that acetylation of the proteins additional to GFAP is differently regulated, suggesting that acetylation and/or deacetylation play an important role in pathogenesis of ALS. PMID:24312501

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

PubMed

Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

2018-05-01

The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

Parenting stress and anger expression as predictors of child abuse potential.

PubMed

Rodriguez, C M; Green, A J

1997-04-01

To explore one potential pathway to physical child abuse, the present investigation used hierarchical regression analysis using measures of parenting stress and anger expression to jointly predict child abuse potential. The Parenting Stress Index, State-Trait Anger Expression Inventory, and the Child Abuse Potential Inventory were administered to two different samples of New Zealand parents. As expected, both studies revealed parenting stress and anger expression and were individually positively correlated with child abuse potential: the major finding involved the strong point contribution of parenting stress and anger expression in predicting Child Abuse Potential Inventory scores. Application of findings for intervention and prevention are discussed.

[Localization of attention related cortical structures by evoked potentials].

PubMed

Szelenberger, W

2000-01-01

Attention is an ambiguous concept, difficult to direct implementation in neurophysiological studies. The paper presents application of the Continuous Attention Test (CAT) items as stimuli in event related potential (ERP) studies on attention. Stimuli with high demand of attention result in enlarged N1 component in occipital derivations. Spatial analysis revealed increased positivity in frontal derivations. Three-dimensional image of cortical current density by means of Low Resolution Electromagnetic Tomography (LORETA) revealed sources of N1 component in occipital, parietal and postero-temporal derivations with the maximal current value at 17 Brodmann area. After target stimuli increase of current density in frontal derivations was observed, with the maximal value in the left 9 Brodmann area.

Oocytes express an endogenous red fluorescent protein in a stony coral, Euphyllia ancora: a potential involvement in coral oogenesis

PubMed Central

Shikina, Shinya; Chiu, Yi-Ling; Chung, Yi-Jou; Chen, Chieh-Jhen; Lee, Yan-Horn; Chang, Ching-Fong

2016-01-01

To date,the molecular and cellular mechanisms underlying coral sexual reproduction remain largely unknown. We then performed a differential screen to identify genes related to oogenesis in the stony coral Euphyllia ancora. We identified a clone encoding a novel red fluorescent protein cDNA of E. ancora (named EaRFP). Microscopic observation and quantitative RT-PCR revealed that EaRFP is almost exclusively expressed in the ovary of the adult coral. The combination of the ovarian-cell separation method and the RT-PCR analysis revealed that the oocytes, but not the ovarian somatic cells, are the cells expressing EaRFP. Immunohistochemical analysis revealed that the expression of EaRFP starts in the early stage of the oocyte and continues until the maturation period. Furthermore, recombinant EaRFP was shown to possess an H2O2 degradation activity. These results raise the possibility that EaRFP plays a role in protecting the oocytes from oxidative stress from the early to late stages of oogenesis. The present study provides not only the first evidence for the potential involvement of FPs in coral oogenesis but also an insight into a cellular strategy underlying coral sexual reproduction. PMID:27167722

Oocytes express an endogenous red fluorescent protein in a stony coral, Euphyllia ancora: a potential involvement in coral oogenesis.

PubMed

Shikina, Shinya; Chiu, Yi-Ling; Chung, Yi-Jou; Chen, Chieh-Jhen; Lee, Yan-Horn; Chang, Ching-Fong

2016-05-11

To date,the molecular and cellular mechanisms underlying coral sexual reproduction remain largely unknown. We then performed a differential screen to identify genes related to oogenesis in the stony coral Euphyllia ancora. We identified a clone encoding a novel red fluorescent protein cDNA of E. ancora (named EaRFP). Microscopic observation and quantitative RT-PCR revealed that EaRFP is almost exclusively expressed in the ovary of the adult coral. The combination of the ovarian-cell separation method and the RT-PCR analysis revealed that the oocytes, but not the ovarian somatic cells, are the cells expressing EaRFP. Immunohistochemical analysis revealed that the expression of EaRFP starts in the early stage of the oocyte and continues until the maturation period. Furthermore, recombinant EaRFP was shown to possess an H2O2 degradation activity. These results raise the possibility that EaRFP plays a role in protecting the oocytes from oxidative stress from the early to late stages of oogenesis. The present study provides not only the first evidence for the potential involvement of FPs in coral oogenesis but also an insight into a cellular strategy underlying coral sexual reproduction.

Biological activities of the polysaccharides produced in submerged culture of two edible Pleurotus ostreatus mushrooms.

PubMed

Vamanu, Emanuel

2012-01-01

Exopolysaccharides (EPS) and internal (intracellular) polysaccharides (IPS) obtained from the Pleurotus ostreatus M2191 and PBS281009 cultivated using the batch system revealed an average of between 0.1-2 (EPS) and 0.07-1.5 g/L/day (IPS). The carbohydrate analysis revealed that the polysaccharides comprised 87-89% EPS and 68-74% IPS. The investigation of antioxidant activity in vitro revealed a good antioxidant potential, particularly for the IPS and EPS isolated from PBS281009, as proved by the EC(50) value for DPPH, ABTS scavenging activity, reducing power, and iron chelating activity.

Rapid Presentation of Emotional Expressions Reveals New Emotional Impairments in Tourette’s Syndrome

PubMed Central

Mermillod, Martial; Devaux, Damien; Derost, Philippe; Rieu, Isabelle; Chambres, Patrick; Auxiette, Catherine; Legrand, Guillaume; Galland, Fabienne; Dalens, Hélène; Coulangeon, Louise Marie; Broussolle, Emmanuel; Durif, Franck; Jalenques, Isabelle

2013-01-01

Objective: Based on a variety of empirical evidence obtained within the theoretical framework of embodiment theory, we considered it likely that motor disorders in Tourette’s syndrome (TS) would have emotional consequences for TS patients. However, previous research using emotional facial categorization tasks suggests that these consequences are limited to TS patients with obsessive-compulsive behaviors (OCB). Method: These studies used long stimulus presentations which allowed the participants to categorize the different emotional facial expressions (EFEs) on the basis of a perceptual analysis that might potentially hide a lack of emotional feeling for certain emotions. In order to reduce this perceptual bias, we used a rapid visual presentation procedure. Results: Using this new experimental method, we revealed different and surprising impairments on several EFEs in TS patients compared to matched healthy control participants. Moreover, a spatial frequency analysis of the visual signal processed by the patients suggests that these impairments may be located at a cortical level. Conclusion: The current study indicates that the rapid visual presentation paradigm makes it possible to identify various potential emotional disorders that were not revealed by the standard visual presentation procedures previously reported in the literature. Moreover, the spatial frequency analysis performed in our study suggests that emotional deficit in TS might lie at the level of temporal cortical areas dedicated to the processing of HSF visual information. PMID:23630481

Culture-independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil-bioremediation.

PubMed

Dashti, Narjes; Ali, Nedaa; Salamah, Samar; Khanafer, Majida; Al-Shamy, Ghada; Al-Awadhi, Husain; Radwan, Samir S

2018-04-15

To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA-genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture-dependent method we had used in an earlier study for the analysis of the same samples. The study described the dynamics of bacterial communities during bioremediation. The main limitation associated with this molecular approach, namely of not distinguishing hydrocarbonoclastic taxa from others, was overcome by consulting the literature for the hydrocarbonoclastic potential of taxa related to those identified in this study. By doing so, it was concluded that the hydrocarbonoclastic bacterial taxa were much more diverse than those captured by the culture-dependent approach. The molecular analysis also revealed the frequent occurrence of nifH-genes in the total genomic DNA extracts of all the studied environmental samples, which reflects a nitrogen-fixation potential. Nitrogen fertilization is long known to enhance microbial oil-bioremediation. The study revealed that bioaugmentation using plant rhizospheres or soil with long history of oil-pollution was more effective in oil-removal in the desert soil than in seawater microcosms. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Not worth the fuss after all? cross-sectional and prospective data on violent video game influences on aggression, visuospatial cognition and mathematics ability in a sample of youth.

PubMed

Ferguson, Christopher J; Garza, Adolfo; Jerabeck, Jessica; Ramos, Raul; Galindo, Mariza

2013-01-01

The United States Supreme Court's recent decision relating to violent video games revealed divisions within the scientific community about the potential for negative effects of such games as well as the need for more, higher quality research. Scholars also have debated the potential for violent games to have positive effects such as on visuospatial cognition or math ability. The current study sought to extend previous literature by using well-validated clinical outcome measures for relevant constructs, which have generally been lacking in past research. Cross-section data on aggression, visuospatial cognition, and math achievement were available for a sample of 333 (51.7 % female) mostly Hispanic youth (mean age = 12.76). Prospective 1-year data on aggression and school GPA were available for 143 (46.2 % female) of those youth. Results from both sets of analysis revealed that exposure to violent game had neither short-term nor long-term predictive influences on either positive or negative outcomes. A developmental analysis of the cross-sectional data revealed that results did not differ across age categories of older children, preadolescents or adolescents. Analysis of effect sizes largely ruled out Type II error as a possible explanation for null results. Suggestions for new directions in the field of video game research are proffered.

PRODUCTION ENGINEERING AND MARKETING ANALYSIS OF THE ROTATING DISK EVAPORATOR

EPA Science Inventory

Recent EPA-funded research into the onsite, mechanical evaporation of wastewater from single family homes revealed that a rotating disk evaporator (RDE) could function in a nondischarging mode. Such a device has potential use where site limitations preclude conventional methods o...

Glycomics meets artificial intelligence - Potential of glycan analysis for identification of seropositive and seronegative rheumatoid arthritis patients revealed.

PubMed

Chocholova, Erika; Bertok, Tomas; Jane, Eduard; Lorencova, Lenka; Holazova, Alena; Belicka, Ludmila; Belicky, Stefan; Mislovicova, Danica; Vikartovska, Alica; Imrich, Richard; Kasak, Peter; Tkac, Jan

2018-06-01

In this study, one hundred serum samples from healthy people and patients with rheumatoid arthritis (RA) were analyzed. Standard immunoassays for detection of 10 different RA markers and analysis of glycan markers on antibodies in 10 different assay formats with several lectins were applied for each serum sample. A dataset containing 2000 data points was data mined using artificial neural networks (ANN). We identified key RA markers, which can discriminate between healthy people and seropositive RA patients (serum containing autoantibodies) with accuracy of 83.3%. Combination of RA markers with glycan analysis provided much better discrimination accuracy of 92.5%. Immunoassays completely failed to identify seronegative RA patients (serum not containing autoantibodies), while glycan analysis correctly identified 43.8% of these patients. Further, we revealed other critical parameters for successful glycan analysis such as type of a sample, format of analysis and orientation of captured antibodies for glycan analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'.

PubMed

Nakashima, Yu; Egami, Yoko; Kimura, Miki; Wakimoto, Toshiyuki; Abe, Ikuro

2016-01-01

Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an 'Entotheonella' sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.

Factor structure of DSM-IV criteria for obsessive compulsive personality disorder in patients with binge eating disorder.

PubMed

Grilo, C M

2004-01-01

To examine the factor structure of DSM-IV criteria for obsessive compulsive personality disorder (OCPD) in patients with binge eating disorder (BED). Two hundred and eleven consecutive out-patients with axis I diagnoses of BED were reliably assessed with semi-structured diagnostic interviews. The eight criteria for the OCPD diagnosis were examined with reliability and correlational analyses. Exploratory factor analysis was performed to identify potential components. Cronbach's coefficient alpha for the OCPD criteria was 0.77. Principal components factor analysis with varimax rotation revealed a three-factor solution (rigidity, perfectionism, and miserliness), which accounted for 65% of variance. The DSM-IV criteria for OCPD showed good internal consistency. Exploratory factor analysis, however, revealed three components that may reflect distinct interpersonal, intrapersonal (cognitive), and behavioral features.

Potential safety benefits of intelligent cruise control systems.

PubMed

Chira-Chavala, T; Yoo, S M

1994-04-01

Potential safety impact of a hypothetical intelligent cruise control system (ICCS) is evaluated in terms of changes in traffic accidents and some traffic operation characteristics affecting safety. The analysis of changes in traffic accidents is accomplished by in-depth examinations of police accident reports for four major counties in California. The evaluation of changes in traffic operation characteristics affecting safety is accomplished by vehicle simulation. The accident analysis reveals that the use of the hypothetical ICCS could potentially reduce traffic accidents by up to 7.5%. Preliminary vehicle simulation results based on a 10-vehicle convoy indicate that the use of the hypothetical ICCS could reduce frequencies of hard acceleration and deceleration, enhance speed harmonization among vehicles, and reduce incidence of "less-safe" headway.

Robust Nonlinear Causality Analysis of Nonstationary Multivariate Physiological Time Series.

PubMed

Schack, Tim; Muma, Michael; Feng, Mengling; Guan, Cuntai; Zoubir, Abdelhak M

2018-06-01

An important research area in biomedical signal processing is that of quantifying the relationship between simultaneously observed time series and to reveal interactions between the signals. Since biomedical signals are potentially nonstationary and the measurements may contain outliers and artifacts, we introduce a robust time-varying generalized partial directed coherence (rTV-gPDC) function. The proposed method, which is based on a robust estimator of the time-varying autoregressive (TVAR) parameters, is capable of revealing directed interactions between signals. By definition, the rTV-gPDC only displays the linear relationships between the signals. We therefore suggest to approximate the residuals of the TVAR process, which potentially carry information about the nonlinear causality by a piece-wise linear time-varying moving-average model. The performance of the proposed method is assessed via extensive simulations. To illustrate the method's applicability to real-world problems, it is applied to a neurophysiological study that involves intracranial pressure, arterial blood pressure, and brain tissue oxygenation level (PtiO2) measurements. The rTV-gPDC reveals causal patterns that are in accordance with expected cardiosudoral meachanisms and potentially provides new insights regarding traumatic brain injuries. The rTV-gPDC is not restricted to the above problem but can be useful in revealing interactions in a broad range of applications.

Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells

PubMed Central

Liu, Bing; Gao, Yankun; Ruan, Hai-Bin; Chen, Yue

2016-01-01

Proline hydroxylation is a critical cellular mechanism regulating oxygen-response pathways in tumor initiation and progression. Yet, its substrate diversity and functions remain largely unknown. Here, we report a system-wide analysis to characterize proline hydroxylation substrates in cancer cells using an immunoaffinity-purification assisted proteomics strategy. We identified 562 sites from 272 proteins in HeLa cells. Bioinformatic analysis revealed that proline hydroxylation substrates are significantly enriched with mRNA processing and stress-response cellular pathways with canonical and diverse flanking sequence motifs. Structural analysis indicates a significant enrichment of proline hydroxylation participating in the secondary structure of substrate proteins. Our study identified and validated Brd4, a key transcription factor, as a novel proline hydroxylation substrate. Functional analysis showed that the inhibition of proline hydroxylation pathway significantly reduced the proline hydroxylation abundance on Brd4 and affected Brd4-mediated transcriptional activity as well as cell proliferation in AML leukemia cells. Taken together, our study identified a broad regulatory role of proline hydroxylation in cellular oxygen-sensing pathways and revealed potentially new targets that dynamically respond to hypoxia microenvironment in tumor cells. PMID:27764789

Microbiome Analysis of Stool Samples from African Americans with Colon Polyps

PubMed Central

Brim, Hassan; Yooseph, Shibu; Zoetendal, Erwin G.; Lee, Edward; Torralbo, Manolito; Laiyemo, Adeyinka O.; Shokrani, Babak; Nelson, Karen; Ashktorab, Hassan

2013-01-01

Background Colonic polyps are common tumors occurring in ~50% of Western populations with ~10% risk of malignant progression. Dietary agents have been considered the primary environmental exposure to promote colorectal cancer (CRC) development. However, the colonic mucosa is permanently in contact with the microbiota and its metabolic products including toxins that also have the potential to trigger oncogenic transformation. Aim To analyze fecal DNA for microbiota composition and functional potential in African Americans with pre-neoplastic lesions. Materials & Methods We analyzed the bacterial composition of stool samples from 6 healthy individuals and 6 patients with colon polyps using 16S ribosomal RNA-based phylogenetic microarray; the Human intestinal Tract Chip (HITChip) and 16S rRNA gene barcoded 454 pyrosequencing. The functional potential was determined by sequence-based metagenomics using 454 pyrosequencing. Results Fecal microbiota profiling of samples from the healthy and polyp patients using both a phylogenetic microarraying (HITChip) and barcoded 454 pyrosequencing generated similar results. A distinction between both sets of samples was only obtained when the analysis was performed at the sub-genus level. Most of the species leading to the dissociation were from the Bacteroides group. The metagenomic analysis did not reveal major differences in bacterial gene prevalence/abundances between the two groups even when the analysis and comparisons were restricted to available Bacteroides genomes. Conclusion This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level. These differences were not reflected at the genome/functions levels. Bacteria and associated functions within the Bacteroides group need to be further analyzed and dissected to pinpoint potential actors in the early colon oncogenic transformation in a large sample size. PMID:24376500

Genetic analysis reveals multiple cryptic invasive species of the hydrozoan gene Cordylophora

EPA Science Inventory

Understanding the patterns and dynamics of biological invasions is a crucial prerequisite to predicting and mitigating their potential ecological and economic impacts. Unfortunately, in many cases such understanding is limited not only by ignorance of invasion history, but also b...

Enhancing Electromagnetic Side-Channel Analysis in an Operational Environment

DTIC Science & Technology

2013-09-01

phenomenon of compromising power and EM emissions has been known and exploited for decades. Declassified TEMPEST documents reveal vulnerabilities of...Components. One technique to detect potentially compromising emissions is to use a wide-band receiver tuned to a specific frequency. High-end TEMPEST

Structural Investigations of Afghanistan Deduced from Remote Sensing and Potential Field Data

NASA Astrophysics Data System (ADS)

Saibi, Hakim; Azizi, Masood; Mogren, Saad

2016-08-01

This study integrates potential gravity and magnetic field data with remotely sensed images and geological data in an effort to understand the subsurface major geological structures in Afghanistan. Integrated analysis of Landsat SRTM data was applied for extraction of geological lineaments. The potential field data were analyzed using gradient interpretation techniques, such as analytic signal (AS), tilt derivative (TDR), horizontal gradient of the tilt derivative (HG-TDR), Euler Deconvolution (ED) and power spectrum methods, and results were correlated with known geological structures. The analysis of remote sensing data and potential field data reveals the regional geological structural characteristics of Afghanistan. The power spectrum analysis of magnetic and gravity data suggests shallow basement rocks at around 1 to 1.5 km depth. The results of TDR of potential field data are in agreement with the location of the major regional fault structures and also the location of the basins and swells, except in the Helmand region (SW Afghanistan) where many high potential field anomalies are observed and attributed to batholiths and near-surface volcanic rocks intrusions. A high-resolution airborne geophysical survey in the data sparse region of eastern Afghanistan is recommended in order to have a complete image of the potential field anomalies.

Temporal analysis of mtDNA variation reveals decreased genetic diversity in least terns

USGS Publications Warehouse

Draheim, Hope M.; Baird, Patricia; Haig, Susan M.

2012-01-01

The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. We used historical museum specimens (pre-1960) and contemporary (2001–2005) samples to examine range-wide phylogeographic patterns and investigate potential loss in the species' genetic variation. We obtained sequences (522 bp) of the mitochondrial gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species' range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. However, we detected potential reductions in genetic diversity in contemporary samples from California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Our results offer unique insights into changes in the Least Tern's genetic diversity over the past century and highlight the importance and utility of museum specimens in studies of conservation genetics.

Functional annotation of the genome unravels probiotic potential of Bacillus coagulans HS243.

PubMed

Kapse, N G; Engineer, A S; Gowdaman, V; Wagh, S; Dhakephalkar, P K

2018-05-30

Spore forming Bacillus species are widely used as probiotics for human dietary supplements and in animal feeds. However, information on genetic basis of their probiotic action is obscure. Therefore, the present investigation was undertaken to elucidate probiotic traits of B. coagulans HS243 through its genome analysis. Genome mining revealed the presence of an arsenal of marker genes attributed to genuine probiotic traits. In silico analysis of HS243 genome revealed the presence of multi subunit ATPases, ADI pathway genes, chologlycine hydrolase, adhesion proteins for surviving and colonizing harsh gastric transit. HS243 genome harbored vitamin and essential amino acid biosynthetic genes, suggesting the use of HS243 as a nutrient supplement. Bacteriocin producing genes highlighted the disease preventing potential of HS243. Thus, this work established that HS243 possessed the genetic repertoire required for surviving harsh gastric transit and conferring health benefits to the host which were further validated by wet lab evidences. Copyright © 2018. Published by Elsevier Inc.

Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making

PubMed Central

Chahal, Manik; Pleasance, Erin; Grewal, Jasleen; Zhao, Eric; Ng, Tony; Chapman, Erin; Jones, Martin R.; Shen, Yaoqing; Mungall, Karen L.; Bonakdar, Melika; Taylor, Gregory A.; Ma, Yussanne; Mungall, Andrew J.; Moore, Richard A.; Lim, Howard; Renouf, Daniel; Yip, Stephen; Jones, Steven J.M.; Marra, Marco A.; Laskin, Janessa

2018-01-01

Metastatic adenoid cystic carcinomas (ACCs) can cause significant morbidity and mortality. Because of their slow growth and relative rarity, there is limited evidence for systemic therapy regimens. Recently, molecular profiling studies have begun to reveal the genetic landscape of these poorly understood cancers, and new treatment possibilities are beginning to emerge. The objective is to use whole-genome and transcriptome sequencing and analysis to better understand the genetic alterations underlying the pathology of metastatic and rare ACCs and determine potentially actionable therapeutic targets. We report five cases of metastatic ACC, not originating in the salivary glands, in patients enrolled in the Personalized Oncogenomics (POG) Program at the BC Cancer Agency. Genomic workup included whole-genome and transcriptome sequencing, detailed analysis of tumor alterations, and integration with existing knowledge of drug–target combinations to identify potential therapeutic targets. Analysis reveals low mutational burden in these five ACC cases, and mutation signatures that are commonly observed in multiple cancer types. Notably, the only recurrent structural aberration identified was the well-described MYB-NFIB fusion that was present in four of five cases, and one case exhibited a closely related MYBL1-NFIB fusion. Recurrent mutations were also identified in BAP1 and BCOR, with additional mutations in individual samples affecting NOTCH1 and the epigenetic regulators ARID2, SMARCA2, and SMARCB1. Copy changes were rare, and they included amplification of MYC and homozygous loss of CDKN2A in individual samples. Genomic analysis revealed therapeutic targets in all five cases and served to inform a therapeutic choice in three of the cases to date. PMID:29610392

Conservation of tubulin-binding sequences in TRPV1 throughout evolution.

PubMed

Sardar, Puspendu; Kumar, Abhishek; Bhandari, Anita; Goswami, Chandan

2012-01-01

Transient Receptor Potential Vanilloid sub type 1 (TRPV1), commonly known as capsaicin receptor can detect multiple stimuli ranging from noxious compounds, low pH, temperature as well as electromagnetic wave at different ranges. In addition, this receptor is involved in multiple physiological and sensory processes. Therefore, functions of TRPV1 have direct influences on adaptation and further evolution also. Availability of various eukaryotic genomic sequences in public domain facilitates us in studying the molecular evolution of TRPV1 protein and the respective conservation of certain domains, motifs and interacting regions that are functionally important. Using statistical and bioinformatics tools, our analysis reveals that TRPV1 has evolved about ∼420 million years ago (MYA). Our analysis reveals that specific regions, domains and motifs of TRPV1 has gone through different selection pressure and thus have different levels of conservation. We found that among all, TRP box is the most conserved and thus have functional significance. Our results also indicate that the tubulin binding sequences (TBS) have evolutionary significance as these stretch sequences are more conserved than many other essential regions of TRPV1. The overall distribution of positively charged residues within the TBS motifs is conserved throughout evolution. In silico analysis reveals that the TBS-1 and TBS-2 of TRPV1 can form helical structures and may play important role in TRPV1 function. Our analysis identifies the regions of TRPV1, which are important for structure-function relationship. This analysis indicates that tubulin binding sequence-1 (TBS-1) near the TRP-box forms a potential helix and the tubulin interactions with TRPV1 via TBS-1 have evolutionary significance. This interaction may be required for the proper channel function and regulation and may also have significance in the context of Taxol®-induced neuropathy.

Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor.

PubMed

Chen, Xin; Xia, Jing; Xia, Zhiqiang; Zhang, Hefang; Zeng, Changying; Lu, Cheng; Zhang, Weixiong; Wang, Wenquan

2015-02-04

MicroRNAs (miRNAs) are small (approximately 21 nucleotide) non-coding RNAs that are key post-transcriptional gene regulators in eukaryotic organisms. More than 100 cassava miRNAs have been identified in a conservation analysis and a repertoire of cassava miRNAs have also been characterised by next-generation sequencing (NGS) in recent studies. Here, using NGS, we profiled small non-coding RNAs and mRNA genes in two cassava cultivars and their wild progenitor to identify and characterise miRNAs that are potentially involved in plant growth and starch biosynthesis. Six small RNA and six mRNA libraries from leaves and roots of the two cultivars, KU50 and Arg7, and their wild progenitor, W14, were subjected to NGS. Analysis of the sequencing data revealed 29 conserved miRNA families and 33 new miRNA families. Together, these miRNAs potentially targeted a total of 360 putative target genes. Whereas 16 miRNA families were highly expressed in cultivar leaves, another 13 miRNA families were highly expressed in storage roots of cultivars. Co-expression analysis revealed that the expression level of some targets had negative relationship with their corresponding miRNAs in storage roots and leaves; these targets included MYB33, ARF10, GRF1, RD19, APL2, NF-YA3 and SPL2, which are known to be involved in plant development, starch biosynthesis and response to environmental stimuli. The identified miRNAs, target mRNAs and target gene ontology annotation all shed light on the possible functions of miRNAs in Manihot species. The differential expression of miRNAs between cultivars and their wild progenitor, together with our analysis of GO annotation and confirmation of miRNA: target pairs, might provide insight into know the differences between wild progenitor and cultivated cassava.

Transcriptome analysis of Spodoptera frugiperda Sf9 cells reveals putative apoptosis-related genes and a preliminary apoptosis mechanism induced by azadirachtin.

PubMed

Shu, Benshui; Zhang, Jingjing; Sethuraman, Veeran; Cui, Gaofeng; Yi, Xin; Zhong, Guohua

2017-10-16

As an important botanical pesticide, azadirachtin demonstrates broad insecticidal activity against many agricultural pests. The results of a previous study indicated the toxicity and apoptosis induction of azadirachtin in Spodoptera frugiperda Sf9 cells. However, the lack of genomic data has hindered a deeper investigation of apoptosis in Sf9 cells at a molecular level. In the present study, the complete transcriptome data for Sf9 cell line was accomplished using Illumina sequencing technology, and 97 putative apoptosis-related genes were identified through BLAST and KEGG orthologue annotations. Fragments of potential candidate apoptosis-related genes were cloned, and the mRNA expression patterns of ten identified genes regulated by azadirachtin were examined using qRT-PCR. Furthermore, Western blot analysis showed that six putative apoptosis-related proteins were upregulated after being treated with azadirachtin while the protein Bcl-2 were downregulated. These data suggested that both intrinsic and extrinsic apoptotic signal pathways comprising the identified potential apoptosis-related genes were potentially active in S. frugiperda. In addition, the preliminary results revealed that caspase-dependent or caspase-independent apoptotic pathways could function in azadirachtin-induced apoptosis in Sf9 cells.

Analysis of Gastric Adenocarcinoma Data in a Pan-GI Context to Reveal Genes, Pathways, and Interactions that Yield Novel Therapeutic Advantages

DTIC Science & Technology

2017-09-01

that Yield Novel Therapeutic Advantages PRINCIPAL INVESTIGATOR: Rehan Akbani CONTRACTING ORGANIZATION: University of Texas MD Anderson Cancer ...mdanderson.org, jajani@mdanderson.org 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) The University of Texas MD Anderson Cancer Center...is the study of gastric cancer , where the purpose is to reveal new insights into the biology of the disease that could potentially have therapeutic

The Sea Urchin Arbacia lixula: A Novel Natural Source of Astaxanthin

PubMed Central

Cirino, Paola; Brunet, Christophe; Ciaravolo, Martina; Galasso, Christian; Musco, Luigi; Vega Fernández, Tomás; Sansone, Clementina; Toscano, Alfonso

2017-01-01

Several echinoderms, including sea urchins, are valuable sources of bioactive compounds but their nutraceutical potential is largely unexplored. In fact, the gonads of some sea urchin species contain antioxidants including carotenoids and polyhydroxylated naphthoquinones (PHNQ’s), such as echinochrome A. Astaxanthin is known to have particular bioactivity for the prevention of neurodegenerative diseases. This carotenoid is produced by microalgae, while several marine invertebrates can bioaccumulate or synthetize it from metabolic precursors. We determined the carotenoid content and analyzed the bioactivity potential of non-harvested Atlantic-Mediterranean sea urchin Arbacia lixula. The comparison of methanol crude extracts obtained from eggs of farmed and wild specimens revealed a higher bioactivity in farmed individuals fed with a customized fodder. HPLC-analysis revealed a high concentration of astaxanthin (27.0 μg/mg), which was the only pigment observed. This study highlights the potential of farmed A. lixula as a new source of the active stereoisomer of astaxanthin. PMID:28635649

Exome Sequencing Identifies Potentially Druggable Mutations in Nasopharyngeal Carcinoma.

PubMed

Chow, Yock Ping; Tan, Lu Ping; Chai, San Jiun; Abdul Aziz, Norazlin; Choo, Siew Woh; Lim, Paul Vey Hong; Pathmanathan, Rajadurai; Mohd Kornain, Noor Kaslina; Lum, Chee Lun; Pua, Kin Choo; Yap, Yoke Yeow; Tan, Tee Yong; Teo, Soo Hwang; Khoo, Alan Soo-Beng; Patel, Vyomesh

2017-03-03

In this study, we first performed whole exome sequencing of DNA from 10 untreated and clinically annotated fresh frozen nasopharyngeal carcinoma (NPC) biopsies and matched bloods to identify somatically mutated genes that may be amenable to targeted therapeutic strategies. We identified a total of 323 mutations which were either non-synonymous (n = 238) or synonymous (n = 85). Furthermore, our analysis revealed genes in key cancer pathways (DNA repair, cell cycle regulation, apoptosis, immune response, lipid signaling) were mutated, of which those in the lipid-signaling pathway were the most enriched. We next extended our analysis on a prioritized sub-set of 37 mutated genes plus top 5 mutated cancer genes listed in COSMIC using a custom designed HaloPlex target enrichment panel with an additional 88 NPC samples. Our analysis identified 160 additional non-synonymous mutations in 37/42 genes in 66/88 samples. Of these, 99/160 mutations within potentially druggable pathways were further selected for validation. Sanger sequencing revealed that 77/99 variants were true positives, giving an accuracy of 78%. Taken together, our study indicated that ~72% (n = 71/98) of NPC samples harbored mutations in one of the four cancer pathways (EGFR-PI3K-Akt-mTOR, NOTCH, NF-κB, DNA repair) which may be potentially useful as predictive biomarkers of response to matched targeted therapies.

Exome Sequencing Identifies Potentially Druggable Mutations in Nasopharyngeal Carcinoma

PubMed Central

Chow, Yock Ping; Tan, Lu Ping; Chai, San Jiun; Abdul Aziz, Norazlin; Choo, Siew Woh; Lim, Paul Vey Hong; Pathmanathan, Rajadurai; Mohd Kornain, Noor Kaslina; Lum, Chee Lun; Pua, Kin Choo; Yap, Yoke Yeow; Tan, Tee Yong; Teo, Soo Hwang; Khoo, Alan Soo-Beng; Patel, Vyomesh

2017-01-01

In this study, we first performed whole exome sequencing of DNA from 10 untreated and clinically annotated fresh frozen nasopharyngeal carcinoma (NPC) biopsies and matched bloods to identify somatically mutated genes that may be amenable to targeted therapeutic strategies. We identified a total of 323 mutations which were either non-synonymous (n = 238) or synonymous (n = 85). Furthermore, our analysis revealed genes in key cancer pathways (DNA repair, cell cycle regulation, apoptosis, immune response, lipid signaling) were mutated, of which those in the lipid-signaling pathway were the most enriched. We next extended our analysis on a prioritized sub-set of 37 mutated genes plus top 5 mutated cancer genes listed in COSMIC using a custom designed HaloPlex target enrichment panel with an additional 88 NPC samples. Our analysis identified 160 additional non-synonymous mutations in 37/42 genes in 66/88 samples. Of these, 99/160 mutations within potentially druggable pathways were further selected for validation. Sanger sequencing revealed that 77/99 variants were true positives, giving an accuracy of 78%. Taken together, our study indicated that ~72% (n = 71/98) of NPC samples harbored mutations in one of the four cancer pathways (EGFR-PI3K-Akt-mTOR, NOTCH, NF-κB, DNA repair) which may be potentially useful as predictive biomarkers of response to matched targeted therapies. PMID:28256603

Phytoremediation potential of Arabidopsis with reference to acrylamide and microarray analysis of acrylamide-response genes.

PubMed

Gao, Jian-Jie; Peng, Ri-He; Zhu, Bo; Wang, Bo; Wang, Li-Juan; Xu, Jing; Sun, Miao; Yao, Quan-Hong

2015-10-01

Acrylamide (ACR) is a widely used industrial chemical. However, it is a dangerous compound because it showed neurotoxic effects in humans and act as reproductive toxicant and carcinogen in many animal species. In the environment, acrylamide has high soil mobility and may travel via groundwater. Phytoremediation is an effective method to remove the environmental pollutants, but the mechanism of plant response to acrylamide remains unknown. With the purpose of assessing remediation potentials of plants for acrylamide, we have examined acrylamide uptake by the model plant Arabidopsis grown on contaminated substrates with high performance liquid chromatography (HPLC) analysis. The result revealed that acrylamide could be absorbed and degraded by Arabidopsis. Further microarray analysis showed that 527 transcripts were up-regulated within 2-days under acrylamide exposure condition. We have found many potential acrylamide-induced genes playing a major role in plant metabolism and phytoremediation. Copyright © 2015 Elsevier Inc. All rights reserved.

The zoonotic potential of Clostridium difficile from small companion animals and their owners.

PubMed

Rabold, Denise; Espelage, Werner; Abu Sin, Muna; Eckmanns, Tim; Schneeberg, Alexander; Neubauer, Heinrich; Möbius, Nadine; Hille, Katja; Wieler, Lothar H; Seyboldt, Christian; Lübke-Becker, Antina

2018-01-01

Clostridium difficile infections (CDI) in humans range from asymptomatic carriage to life-threatening intestinal disease. Findings on C. difficile in various animal species and an overlap in ribotypes (RTs) suggest potential zoonotic transmission. However, the impact of animals for human CDI remains unclear. In a large-scale survey we collected 1,447 fecal samples to determine the occurrence of C. difficile in small companion animals (dogs and cats) and their owners and to assess potential epidemiological links within the community. The Germany-wide survey was conducted from July 2012-August 2013. PCR ribotyping, Multilocus VNTR Analysis (MLVA) and PCR detection of toxin genes were used to characterize isolated C. difficile strains. A database was defined and logistic regression used to identify putative factors associated with fecal shedding of C. difficile. In total, 1,418 samples met the inclusion criteria. The isolation rates for small companion animals and their owners within the community were similarly low with 3.0% (25/840) and 2.9% (17/578), respectively. PCR ribotyping revealed eight and twelve different RTs in animals and humans, respectively, whereas three RTs were isolated in both, humans and animals. RT 014/0, a well-known human hospital-associated lineage, was predominantly detected in animal samples. Moreover, the potentially highly pathogenic RTs 027 and 078 were isolated from dogs. Even though, C. difficile did not occur simultaneously in animals and humans sharing the same household. The results of the epidemiological analysis of factors associated with fecal shedding of C. difficile support the hypothesis of a zoonotic potential. Molecular characterization and epidemiological analysis revealed that the zoonotic risk for C. difficile associated with dogs and cats within the community is low but cannot be excluded.

Evaluating the Energy Recovery Potential of Nigerian Coals under Non-Isothermal Thermogravimetry

NASA Astrophysics Data System (ADS)

Bevan Nyakuma, Bemgba; Oladokun, Olagoke; Jauro, Aliyu; Damian Nyakuma, Denen

2017-07-01

This study investigated the fuel properties and energy recovery potential of two coal samples from Ihioma (IHM) and Ogboligbo (OGB) environs in Nigeria. The ultimate, proximate, and bomb calorimetric analyses of the coal were examined. Next, the rank classification and potential application of the coals were evaluated according to the ASTM standard D388. Lastly, thermal decomposition behaviour was examined by non-isothermal thermogravimetry (TG) under pyrolysis conditions from 30 - 900 °C. The results indicated IHM and OGB contain high proportions of combustible elements for potential thermal conversion. The higher heating value (HHV) of IHM was 20.37 MJ/kg whereas OGB was 16.33 MJ/kg. TG analysis revealed 55% weight loss for OGB and 76% for IHM. The residual mass was 23% for IHM and 44% for OGB. Based on the temperature profile characteristics (TPCs); Ton , Tmax , and Toff , IHM was more reactive than OGB due to its higher volatile matter (VM). Overall, results revealed the coals are Lignite (Brown) low-rank coals (LRCs) with potential for electric power generation.

Single-Pixel Optical Fluctuation Analysis of Calcium Channel Function in Active Zones of Motor Nerve Terminals

PubMed Central

Luo, Fujun; Dittrich, Markus; Stiles, Joel R.; Meriney, Stephen D.

2011-01-01

We used high-resolution fluorescence imaging and single-pixel optical fluctuation analysis to estimate the opening probability of individual voltage-gated calcium (Ca2+) channels during an action potential and the number of such Ca2+ channels within active zones of frog neuromuscular junctions. Analysis revealed ~36 Ca2+ channels within each active zone, similar to the number of docked synaptic vesicles but far less than the total number of transmembrane particles reported based on freeze-fracture analysis (~200–250). The probability that each channel opened during an action potential was only ~0.2. These results suggest why each active zone averages only one quantal release event during every other action potential, despite a substantial number of docked vesicles. With sparse Ca2+ channels and low opening probability, triggering of fusion for each vesicle is primarily controlled by Ca2+ influx through individual Ca2+ channels. In contrast, the entire synapse is highly reliable because it contains hundreds of active zones. PMID:21813687

Laser-induced breakdown spectroscopy (LIBS) for rapid analysis of ash, potassium and magnesium in gluten free flours.

PubMed

Markiewicz-Keszycka, Maria; Casado-Gavalda, Maria P; Cama-Moncunill, Xavier; Cama-Moncunill, Raquel; Dixit, Yash; Cullen, Patrick J; Sullivan, Carl

2018-04-01

Gluten free (GF) diets are prone to mineral deficiency, thus effective monitoring of the elemental composition of GF products is important to ensure a balanced micronutrient diet. The objective of this study was to test the potential of laser-induced breakdown spectroscopy (LIBS) analysis combined with chemometrics for at-line monitoring of ash, potassium and magnesium content of GF flours: tapioca, potato, maize, buckwheat, brown rice and a GF flour mixture. Concentrations of ash, potassium and magnesium were determined with reference methods and LIBS. PCA analysis was performed and presented the potential for discrimination of the six GF flours. For the quantification analysis PLSR models were developed; R 2 cal were 0.99 for magnesium and potassium and 0.97 for ash. The study revealed that LIBS combined with chemometrics is a convenient method to quantify concentrations of ash, potassium and magnesium and present the potential to classify different types of flours. Copyright © 2017 Elsevier Ltd. All rights reserved.

Learning Potentials and Limitations under Globalisation in Aged Care Workplaces.

ERIC Educational Resources Information Center

Somerville, Margaret

2002-01-01

Analysis of research on the Australian elder care industry used the categories of gender equity, gender differences, and gender deconstruction. Findings revealed the gender segregation of the industry, devaluing of women's work, and persistence of body/mind, male/female dualism. (Contains 16 references.) (SK)

Acute Hepatopancreatic Necrosis Disease (AHPND) related microRNAs in Litopenaeus vannamei infected with AHPND-causing strain of Vibrio parahemolyticus.

PubMed

Zheng, Zhihong; Aweya, Jude Juventus; Wang, Fan; Yao, Defu; Lun, Jingsheng; Li, Shengkang; Ma, Hongyu; Zhang, Yueling

2018-05-08

Acute hepatopancreatic necrosis disease (AHPND) has emerged as a major debilitating disease that causes massive shrimp death resulting in substantial economic losses in shrimp aquaculture. Given that several diseases and infections have been associated with microRNAs (miRNAs), we conducted a comparative transcriptomic analysis using the AHPND (VA) and non-AHPND (VN) strains of Vibrio parahemolyticus to identify miRNAs potentially involved in AHPND pathogenesis in Litopenaeus vannamei. A total of 83 miRNAs (47 upregulated and 36 downregulated) were significantly differentially expressed between the VA and VN challenged groups, while 222 target genes of these miRNAs were predicted. Functional enrichment analysis revealed that the miRNAs target genes were involved in multiple biological processes including metabolic pathways, amoebiasis, Vibrio cholerae infection etc. Finally, interaction network and qPCR (Real-time Quantitative PCR) analysis of 12 potential key AHPND-related miRNAs and their predicted target genes, revealed their possible involvement in modulating several immune-related processes in the pathogenesis of AHPND. We have shown using comparative transcriptomic analysis, miRNAs and their target genes that are responsive to AHPND V. parahemolyticus infection in shrimp, therefore suggesting their possible role in defense response to AHPND V. parahemolyticus infection.

A Detailed Analysis of Visible Defects Formed in Commercial Silicon Thin-Film Modules During Outdoor Exposure

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

Gerber, Andreas; Johnston, Steve; Olivera-Pimentel, Guillermo

We analyzed defects in silicon thin-film tandem (a-Si:H/..mu..c-Si:H) modules from an outdoor installation in India. The inspection of several affected modules reveals that most of the defects -- which optically appear as bright spots -- were formed primarily nearby the separation and series connection laser lines. Cross-sectional SEM analysis reveals that the bright spots emerge due to electrical isolation, caused by a delamination of the cell from the front TCO in the affected area. In addition, the morphology of the a-Si:H top cell differs in the delaminated area compared to the surrounding unaffected area. We propose that these effects aremore » potentially caused by an explosive and thermally triggered liberation of hydrogen from the a-Si:H layer. Electrical and thermal measurements reveal that these defects can impact the cell performance significantly.« less

CHILDHOOD DEPRESSION. Exploring the association between family violence and other psychosocial factors in low-income Brazilian schoolchildren

PubMed Central

2012-01-01

Background Childhood depression affects the morbidity, mortality and life functions of children. Individual, family and environmental factors have been documented as psychosocial risk factors for childhood depression, especially family violence, which results in inadequate support, low family cohesion and poor communication. This study investigates the association between psychosocial depression factors in low-income schoolchildren and reveals the potential trouble spots, highlighting several forms of violence that take place within the family context. Methods The study was based on a cross-sectional analysis of 464 schoolchildren aged between 6 and 10, selected by random sampling from a city in the state of Rio de Janeiro, Brazil. Socio-economic, family and individual variables were investigated on the strength of the caregivers’ information and organized in blocks for analysis. A binary logistic regression model was applied, according to hierarchical blocks. Results The final hierarchical regression analysis showed that the following variables are potential psychosocial factors associated with depression in childhood: average/poor relationship with the father (OR 3.24, 95% CI 1.32-7.94), high frequency of victimization by psychological violence (humiliation) (OR 6.13, 95% CI 2.06-18.31), parental divorce (OR 2.89, 95% CI 1.14-7.32) and externalizing behavior problems (OR 3.53 IC 1.51-8.23). Conclusions The results point to multiple determinants of depressive behavior in children, as well as the potential contribution of psychological family violence. The study also reveals potential key targets for early intervention, especially for children from highly vulnerable families. PMID:22776354

Genome-Wide Analysis of Mycoplasma bovirhinis GS01 Reveals Potential Virulence Factors and Phylogenetic Relationships.

PubMed

Chen, Shengli; Hao, Huafang; Zhao, Ping; Liu, Yongsheng; Chu, Yuefeng

2018-05-04

Mycoplasma bovirhinis is a significant etiology in bovine pneumonia and mastitis, but our knowledge about the genetic and pathogenic mechanisms of M. bovirhinis is very limited. In this study, we sequenced the complete genome of M. bovirhinis strain GS01 isolated from the nasal swab of pneumonic calves in Gansu, China, and we found that its genome forms a 847,985 bp single circular chromosome with a GC content of 27.57% and with 707 protein-coding genes. The putative virulence determinants of M. bovirhinis were then analyzed. Results showed that three genomic islands and 16 putative virulence genes, including one adhesion gene enolase, seven surface lipoproteins, proteins involved in glycerol metabolism, and cation transporters, might be potential virulence factors. Glycerol and pyruvate metabolic pathways were defective. Comparative analysis revealed remarkable genome variations between GS01 and a recently reported HAZ141_2 strain, and extremely low homology with others mycoplasma species. Phylogenetic analysis demonstrated that M. bovirhinis was most genetically close to M. canis , distant from other bovine Mycoplasma species. Genomic dissection may provide useful information on the pathogenic mechanisms and genetics of M. bovirhinis . Copyright © 2018 Chen et al.

Alkaline active cyanide dihydratase of Flavobacterium indicum MTCC 6936: Growth optimization, purification, characterization and in silico analysis.

PubMed

Kumar, Virender; Kumar, Vijay; Bhalla, Tek Chand

2018-05-15

The present work explores a rare cyanide dihydratase of Flavobacterium indicum MTCC 6936 for its potential of cyanide degradation. The enzyme is purified to 12 fold with a yield of 76%. SDS and native-PAGE analysis revealed that enzyme was monomer of 40 kDa size. The enzyme works well in mesophilic range at wide array of pH. The thermostability profile of cyanide dihydratase revealed that the enzyme is quite stable at 30 °C and 35 °C with half-life of 6 h 30 min and 5 h respectively. K m and V max for cyanide dihydratase of F. indicum was measured to be 4.76 mM and 45 U mg -1 with k cat calculated to be 27.3 s -1 and specificity constant (k cat /K m ) to be around 5.67 mM -1  s -1 . MALDI-TOF analysis of purified protein revealed that the amino acid sequence has 50% and 43% sequence identity with putative amino acid sequence of F. indicum and earlier reported cyanide dihydratase of Bacillus pumilus respectively. Homology modeling studies of cyanide dihydratase of F. indicum predicted the catalytic triad of the enzyme indicating Cys at 164, Glu at 46 and Lys at 130th position. The purified enzyme has potential applications in bioremediation and analytical sector. Copyright © 2018 Elsevier B.V. All rights reserved.

Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs.

PubMed

Verardo, Lucas L; Sevón-Aimonen, Marja-Liisa; Serenius, Timo; Hietakangas, Ville; Uimari, Pekka

2017-02-13

One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. In this study, we used whole-genome SNP genotypes of over 700 AI boars; after a quality check, 42,385 SNPs remained for association analysis. All the boars were purebred Finnish Yorkshire. To account for relatedness of the animals, a pedigree-based relationship matrix was used in a mixed linear model to test the effect of SNPs on pH measured from loin. A bioinformatics analysis was performed to identify the most promising genes in the significant regions related to meat quality. Genome-wide association study (GWAS) revealed three significant chromosomal regions: one on chromosome 3 (39.9 Mb-40.1 Mb) and two on chromosome 15 (58.5 Mb-60.5 Mb and 132 Mb-135 Mb including PRKAG3). A conditional analysis with a significant SNP in the PRKAG3 region, MARC0083357, as a covariate in the model retained the significant SNPs on chromosome 3. Even though linkage disequilibrium was relatively high over a long distance between MARC0083357 and other significant SNPs on chromosome 15, some SNPs retained their significance in the conditional analysis, even in the vicinity of PRKAG3. The significant regions harbored several genes, including two genes involved in cyclic AMP (cAMP) signaling: ADCY9 and CREBBP. Based on functional and transcription factor-gene networks, the most promising candidate genes for meat pH are ADCY9, CREBBP, TRAP1, NRG1, PRKAG3, VIL1, TNS1, and IGFBP5, and the key transcription factors related to these genes are HNF4A, PPARG, and Nkx2-5. Based on SNP association, pathway, and transcription factor analysis, we were able to identify several genes with potential to control muscle cell homeostasis and meat quality. The associated SNPs can be used in selection for better pork. We also showed that post-GWAS analysis reveals important information about the genes' potential role on meat quality. The gained information can be used in later functional studies.

Study of 11Li+p elastic scattering using BHF formalism with three body force

NASA Astrophysics Data System (ADS)

Sharma, Manjari; Haider, W.

2018-04-01

In the present work we have analyzed the elastic scattering data of 11Li + p at 62, 68.4 and 75 MeV/nucleon, using the microscopic optical potential calculated within the framework of Brueckner-Hartree-Fock formalism (BHF). The calculation uses Argonne v18 and Urbana v14 inter-nucleon potentials and the Urbana IX (UVIX) model of three body force. The required nucleon-density distributions for 11Li are obtained using the semi-phenomenological model for nuclear density distributions. The optical potential has been obtained by folding the g-matrices as calculated in BHF (with and without three body forces) over the nucleon density distributions. We have used the exact method for calculating both the direct and the exchange parts of the spin-orbit potential. Our results reveal that the spin-orbit potential significantly contributes to 11Li+p elastic scattering at all three incident energies. Further, the calculated spin-orbit potential in BHF is much smaller and more diffused as compared with the phenomenological spin-orbit potential. The analysis reveals that the calculated microscopic optical potentials, with and without three body force using BHF approach with phenomenological form of density distribution, provides satisfactory agreement with the elastic scattering data for 11Li+p.

Deppdb--DNA electrostatic potential properties database: electrostatic properties of genome DNA.

PubMed

Osypov, Alexander A; Krutinin, Gleb G; Kamzolova, Svetlana G

2010-06-01

The electrostatic properties of genome DNA influence its interactions with different proteins, in particular, the regulation of transcription by RNA-polymerases. DEPPDB--DNA Electrostatic Potential Properties Database--was developed to hold and provide all available information on the electrostatic properties of genome DNA combined with its sequence and annotation of biological and structural properties of genome elements and whole genomes. Genomes in DEPPDB are organized on a taxonomical basis. Currently, the database contains all the completely sequenced bacterial and viral genomes according to NCBI RefSeq. General properties of the genome DNA electrostatic potential profile and principles of its formation are revealed. This potential correlates with the GC content but does not correspond to it exactly and strongly depends on both the sequence arrangement and its context (flanking regions). Analysis of the promoter regions for bacterial and viral RNA polymerases revealed a correspondence between the scale of these proteins' physical properties and electrostatic profile patterns. We also discovered a direct correlation between the potential value and the binding frequency of RNA polymerase to DNA, supporting the idea of the role of electrostatics in these interactions. This matches a pronounced tendency of the promoter regions to possess higher values of the electrostatic potential.

The Potential for Development of Russian Youth Social Activity

ERIC Educational Resources Information Center

Savotina, Nataliya

2016-01-01

The article deals with scientific and applied topicality of studying the problem of children and youth social activity. Spheres of social activity display in European tradition, in particular, the European Charter, Great Britain, have been revealed. Comparative analysis of understanding the essence of such a phenomenon in Western theories and…

Coping with Relationship Stressors: A Decade Review

ERIC Educational Resources Information Center

Seiffge-Krenke, Inge

2011-01-01

This review identifies key issues in research on adolescent coping with stress with parents, friends, and romantic partners during the past decade. An analysis of 78 studies revealed findings on relationship stressors and the potential links between the use of different coping styles for different relationship types. Research has confirmed…

Economically Disadvantaged Children's Transitions into Elementary School: Linking Family Processes, School Contexts, and Educational Policy

ERIC Educational Resources Information Center

Crosnoe, Robert; Cooper, Carey E.

2010-01-01

Working from a core perspective on the developmental implications of economic disadvantage, this study attempted to identify "family-based" mechanisms of economic effects on early learning and their potential "school-based" remedies. Multilevel analysis of the Early Childhood Longitudinal Study-Kindergarten Cohort revealed that…

A Marketing Strategy for Spanish for Business.

ERIC Educational Resources Information Center

Grosse, Christine Uber

The development of a marketing strategy for business Spanish courses by means of situational analysis is described. The planner of marketing strategy must consider demand for a course, institutional acceptance, and financial support. A survey of 508 universities revealed a low level of demand for business Spanish which could potentially be…

Leading Professional Learning to Develop Professional Capital: The Saskatchewan Professional Development Unit's Facilitator Community

ERIC Educational Resources Information Center

Osmond-Johnson, Pamela

2017-01-01

Drawing on data from a mixed methods study of the Saskatchewan Professional Development Unit's (SPDU) Facilitator Community, this paper highlights the potential of teacher-led professional learning in developing professional capital through engagement in teacher leadership. Analysis of survey, interview, and observational data revealed the…

Two Medical Literatures That Are Logically But Not Bibliographically Connected.

ERIC Educational Resources Information Center

Swanson, Don R.

1987-01-01

Describes a study which demonstrates that unintended logical connections within scientific literature, which potentially reveal new knowledge, are unmarked by reference citations or other bibliographic clues. Citation analysis of two separate literatures in biomedicine that have a logical link is used to support this hypothesis. (Author/CLB)

Rural Economic Development: What Makes Rural Communities Grow?

ERIC Educational Resources Information Center

Aldrich, Lorna; Kusmin, Lorin

This report identifies local factors that foster rural economic growth. A review of the literature revealed potential indicators of county economic growth, and those indicators were then tested against data for nonmetro counties during the 1980s using multiple regression analysis. The principal variables examined included demographic and labor…

Silvicultural cutting opportunities in oak-hickory forests of West Virginia

Treesearch

S. L. Arner; D.A. Gansner; M.E. Dale; H.C. Smith

1991-01-01

Analysis of cutting opportunities of oak-hickory forests of West Virginia reveals a storehouse of economic opportunity. The potential cut from silviculturally sound thinning, regeneration, and harvest opportunities totals 100 million cords, or 60 times the current annual harvest of growing stock volume from the state.

Thai Students' Choices of Vocational Education: Marketing Factors and Reference Groups

ERIC Educational Resources Information Center

Pimpa, Nattavud; Suwannapirom, Suda

2008-01-01

This study aims to identify factors influencing Thai students' choices of vocational education. By using factor analysis, it reveals five key influencing factors: personal attitude, curriculum, potential employment, attractiveness of campus, and tuition fees. Furthermore, this study also indicates that teachers from secondary school, and parents…

The Limits of Empowerment in Anti-Nuclear Advocacy: A Case Study of Adult Education for Technological Literacy.

ERIC Educational Resources Information Center

Regnier, Robert; Penna, Phillip

1996-01-01

Using a theory of technological literacy, analysis of a project to oppose uranium mining in Saskatchewan revealed how the potential for empowerment is often overstated. Informing citizens to participate in critical discourse does not always lead to decisions reflecting their interests. (SK)

Italian Neo-Ethnicity: The Search for Self-Identity.

ERIC Educational Resources Information Center

Aversa, Alfred, Jr.

1978-01-01

After a review of how Blacks went about constructing a new self-identity, an analysis of the Italian-American case reveals three motifs to be introduced as a potential frame of reference for identity building: the grandeur of Renaissance Italy; pastoralism; and the immigrant experience (family and work). (Author/EB)

Molecular characterization and pathogenicity of fungal isolates for use against the small hive beetle (Aethina tumida)

USDA-ARS?s Scientific Manuscript database

The analysis of DNA sequences from fungal pathogens obtained from cadavers of the small hive beetle (SHB) collected from several apiaries in Florida revealed a mixture of saprobes and two potential primary entomopathogens, Metarhizium anisopliae and Beauveria bassiana. Spray tower bioassays indicate...

An Analysis of the Performance-Based Service Acquisition (PBSA) and Its Applicability to Hellenic Navy Service Acquisition Activities

DTIC Science & Technology

2012-12-01

potential offeror in response to its request must not be disclosed if doing so would reveal the potential offeror’s confidential business strategy...also the Navy Academy and the Navy hospital have and operate kitchen facilities. Ships have their own kitchen facilities too and dedicated personnel...abandoned. Now the HN dedicates personnel, has kitchen facilities to provide the food services and doing the whole process. The HN could outsource

Molecular Heterogeneity in Glioblastoma: Potential Clinical Implications

PubMed Central

Parker, Nicole Renee; Khong, Peter; Parkinson, Jonathon Fergus; Howell, Viive Maarika; Wheeler, Helen Ruth

2015-01-01

Glioblastomas, (grade 4 astrocytomas), are aggressive primary brain tumors characterized by histopathological heterogeneity. High-resolution sequencing technologies have shown that these tumors also feature significant inter-tumoral molecular heterogeneity. Molecular subtyping of these tumors has revealed several predictive and prognostic biomarkers. However, intra-tumoral heterogeneity may undermine the use of single biopsy analysis for determining tumor genotype and has implications for potential targeted therapies. The clinical relevance and theories of tumoral molecular heterogeneity in glioblastoma are discussed. PMID:25785247

Aligning HIV/AIDS communication with the oral tradition of Africans: a theory-based content analysis of songs' potential in prevention efforts.

PubMed

Bekalu, Mesfin Awoke; Eggermont, Steven

2015-01-01

Despite a growing recognition of songs as a useful HIV/AIDS campaign strategy, little research has investigated their potential and/or actual impact. In this study, through a theory-based content analysis, we have assessed the prevention domains covered and the health-relevant constructs promoted by 23 AIDS songs widely used to aid prevention efforts in Ethiopia. To identify the health-relevant constructs and reveal their potential to facilitate or inhibit positive changes, the Extended Parallel Process Model (EPPM) has been used. The findings revealed that the songs cover most of the prevention domains that constitute the current agenda of behavior change communication in Sub-Saharan Africa. However, although all the EPPM variables have been found in almost every song, there were significantly more efficacy messages than threat messages. This suggests that although the songs may lead to positive changes in HIV/AIDS-related outcomes among audiences who have already perceived the threat posed by HIV/AIDS, they are less likely to motivate and thereby generate responses from audiences who have less or no threat perceptions. It is argued that given their potential as a culturally appropriate strategy in Sub-Saharan Africa where oral channels of communication play significant roles, songs could be harnessed for better outcomes through a theory-based design.

Genetic variability of VEGF pathway genes in six randomized phase III trials assessing the addition of bevacizumab to standard therapy.

PubMed

de Haas, Sanne; Delmar, Paul; Bansal, Aruna T; Moisse, Matthieu; Miles, David W; Leighl, Natasha; Escudier, Bernard; Van Cutsem, Eric; Carmeliet, Peter; Scherer, Stefan J; Pallaud, Celine; Lambrechts, Diether

2014-10-01

Despite extensive translational research, no validated biomarkers predictive of bevacizumab treatment outcome have been identified. We performed a meta-analysis of individual patient data from six randomized phase III trials in colorectal, pancreatic, lung, renal, breast, and gastric cancer to explore the potential relationships between 195 common genetic variants in the vascular endothelial growth factor (VEGF) pathway and bevacizumab treatment outcome. The analysis included 1,402 patients (716 bevacizumab-treated and 686 placebo-treated). Twenty variants were associated (P < 0.05) with progression-free survival (PFS) in bevacizumab-treated patients. Of these, 4 variants in EPAS1 survived correction for multiple testing (q < 0.05). Genotype-by-treatment interaction tests revealed that, across these 20 variants, 3 variants in VEGF-C (rs12510099), EPAS1 (rs4953344), and IL8RA (rs2234671) were potentially predictive (P < 0.05), but not resistant to multiple testing (q > 0.05). A weak genotype-by-treatment interaction effect was also observed for rs699946 in VEGF-A, whereas Bayesian genewise analysis revealed that genetic variability in VHL was associated with PFS in the bevacizumab arm (q < 0.05). Variants in VEGF-A, EPAS1, and VHL were located in expression quantitative loci derived from lymphoblastoid cell lines, indicating that they affect the expression levels of their respective gene. This large genetic analysis suggests that variants in VEGF-A, EPAS1, IL8RA, VHL, and VEGF-C have potential value in predicting bevacizumab treatment outcome across tumor types. Although these associations did not survive correction for multiple testing in a genotype-by-interaction analysis, they are among the strongest predictive effects reported to date for genetic variants and bevacizumab efficacy.

A mean spherical model for soft potentials: The hard core revealed as a perturbation

NASA Technical Reports Server (NTRS)

Rosenfeld, Y.; Ashcroft, N. W.

1978-01-01

The mean spherical approximation for fluids is extended to treat the case of dense systems interacting via soft-potentials. The extension takes the form of a generalized statement concerning the behavior of the direct correlation function c(r) and radial distribution g(r). From a detailed analysis that views the hard core portion of a potential as a perturbation on the whole, a specific model is proposed which possesses analytic solutions for both Coulomb and Yukawa potentials, in addition to certain other remarkable properties. A variational principle for the model leads to a relatively simple method for obtaining numerical solutions.

Quasi-targeted analysis of hydroxylation-related metabolites of polycyclic aromatic hydrocarbons in human urine by liquid chromatography-mass spectrometry.

PubMed

Tang, Caiming; Tan, Jianhua; Fan, Ruifang; Zhao, Bo; Tang, Caixing; Ou, Weihui; Jin, Jiabin; Peng, Xianzhi

2016-08-26

Metabolite identification is crucial for revealing metabolic pathways and comprehensive potential toxicities of polycyclic aromatic hydrocarbons (PAHs) in human body. In this work, a quasi-targeted analysis strategy was proposed for metabolite identification of monohydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) in human urine using liquid chromatography triple quadruple mass spectrometry (LC-QqQ-MS/MS) combined with liquid chromatography high resolution mass spectrometry (LC-HRMS). Potential metabolites of OH-PAHs were preliminarily screened out by LC-QqQ-MS/MS in association with filtering in a self-constructed information list of possible metabolites, followed by further identification and confirmation with LC-HRMS. The developed method can provide more reliable and systematic results compared with traditional untargeted analysis using LC-HRMS. In addition, data processing for LC-HRMS analysis were greatly simplified. This quasi-targeted analysis method was successfully applied to identifying phase I and phase II metabolites of OH-PAHs in human urine. Five metabolites of hydroxynaphthalene, seven of hydroxyfluorene, four of hydroxyphenanthrene, and three of hydroxypyrene were tentatively identified. Metabolic pathways of PAHs in human body were putatively revealed based on the identified metabolites. The experimental results will be valuable for investigating the metabolic processes of PAHs in human body, and the quasi-targeted analysis strategy can be expanded to the metabolite identification and profiling of other compounds in vivo. Copyright © 2016 Elsevier B.V. All rights reserved.

Proteomics Analysis of Tissue Samples Reveals Changes in Mitochondrial Protein Levels in Parathyroid Hyperplasia over Adenoma

PubMed Central

AKPINAR, GURLER; KASAP, MURAT; CANTURK, NUH ZAFER; ZULFIGAROVA, MEHIN; ISLEK, EYLÜL ECE; GULER, SERTAC ATA; SIMSEK, TURGAY; CANTURK, ZEYNEP

2017-01-01

Background/Aim: To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. Materials and Methods: Protein extracts were prepared from tissue samples (n=8 per group). Protein pools were created for each group and subjected to DIGE and conventional 2DE. Following image analysis, spots representing the differentially regulated proteins were excised from the and used for identification via MALDI-TOF/TOF analysis. Results: The identities of 40 differentially-expressed proteins were revealed. Fourteen of these proteins were over-expressed in the hyperplasia while 26 of them were over-expressed in the adenoma. Conclusion: Most proteins found to be over-expressed in the hyperplasia samples were mitochondrial, underlying the importance of the mitochondrial activity as a potential biomarker for differentiation of parathyroid hyperplasia from adenoma. PMID:28446534

Flexible traffic control of the synfire-mode transmission by inhibitory modulation: Nonlinear noise reduction

NASA Astrophysics Data System (ADS)

Shinozaki, Takashi; Okada, Masato; Reyes, Alex D.; Câteau, Hideyuki

2010-01-01

Intermingled neural connections apparent in the brain make us wonder what controls the traffic of propagating activity in the brain to secure signal transmission without harmful crosstalk. Here, we reveal that inhibitory input but not excitatory input works as a particularly useful traffic controller because it controls the degree of synchrony of population firing of neurons as well as controlling the size of the population firing bidirectionally. Our dynamical system analysis reveals that the synchrony enhancement depends crucially on the nonlinear membrane potential dynamics and a hidden slow dynamical variable. Our electrophysiological study with rodent slice preparations show that the phenomenon happens in real neurons. Furthermore, our analysis with the Fokker-Planck equations demonstrates the phenomenon in a semianalytical manner.

Essay Contest Reveals Misconceptions of High School Students in Genetics Content

PubMed Central

Mills Shaw, Kenna R.; Van Horne, Katie; Zhang, Hubert; Boughman, Joann

2008-01-01

National educational organizations have called upon scientists to become involved in K–12 education reform. From sporadic interaction with students to more sustained partnerships with teachers, the engagement of scientists takes many forms. In this case, scientists from the American Society of Human Genetics (ASHG), the Genetics Society of America (GSA), and the National Society of Genetic Counselors (NSGC) have partnered to organize an essay contest for high school students as part of the activities surrounding National DNA Day. We describe a systematic analysis of 500 of 2443 total essays submitted in response to this contest over 2 years. Our analysis reveals the nature of student misconceptions in genetics, the possible sources of these misconceptions, and potential ways to galvanize genetics education. PMID:18245328

Novel green synthesis of gold nanoparticles using Citrullus lanatus rind and investigation of proteasome inhibitory activity, antibacterial, and antioxidant potential

PubMed Central

Patra, Jayanta Kumar; Baek, Kwang-Hyun

2015-01-01

Biological synthesis of nanoparticles using nontoxic, eco-friendly approaches is gaining importance owing to their fascinating biocompatibility and environmentally benign nature. This study describes the green synthesis approach for synthesis of gold nanoparticles (ANPs) using aqueous extract of the rind of watermelon as a fruit waste and evaluate its biopotential in terms of proteasome inhibitory activity, antibacterial, and antioxidant potential. The synthesized ANPs were characterized using UV–vis spectroscopy, scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. The surface plasmon resonance spectra of ANPs were obtained at 560 nm. Scanning electron microscopy image revealed that particles had a spherical shape and have a size distribution of 20–140 nm, followed by the elemental analysis by energy-dispersive X-ray spectroscopy. X-ray diffraction analysis confirmed the crystallite nature of the ANPs and Fourier-transform infrared spectroscopy revealed the involvement of bioactive compounds from watermelon rind in the synthesis, capping, and stabilization of ANPs. ANPs exhibited potential antibacterial activity against five different foodborne pathogenic bacteria with diameter of inhibition zones ranged between 9.23 and 11.58 mm. They also displayed strong synergistic antibacterial activity together with kanamycin (11.93–21.08 mm inhibition zones) and rifampicin (10.32–24.84 mm inhibition zones). ANPs displayed strong antioxidant activity in terms of DPPH radical scavenging (24.69%), nitric oxide scavenging (25.62%), ABTS scavenging (29.42%), and reducing power. Significantly high proteasome inhibitory potential of the ANPs (28.16%) could be highly useful for cancer treatment and targeted cancer drug delivery. Overall, results highlight a potential low-cost green method of synthesizing ANPs from food waste materials. Significant biopotentials of synthesized ANPs could make it a potential candidate for its application in the biomedical, pharmaceutical, cosmetics, and food sectors. PMID:26664116

Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis

PubMed Central

Khan, Raees; Roy, Nazish; Choi, Kihyuck

2018-01-01

The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed. Further, the excessive use of this biocide in natural environments may selectively enrich for not only TCS-resistant bacterial pathogens, but possibly for additional resistance to multiple antibiotics. PMID:29420585

Bioengineered silver nanoparticles as potent anti-corrosive inhibitor for mild steel in cooling towers.

PubMed

Narenkumar, Jayaraman; Parthipan, Punniyakotti; Madhavan, Jagannathan; Murugan, Kadarkarai; Marpu, Sreekar Babu; Suresh, Anil Kumar; Rajasekar, Aruliah

2018-02-01

Silver nanoparticle-aided enhancement in the anti-corrosion potential and stability of plant extract as ecologically benign alternative for microbially induced corrosion treatment is demonstrated. Bioengineered silver nanoparticles (AgNPs) surface functionalized with plant extract material (proteinacious) was generated in vitro in a test tube by treating ionic AgNO 3 with the leaf extract of Azadirachta indica that acted as dual reducing as well as stabilizing agent. Purity and crystallinity of the AgNPs, along with physical and surface characterizations, were evaluated by performing transmission electron microscopy, Fourier transform infrared spectroscopy, energy dispersive x-ray spectra, single-area electron diffractions, zeta potential, and dynamic light scattering measurements. Anti-corrosion studies against mild steel (MS1010) by corrosion-inducive bacterium, Bacillus thuringiensis EN2 isolated from cooling towers, were evaluated by performing electrochemical impedance spectroscopy (EIS), weight loss analysis, and surface analysis by infrared spectroscopy. Our studies revealed that AgNPs profoundly inhibited the biofilm on MS1010 surface and reduced the corrosion rates with the CR of 0.5 mm/y and an inhibition efficiency of 77% when compared to plant extract alone with a CR of 2.2 mm/y and an inhibition efficiency of 52%. Further surface analysis by infrared spectra revealed that AgNPs formed a protective layer of self-assembled film on the surface of MS1010. Additionally, EIS and surface analysis revealed that the AgNPs have inhibited the bacterial biofilm and reduced the pit on MS1010. This is the first report disclosing the application of bioengineered AgNP formulations as potent anti-corrosive inhibitor upon forming a protective layer over mild steel in cooling water towers. Graphical Abstract ᅟ.

Component analysis and free radicals scavenging activity of Cicer arietinum L. husk pectin.

PubMed

Urias-Orona, Vania; Huerta-Oros, Joselina; Carvajal-Millán, Elizabeth; Lizardi-Mendoza, Jaime; Rascón-Chu, Agustin; Gardea, Alfonso A

2010-10-11

A pectin (CAP) was extracted from the husk of Cicer arietinum L. Monosaccharide analysis of CAP revealed the dominance of galacturonic acid and smaller amounts of galactose, arabinose, rhamnose, glucose, xylose and mannose. Viscosimetric analysis showed that the intrinsic viscosity ([η]) and the molecular weight (MW) of CAP were 296 mL/g and 105 kDa, respectively. The degree of esterification (DE = 10%) was determined by FTIR spectroscopy. CAP exhibited a dose-dependent free radical scavenging activity, as shown by its DPPH radical inhibition. At 1.0 mg/mL CAP exhibited a scavenging rate of 29% on DPPH radicals. The evaluation of antioxidant activity suggested that CAP had good potential for DPPH radical scavenging activity and should be explored as a novel potential antioxidant.

Single-Cell Sequencing Technologies for Cardiac Stem Cell Studies.

PubMed

Liu, Tiantian; Wu, Hongjin; Wu, Shixiu; Wang, Charles

2017-11-01

Today with the rapid advancements in stem cell studies and the promising potential of using stem cells in clinical therapy, there is an increasing demand for in-depth comprehensive analysis on individual cell transcriptome and epigenome, as they play critical roles in a number of cell functions such as cell differentiation, growth, and reprogramming. The development of single-cell sequencing technologies has helped in revealing some exciting new perspectives in stem cells and regenerative medicine research. Among the various potential applications, single-cell analysis for cardiac stem cells (CSCs) holds tremendous promises in understanding the mechanisms of heart development and regeneration, which might light up the path toward cell therapy for cardiovascular diseases. This review briefly highlights the recent progresses in single-cell sequencing analysis technologies and their applications in CSC research.

Bioinspired green synthesis of copper oxide nanoparticles from Syzygium alternifolium (Wt.) Walp: characterization and evaluation of its synergistic antimicrobial and anticancer activity

NASA Astrophysics Data System (ADS)

Yugandhar, Pulicherla; Vasavi, Thirumalanadhuni; Uma Maheswari Devi, Palempalli; Savithramma, Nataru

2017-10-01

In recent times, nanoparticles are attributed to green nanotechnology methods to know the synergistic biological activities. To accomplish this phenomenon, present study was aimed to synthesize copper oxide nanoparticles (CuO NPs) by using Syzygium alternifolium stem bark, characterized those NPs using expository tools and to elucidate high prioritized antimicrobial and anticancer activities. Synthesized particles exhibited a color change pattern upon synthesis and affirmed its respective broad peak at 285 nm which was analyzed through UV-vis spectroscopy. FT-IR study confirmed that phenols and primary amines were mainly involved in capping and stabilization of nanoparticles. DLS and Zeta potential studies revealed narrow size of particles with greater stability. XRD studies revealed the crystallographic nature of particles with 17.2 nm average size. Microscopic analysis by using TEM revealed that particle size range from 5-13 nm and most of them were spherical in shape, non-agglomerated and poly-dispersed in condition. Antimicrobial studies of particles showed highest inhibitory activity against E. coli and T. harzianum among bacterial and fungal strains, respectively. The scope of this study is extended by examining anticancer activity of CuO NPs. This study exhibited potential anticancer activity towards MDA-MB-231 human breast cancer lines. Overall, these examinations relate that the S. alternifolium is described as efficient well-being plant and probabilistically for the design and synthesis of nanoparticles for human health. This study paves a way to better understand antimicrobial and anticancer therapeutic drug potentials of nanoparticles to design and analysis of pharmaceuticals by in vivo and in vitro approaches.

COMBINED DELAY AND GRAPH EMBEDDING OF EPILEPTIC DISCHARGES IN EEG REVEALS COMPLEX AND RECURRENT NONLINEAR DYNAMICS.

PubMed

Erem, B; Hyde, D E; Peters, J M; Duffy, F H; Brooks, D H; Warfield, S K

2015-04-01

The dynamical structure of the brain's electrical signals contains valuable information about its physiology. Here we combine techniques for nonlinear dynamical analysis and manifold identification to reveal complex and recurrent dynamics in interictal epileptiform discharges (IEDs). Our results suggest that recurrent IEDs exhibit some consistent dynamics, which may only last briefly, and so individual IED dynamics may need to be considered in order to understand their genesis. This could potentially serve to constrain the dynamics of the inverse source localization problem.

Halogenated arsenenes as Dirac materials

NASA Astrophysics Data System (ADS)

Tang, Wencheng; Sun, Minglei; Ren, Qingqiang; Wang, Sake; Yu, Jin

2016-07-01

Arsenene is the graphene-like arsenic nanosheet, which has been predicted very recently [S. Zhang, Z. Yan, Y. Li, Z. Chen, and H. Zeng, Angewandte Chemie, 127 (2015) 3155-3158]. Using first-principles calculations, we systematically investigate the structures and electronic properties of fully-halogenated arsenenes. Formation energy analysis reveals that all the fully-halogenated arsenenes except iodinated arsenene are energetically favorable and could be synthesized. We have revealed the presence of Dirac cone in fully-halogenated arsenene compounds. They may have great potential applications in next generation of high-performance devices.

NMR-based metabonomics and correlation analysis reveal potential biomarkers associated with chronic atrophic gastritis.

PubMed

Cui, Jiajia; Liu, Yuetao; Hu, Yinghuan; Tong, Jiayu; Li, Aiping; Qu, Tingli; Qin, Xuemei; Du, Guanhua

2017-01-05

Chronic atrophic gastritis (CAG) is one of the most important pre-cancerous states with a high prevalence. Exploring of the underlying mechanism and potential biomarkers is of significant importance for CAG. In the present work, 1 H NMR-based metabonomics with correlative analysis was performed to analyze the metabolic features of CAG. 19 plasma metabolites and 18 urine metabolites were enrolled to construct the circulatory and excretory metabolome of CAG, which was in response to alterations of energy metabolism, inflammation, immune dysfunction, as well as oxidative stress. 7 plasma biomarkers and 7 urine biomarkers were screened to elucidate the pathogenesis of CAG based on the further correlation analysis with biochemical indexes. Finally, 3 plasma biomarkers (arginine, succinate and 3-hydroxybutyrate) and 2 urine biomarkers (α-ketoglutarate and valine) highlighted the potential to indicate risks of CAG in virtue of correlation with pepsin activity and ROC analysis. Here, our results paved a way for elucidating the underlying mechanisms in the development of CAG, and provided new avenues for the diagnosis of CAG and presented potential drug targets for treatment of CAG. Copyright © 2016 Elsevier B.V. All rights reserved.

Complete genome sequence of probiotic Bacillus coagulans HM-08: A potential lactic acid producer.

PubMed

Yao, Guoqiang; Gao, Pengfei; Zhang, Wenyi

2016-06-20

Bacillus coagulans HM-08 is a commercialized probiotic strain in China. Its genome contains a 3.62Mb circular chromosome with an average GC content of 46.3%. In silico analysis revealed the presence of one xyl operon as well as several other genes that are correlated to xylose utilization. The genetic information provided here may help to expand its future biotechnology potential in lactic acid production. Copyright © 2016 Elsevier B.V. All rights reserved.

An improved infrared technique for sorting pecans

NASA Astrophysics Data System (ADS)

Graeve, Thorsten; Dereniak, Eustace L.; Lamonica, John A., Jr.

1991-10-01

This paper presents the results of a study of pecan spectral reflectances. It describes an experiment for measuring the contrast between several components of raw pecan product to be sorted. An analysis of the experimental data reveals high contrast ratios in the infrared spectrum, suggesting a potential improvement in sorting efficiency when separating pecan meat from shells. It is believed that this technique has the potential to dramatically improve the efficiency of current sorting machinery, and to reduce the cost of processing pecans for the consumer market.

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

DOE PAGES

Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.; ...

2015-03-17

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms weremore » mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.« less

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

PubMed Central

Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.; Mahnert, Alexander; Tom, Lauren; Piceno, Yvette; Andersen, Gary L.; Venkateswaran, Kasthuri; Rettberg, Petra; Barczyk, Simon; Pukall, Rüdiger; Berg, Gabriele

2015-01-01

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms. PMID:25778463

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

NASA Astrophysics Data System (ADS)

Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.; Mahnert, Alexander; Tom, Lauren; Piceno, Yvette; Andersen, Gary L.; Venkateswaran, Kasthuri; Rettberg, Petra; Barczyk, Simon; Pukall, Rüdiger; Berg, Gabriele

2015-03-01

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.

Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano

PubMed Central

Banskar, Sunil; Bhute, Shrikant S.; Suryavanshi, Mangesh V.; Punekar, Sachin; Shouche, Yogesh S.

2016-01-01

Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals. PMID:27845426

Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano.

PubMed

Banskar, Sunil; Bhute, Shrikant S; Suryavanshi, Mangesh V; Punekar, Sachin; Shouche, Yogesh S

2016-11-15

Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals.

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

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

Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms weremore » mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.« less

First Monte Carlo analysis of fragmentation functions from single-inclusive e + e - annihilation

DOE PAGES

Sato, Nobuo; Ethier, J. J.; Melnitchouk, W.; ...

2016-12-02

Here, we perform the first iterative Monte Carlo (IMC) analysis of fragmentation functions constrained by all available data from single-inclusive $e^+ e^-$ annihilation into pions and kaons. The IMC method eliminates potential bias in traditional analyses based on single fits introduced by fixing parameters not well contrained by the data, and provides a statistically rigorous determination of uncertainties. Our analysis reveals specific features of fragmentation functions using the new IMC methodology and those obtained from previous analyses, especially for light quarks and for strange quark fragmentation to kaons.

Multiplex social ecological network analysis reveals how social changes affect community robustness more than resource depletion.

PubMed

Baggio, Jacopo A; BurnSilver, Shauna B; Arenas, Alex; Magdanz, James S; Kofinas, Gary P; De Domenico, Manlio

2016-11-29

Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social-ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic Alaska potentially facing substantial economic and ecological changes. Our analysis of plausible future scenarios suggests that changes to social relations and key households have greater effects on community robustness than changes to specific wild food resources.

The Role of Social and Behavioral Science in Policymaking for Television.

ERIC Educational Resources Information Center

Rand Corp., Santa Monica, CA.

An analysis of the present system of American television broadcasting reveals that social and behavioral science has had very limited influence on its regulatory policymaking. The television advertisement and its potential adverse effect on children have come to the attention of federal regulatory bodies, as well as consumer and children advocacy…

Plastid DNA analysis reveals cryptic hybridization in invasive dalmatian toadflax populations

Treesearch

Andrew Boswell; Sharlene E. Sing; Sarah M. Ward

2016-01-01

Gene flow between Dalmatian toadflax (DT) and yellow toadflax (YT), both aggressive invaders throughout the Intermountain West, is creating hybrid populations potentially more invasive than either parent species. To determine the direction of gene flow in these hybrid populations, species-diagnostic cytoplasmic markers were developed. Markers were based on...

Perspectives of the Titanic: Are We Sinking with the Ship?

ERIC Educational Resources Information Center

Ranz-Smith, Deborah J.

2013-01-01

Teachers are asked to examine the potential opportunities for connecting themes of childhood play to the skills, habits of the mind, and principles of the disciplines. A comparative analysis of the explanations of first graders and the perceptions of their teachers, in separate focus groups, revealed a disparity in the significance of narrative…

Types of Standard Systems and Categories of Measurement.

ERIC Educational Resources Information Center

Aftanas, Marion S.

The term measurement has been used in a number of different sub-areas of psychology without an explicit recognition of the commonalities and potential differences in measurement characteristics. Analysis of these measurement situations reveals that the one common factor is that a mechanism or discriminative process, that is a standard system of…

King Oedipus and the Problem Solving Process.

ERIC Educational Resources Information Center

Borchardt, Donald A.

An analysis of the problem solving process reveals at least three options: (1) finding the cause, (2) solving the problem, and (3) anticipating potential problems. These methods may be illustrated by examining "Oedipus Tyrannus," a play in which a king attempts to deal with a problem that appears to be beyond his ability to solve, and…

Effect of polymer viscosity on physicochemical properties and ocular tolerance of FB-loaded PLGA nanospheres.

PubMed

Araújo, J; Vega, E; Lopes, C; Egea, M A; Garcia, M L; Souto, E B

2009-08-01

Poly(lactide-co-glycolide) acid (PLGA) nanospheres incorporating flurbiprofen (FB) were produced by the solvent displacement technique, for ocular applications aiming to avoid/minimize inflammation induced by surgical trauma. In this work, a PLGA of low viscosity has been tested and the results obtained were compared with those previously reported by Vega et al. The physicochemical properties of the developed formulations were evaluated by measuring particle size, zeta potential and FB entrapment efficiency, showing no significant differences. Release studies demonstrated that the formulation produced with PLGA of higher viscosity revealed a slower drug release rate. Stability analysis, for a period of 75 days, was performed using three complementary methods: (i) turbidity experiments using a Turbiscan optical analyzer, (ii) particle size measurements, and (iii) zeta potential analysis. The results revealed long-term physicochemical stability suitability for ophthalmic use, being independent from the polymer viscosity. The ocular tolerance was assessed by an alternative in vitro method to animal experimentation, the HET-CAM. For all developed formulations no ocular irritancy has been detected.

1,4-Naphthoquinones potently inhibiting P2X7 receptor activity.

PubMed

Faria, R X; Oliveira, F H; Salles, J P; Oliveira, A S; von Ranke, N L; Bello, M L; Rodrigues, C R; Castro, H C; Louvis, A R; Martins, D L; Ferreira, V F

2018-01-01

P2X7 receptor (P2X7R) is an ATP-gated ion-channel with potential therapeutic applications. In this study, we prepared and searched a series of 1,4-naphthoquinones derivatives to evaluate their antagonistic effect on both human and murine P2X7 receptors. We explored the structure-activity relationship and binding mode of the most active compounds using a molecular modeling approach. Biological analysis of this series (eight analogues and two compounds) revealed significant in vitro inhibition against both human and murine P2X7R. Further characterization revealed that AN-03 and AN-04 had greater potency than BBG and A740003 in inhibiting dye uptake, IL-1β release, and carrageenan-induced paw edema in vivo. Moreover, we used electrophysiology and molecular docking analysis for characterizing AN-03 and AN-04 action mechanism. These results suggest 1,4-napthoquinones, mainly AN-04, as potential leads to design new P2X7R blockers and anti-inflammatory drugs. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Acceptability of Pre-Exposure Prophylaxis (PrEP) as an HIV prevention strategy: Barriers and facilitators to PrEP uptake among at-risk Peruvian populations

PubMed Central

Galea, Jerome T.; Kinsler, Janni J.; Salazar, Ximena; Lee, Sung-Jae; Giron, Maziel; Sayles, Jennifer N.; Cáceres, Carlos; Cunningham, William E.

2010-01-01

This study examined Pre-Exposure Prophylaxis (PrEP) acceptability among female sex workers, male-to-female transgendered persons, and men who have sex with men in Lima, Peru. Focus groups explored social issues associated with PrEP acceptability and conjoint analysis assessed preferences among eight hypothetical PrEP scenarios with varying attribute profiles and their relative impact on acceptability. Conjoint analysis revealed that PrEP acceptability ranged from 19.8 to 82.5 out of a possible score of 100 across the eight hypothetical PrEP scenarios. Out-of-pocket cost had the greatest impact on PrEP acceptability (25.2, p <0.001), followed by efficacy (21.4, p <0.001) and potential side effects (14.7, p <0.001). Focus group data supported these findings, and also revealed that potential sexual risk disinhibition, stigma and discrimination associated with PrEP use, and mistrust of health care professionals were also concerns. These issues will require careful attention when planning for PrEP roll-out if proven efficacious in ongoing clinical trials. PMID:21571973

Acceptability of pre-exposure prophylaxis as an HIV prevention strategy: barriers and facilitators to pre-exposure prophylaxis uptake among at-risk Peruvian populations.

PubMed

Galea, J T; Kinsler, J J; Salazar, X; Lee, S-J; Giron, M; Sayles, J N; Cáceres, C; Cunningham, W E

2011-05-01

This study examined pre-exposure prophylaxis (PrEP) acceptability among female sex workers, male-to-female transgendered persons and men who have sex with men in Lima, Peru. Focus groups explored social issues associated with PrEP acceptability and conjoint analysis assessed preferences among eight hypothetical PrEP scenarios with varying attribute profiles and their relative impact on acceptability. Conjoint analysis revealed that PrEP acceptability ranged from 19.8 to 82.5 out of a possible score of 100 across the eight hypothetical PrEP scenarios. Out-of-pocket cost had the greatest impact on PrEP acceptability (25.2, P < 0.001), followed by efficacy (21.4, P < 0.001) and potential side-effects (14.7, P < 0.001). Focus group data supported these findings, and also revealed that potential sexual risk disinhibition, stigma and discrimination associated with PrEP use, and mistrust of health-care professionals were also concerns. These issues will require careful attention when planning for PrEP roll-out.

Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility

PubMed Central

Seumois, Grégory; Chavez, Lukas; Gerasimova, Anna; Lienhard, Matthias; Omran, Nada; Kalinke, Lukas; Vedanayagam, Maria; Ganesan, Asha Purnima V; Chawla, Ashu; Djukanović, Ratko; Ansel, K Mark; Peters, Bjoern; Rao, Anjana; Vijayanand, Pandurangan

2014-01-01

A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce type 2 cytokines (TH2 cells). By mapping genome-wide histone modification profiles for subsets of T cells isolated from peripheral blood of healthy and asthmatic individuals, we identified enhancers with known and potential roles in the normal differentiation of human TH1 cells and TH2 cells. We discovered disease-specific enhancers in T cells that differ between healthy and asthmatic individuals. Enhancers that gained the histone H3 Lys4 dimethyl (H3K4me2) mark during TH2 cell development showed the highest enrichment for asthma-associated single nucleotide polymorphisms (SNPs), which supported a pathogenic role for TH2 cells in asthma. In silico analysis of cell-specific enhancers revealed transcription factors, microRNAs and genes potentially linked to human TH2 cell differentiation. Our results establish the feasibility and utility of enhancer profiling in well-defined populations of specialized cell types involved in disease pathogenesis. PMID:24997565

Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility.

PubMed

Seumois, Grégory; Chavez, Lukas; Gerasimova, Anna; Lienhard, Matthias; Omran, Nada; Kalinke, Lukas; Vedanayagam, Maria; Ganesan, Asha Purnima V; Chawla, Ashu; Djukanović, Ratko; Ansel, K Mark; Peters, Bjoern; Rao, Anjana; Vijayanand, Pandurangan

2014-08-01

A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4(+) T cells that produce type 2 cytokines (TH2 cells). By mapping genome-wide histone modification profiles for subsets of T cells isolated from peripheral blood of healthy and asthmatic individuals, we identified enhancers with known and potential roles in the normal differentiation of human TH1 cells and TH2 cells. We discovered disease-specific enhancers in T cells that differ between healthy and asthmatic individuals. Enhancers that gained the histone H3 Lys4 dimethyl (H3K4me2) mark during TH2 cell development showed the highest enrichment for asthma-associated single nucleotide polymorphisms (SNPs), which supported a pathogenic role for TH2 cells in asthma. In silico analysis of cell-specific enhancers revealed transcription factors, microRNAs and genes potentially linked to human TH2 cell differentiation. Our results establish the feasibility and utility of enhancer profiling in well-defined populations of specialized cell types involved in disease pathogenesis.

Sm@C2v(3)-C80: site-hopping motion of endohedral Sm atom and metal-induced effect on redox profile

NASA Astrophysics Data System (ADS)

Xu, Wei; Niu, Ben; Shi, Zujin; Lian, Yongfu; Feng, Lai

2012-10-01

A new metallofullerene Sm@C2v(3)-C80 was synthesized and characterized. X-Ray analysis showed that the endohedral Sm atom undergoes a hopping motion between several off-center sites, even at low temperature. In addition, a comparative electrochemical study between Sm@C2v(3)-C80 and Yb@C2v(3)-C80 revealed their different redox potentials, suggesting a metal-induced effect on their redox profiles.A new metallofullerene Sm@C2v(3)-C80 was synthesized and characterized. X-Ray analysis showed that the endohedral Sm atom undergoes a hopping motion between several off-center sites, even at low temperature. In addition, a comparative electrochemical study between Sm@C2v(3)-C80 and Yb@C2v(3)-C80 revealed their different redox potentials, suggesting a metal-induced effect on their redox profiles. CCDC reference number 894168. For crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr32193a

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

PubMed

Preissl, Sebastian; Fang, Rongxin; Huang, Hui; Zhao, Yuan; Raviram, Ramya; Gorkin, David U; Zhang, Yanxiao; Sos, Brandon C; Afzal, Veena; Dickel, Diane E; Kuan, Samantha; Visel, Axel; Pennacchio, Len A; Zhang, Kun; Ren, Bing

2018-03-01

Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

[Search for potential gastric cancer biomarkers using low molecular weight blood plasma proteome profiling by mass spectrometry].

PubMed

Shevchenko, V E; Arnotskaia, N E; Ogorodnikova, E V; Davydov, M M; Ibraev, M A; Turkin, I N; Davydov, M I

2014-01-01

Gastric cancer, one of the most widespread malignant tumors, still lacks reliable serum/plasma biomarkers of its early detection. In this study we have developed, unified, and tested a new methodology for search of gastric cancer biomarkers based on profiling of low molecular weight proteome (LMWP) (1-17 kDa). This approach included three main components: sample pre-fractionation, matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS), data analysis by a bioinformatics software package. Applicability and perspectives of the developed approach for detection of potential gastric cancer markers during LMWP analysis have been demonstrated using 69 plasma samples from patients with gastric cancer (stages I-IV) and 238 control samples. The study revealed peptides/polypeptides, which may be potentially used for detection of this pathology.

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing

PubMed Central

Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.

2016-01-01

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. PMID:26950332

U.S. Navy Officer Attitudes on the Repeal of Don’t Ask, Don’t Tell

DTIC Science & Technology

2013-03-01

military units; a pre- test / post - test quasi experiment; survey analysis; relevant media analysis of articles related to the repeal and published within...and 2010. The surveys revealed an increasing acceptance of gays in the Navy. The present study, conducted post - repeal, utilized the same NPS survey...and enlisted personnel. Further, the post -repeal effects on readiness should be monitored, particularly for fairness and potential harassment. The

Mapping the geogenic radon potential: methodology and spatial analysis for central Hungary.

PubMed

Szabó, Katalin Zsuzsanna; Jordan, Gyozo; Horváth, Ákos; Szabó, Csaba

2014-03-01

A detailed geogenic radon potential (GRP) mapping based on field soil gas radon and soil gas permeability measurements was carried out in this study. A conventional continuous variable approach was used in this study for GRP determination and to test its applicability to the selected area of Hungary. Spatial pattern of soil gas radon concentration, soil permeability and GRP and the relationship between geological formations and these parameters were studied by performing detailed spatial analysis. Exploratory data analysis revealed that higher soil gas radon activity concentration and GRP characterizes the mountains and hills than the plains. The highest values were found in the proluvial-deluvial sediments, rock debris on the downhill slopes eroded from hills. Among the Quaternary sediments, which characterize the study area, the fluvial sediment has the highest values, which are also located in the hilly areas. The lowest values were found in the plain areas covered by drift sand, fluvioeolic sand, fluvial sand and loess. As a conclusion, radon is related to the sediment cycle in the study area. A geogenic radon risk map was created, which assists human health risk assessment and risk reduction since it indicates the potential of the source of indoor radon. The map shows that low and medium geogenic radon potential characterizes the study area in central Hungary. High risk occurs only locally. The results reveal that Quaternary sediments are inhomogeneous from a radon point of view, fluvial sediment has medium GRP, whereas the other rock formations such as drift sand, fluioeolic sand, fluvial sand and loess, found in the study area, have low GRP. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cartilaginous Metabolomic Study Reveals Potential Mechanisms of Osteophyte Formation in Osteoarthritis.

PubMed

Xu, Zhongwei; Chen, Tingmei; Luo, Jiao; Ding, Shijia; Gao, Sichuan; Zhang, Jian

2017-04-07

Osteophyte is one of the inevitable consequences of progressive osteoarthritis with the main characteristics of cartilage degeneration and endochondral ossification. The pathogenesis of osteophyte formation is not fully understood to date. In this work, metabolomic approaches were employed to explore potential mechanisms of osteophyte formation by detecting metabolic variations between extracts of osteophyte cartilage tissues (n = 32) and uninvolved control cartilage tissues (n = 34), based on the platform of ultraperformance liquid chromatography tandem quadrupole time-of-flight mass spectrometry, as well as the use of multivariate statistic analysis and univariate statistic analysis. The osteophyte group was significantly separated from the control group by the orthogonal partial least-squares discriminant analysis models, indicating that metabolic state of osteophyte cartilage had been changed. In total, 28 metabolic variations further validated by mass spectrum (MS) match, tandom mass spectrum (MS/MS) match, and standards match mainly included amino acids, sulfonic acids, glycerophospholipids, and fatty acyls. These metabolites were related to some specific physiological or pathological processes (collagen dissolution, boundary layers destroyed, self-restoration triggered, etc.) which might be associated with the procedure of osteophyte formation. Pathway analysis showed phenylalanine metabolism (PI = 0.168, p = 0.004) was highly correlative to this degenerative process. Our findings provided a direction for targeted metabolomic study and an insight into further reveal the molecular mechanisms of ostophyte formation.

A quantitative meta-analysis and review of motor learning in the human brain

PubMed Central

Hardwick, Robert M.; Rottschy, Claudia; Miall, R. Chris; Eickhoff, Simon B.

2013-01-01

Neuroimaging studies have improved our understanding of which brain structures are involved in motor learning. Despite this, questions remain regarding the areas that contribute consistently across paradigms with different task demands. For instance, sensorimotor tasks focus on learning novel movement kinematics and dynamics, while serial response time task (SRTT) variants focus on sequence learning. These differing task demands are likely to elicit quantifiably different patterns of neural activity on top of a potentially consistent core network. The current study identified consistent activations across 70 motor learning experiments using activation likelihood estimation (ALE) meta-analysis. A global analysis of all tasks revealed a bilateral cortical–subcortical network consistently underlying motor learning across tasks. Converging activations were revealed in the dorsal premotor cortex, supplementary motor cortex, primary motor cortex, primary somatosensory cortex, superior parietal lobule, thalamus, putamen and cerebellum. These activations were broadly consistent across task specific analyses that separated sensorimotor tasks and SRTT variants. Contrast analysis indicated that activity in the basal ganglia and cerebellum was significantly stronger for sensorimotor tasks, while activity in cortical structures and the thalamus was significantly stronger for SRTT variants. Additional conjunction analyses then indicated that the left dorsal premotor cortex was activated across all analyses considered, even when controlling for potential motor confounds. The highly consistent activation of the left dorsal premotor cortex suggests it is a critical node in the motor learning network. PMID:23194819

Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.

PubMed

Illeghems, Koen; Weckx, Stefan; De Vuyst, Luc

2015-09-01

A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures. Copyright © 2015 Elsevier Ltd. All rights reserved.

ATR-FTIR spectroscopy reveals polycyclic aromatic hydrocarbon contamination despite relatively pristine site characteristics: Results of a field study in the Niger Delta.

PubMed

Obinaju, Blessing E; Martin, Francis L

2016-01-01

Fourier-transform infrared (FTIR) spectroscopy is an emerging technique to detect biochemical alterations in biological tissues, particularly changes due to sub-lethal exposures to environmental contaminants. We have previously shown the potential of attenuated total reflection FTIR (ATR-FTIR) spectroscopy to detect real-time exposure to contaminants in sentinel organisms as well as the potential to relate spectral alterations to the presence of specific environmental agents. In this study based in the Niger Delta (Nigeria), changes occurring in fish tissues as a result of polycyclic aromatic hydrocarbon (PAH) exposure at contaminated sites are compared to the infrared (IR) spectra of the tissues obtained from a relatively pristine site. Multivariate analysis revealed that PAH contamination could be occurring at the pristine site, based on the IR spectra and significant (P<0.0001) differences between sites. The study provides evidence of the IR spectroscopy techniques' sensitivity and supports their potential application in environmental biomonitoring. Copyright © 2016 Elsevier Ltd. All rights reserved.

Graph-based analysis of kinetics on multidimensional potential-energy surfaces.

PubMed

Okushima, T; Niiyama, T; Ikeda, K S; Shimizu, Y

2009-09-01

The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.

Potential use of hydrocarbons for aging Lucilia sericata blowfly larvae to establish the postmortem interval.

PubMed

Moore, Hannah E; Adam, Craig D; Drijfhout, Falko P

2013-03-01

Previous studies on Diptera have shown the potential for the use of cuticular hydrocarbons' analysis in the determination of larval age and hence the postmortem interval (PMI) for an associated cadaver. In this work, hydrocarbon compounds, extracted daily until pupation from the cuticle of the blowfly Lucilia sericata (Diptera: Calliphoridae), have been analyzed using gas chromatography-mass spectrometry (GC-MS). The results show distinguishing features within the hydrocarbon profile over the period of the larvae life cycle, with significant chemical changes occurring from the younger larvae to the postfeeding larvae. Further interpretation of the chromatograms using principal component analysis revealed a strong correlation between the magnitudes of particular principal components and time. This outcome suggests that, under the conditions of this study, the cuticular hydrocarbons evolve in a systematic fashion with time, thus supporting the potential for GC-MS analysis as a tool for establishing PMI where such a species is present. © 2012 American Academy of Forensic Sciences.

An initial analysis of short- and medium-range correlations potential non-Pt catalysts in CoNx

NASA Astrophysics Data System (ADS)

Peterson, Joe

2009-10-01

A potential show stopper for the development of fuel cells for the commercial automotive industry is the design of low-cost catalysts. The best catalysts are based on platinum, which is a rare and expensive noble metal. Our group has been involved in the characterization of potential materials for non-Pt catalysts. In this presentation, I will present some preliminary neutron scattering data from a nanocrystalline powder sample of CoNx. It is apparent that the diffraction data cannot be analyzed with standard Riedveld refinement, and we have to invoke pair distribution function (PDF) analysis. The PDF provides insight into short-range correlations, as it measures the probabilities of short- and mid-range interatomic distances in a material. The analysis reveals a strong incoherent scattering response, which is indicative of the presence of hydrogen in the sample. After correcting for the incoherent scattering, one obtains the normalized scattering function S(Q), whose Fourier transform yields the PDF.

An initial analysis of short- and medium-range correlations potential non-Pt catalysts in CoNx

NASA Astrophysics Data System (ADS)

Peterson, Joe

2010-03-01

A potential show stopper for the development of fuel cells for the commercial automotive industry is the design of low-cost catalysts. The best catalysts are based on platinum, which is a rare and expensive noble metal. Our group has been involved in the characterization of potential materials for non-Pt catalysts. In this presentation, I will present some preliminary neutron scattering data from a nanocrystalline powder sample of CoNx. It is apparent that the diffraction data cannot be analyzed with standard Riedveld refinement, and we have to invoke pair distribution function (PDF) analysis. The PDF provides insight into short-range correlations, as it measures the probabilities of short- and mid-range interatomic distances in a material. The analysis reveals a strong incoherent scattering response, which is indicative of the presence of hydrogen in the sample. After correcting for the incoherent scattering, one obtains the normalized scattering function S(Q), whose Fourier transform yields the PDF.

LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis.

PubMed

Thomas, James R; Gedeon, Patrick C; Grant, Barry J; Madura, Jeffry D

2012-07-03

Monoamine transporters (MATs) function by coupling ion gradients to the transport of dopamine, norepinephrine, or serotonin. Despite their importance in regulating neurotransmission, the exact conformational mechanism by which MATs function remains elusive. To this end, we have performed seven 250 ns accelerated molecular dynamics simulations of the leucine transporter, a model for neurotransmitter MATs. By varying the presence of binding-pocket leucine substrate and sodium ions, we have sampled plausible conformational states representative of the substrate transport cycle. The resulting trajectories were analyzed using principal component analysis of transmembrane helices 1b and 6a. This analysis revealed seven unique structures: two of the obtained conformations are similar to the currently published crystallographic structures, one conformation is similar to a proposed open inward structure, and four conformations represent novel structures of potential importance to the transport cycle. Further analysis reveals that the presence of binding-pocket sodium ions is necessary to stabilize the locked-occluded and open-inward conformations. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Aspergillus Oryzae S2 α-Amylase Domain C Involvement in Activity and Specificity: In Vivo Proteolysis, Molecular and Docking Studies

PubMed Central

Sahnoun, Mouna; Jemli, Sonia; Trabelsi, Sahar; Ayadi, Leila; Bejar, Samir

2016-01-01

We previously reported that Aspergillus oryzae strain S2 had produced two α-amylase isoforms named AmyA and AmyB. The apparent molecular masses revealed by SDS-PAGE were 50 and 42 kDa, respectively. Yet AmyB has a higher catalytic efficiency. Based on a monitoring study of the α-amylase production in both the presence and absence of different protease inhibitors, a chymotrypsin proteolysis process was detected in vivo generating AmyB. A. oryzae S2 α-amylase gene was amplified, cloned and sequenced. The sequence analysis revealed nine exons, eight introns and an encoding open reading frame of 1500 bp corresponding to AmyA isoform. The amino-acid sequence analysis revealed aY371 potential chymotrypsin cleaving site, likely to be the AmyB C-Terminal end and two other potential sites at Y359, and F379. A zymogram with a high acrylamide concentration was used. It highlighted two other closed apparent molecular mass α-amylases termed AmyB1 and AmyB2 reaching40 kDa and 43 kDa. These isoforms could be possibly generated fromY359, and F379secondary cut, respectively. The molecular modeling study showed that AmyB preserved the (β/α)8 barrel domain and the domain B but lacked the C-terminal domain C. The contact map analysis and the docking studies strongly suggested a higher activity and substrate binding affinity for AmyB than AmyA which was previously experimentally exhibited. This could be explained by the easy catalytic cleft accessibility. PMID:27101008

Adjunctive Nutraceuticals for Depression: A Systematic Review and Meta-Analyses.

PubMed

Sarris, Jerome; Murphy, Jenifer; Mischoulon, David; Papakostas, George I; Fava, Maurizio; Berk, Michael; Ng, Chee H

2016-06-01

There is burgeoning interest in augmentation strategies for improving inadequate response to antidepressants. The adjunctive use of standardized pharmaceutical-grade nutrients, known as nutraceuticals, has the potential to modulate several neurochemical pathways implicated in depression. While many studies have been conducted in this area, to date no specialized systematic review (or meta-analysis) has been conducted. A systematic search of PubMed, CINAHL, Cochrane Library, and Web of Science was conducted up to December 2015 for clinical trials using adjunctive nutrients for depression. Where sufficient data were available, a random-effects model analyzed the standard mean difference between treatment and placebo in the change from baseline to endpoint, combining the effect size data. Funnel plot and heterogeneity analyses were also performed. Primarily positive results were found for replicated studies testing S-adenosylmethionine (SAMe), methylfolate, omega-3 (primarily EPA or ethyl-EPA), and vitamin D, with positive isolated studies for creatine, folinic acid, and an amino acid combination. Mixed results were found for zinc, folic acid, vitamin C, and tryptophan, with nonsignificant results for inositol. No major adverse effects were noted in the studies (aside from minor digestive disturbance). A meta-analysis of adjunctive omega-3 versus placebo revealed a significant and moderate to strong effect in favor of omega-3. Conversely, a meta-analysis of folic acid revealed a nonsignificant difference from placebo. Marked study heterogeneity was found in a Higgins test for both omega-3 and folic acid studies; funnel plots also revealed asymmetry (reflecting potential study bias). Current evidence supports adjunctive use of SAMe, methylfolate, omega-3, and vitamin D with antidepressants to reduce depressive symptoms.

Characterization of Exoelectrogenic Bacteria Enterobacter Strains Isolated from a Microbial Fuel Cell Exposed to Copper Shock Load

PubMed Central

Feng, Cuijie; Li, Jiangwei; Qin, Dan; Chen, Lixiang; Zhao, Feng; Chen, Shaohua; Hu, Hongbo; Yu, Chang-Ping

2014-01-01

Microorganisms capable of generating electricity in microbial fuel cells (MFCs) have gained increasing interest. Here fourteen exoelectrogenic bacterial strains were isolated from the anodic biofilm in an MFC before and after copper (Cu) shock load by Hungate roll-tube technique with solid ferric (III) oxide as an electron acceptor and acetate as an electron donor. Phylogenetic analysis of the 16S rRNA gene sequences revealed that they were all closely related to Enterobacter ludwigii DSM 16688T within the Enterobacteriaceae family, although these isolated bacteria showed slightly different morphology before and after Cu shock load. Two representative strains R2B1 (before Cu shock load) and B4B2 (after Cu shock load) were chosen for further analysis. B4B2 is resistant to 200 mg L−1 of Cu(II) while R2B1 is not, which indicated the potential selection of the Cu shock load. Raman analysis revealed that both R2B1 and B4B2 contained c-type cytochromes. Cyclic voltammetry measurements revealed that strain R2B1 had the capacity to transfer electrons to electrodes. The experimental results demonstrated that strain R2B1 was capable of utilizing a wide range of substrates, including Luria-Bertani (LB) broth, cellulose, acetate, citrate, glucose, sucrose, glycerol and lactose to generate electricity, with the highest current density of 440 mA·m−2 generated from LB-fed MFC. Further experiments indicated that the bacterial cell density had potential correlation with the current density. PMID:25412475

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition.

PubMed

Wang, Cheng; Dong, Da; Wang, Haoshu; Müller, Karin; Qin, Yong; Wang, Hailong; Wu, Weixiang

2016-01-01

Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome. Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed. These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

PubMed

Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

2015-05-19

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

Comprehensive analysis of miRNAs expression profiles revealed potential key miRNA/mRNAs regulating colorectal cancer stem cell self-renewal.

PubMed

Xu, Peng; Wang, Junhua; Sun, Bo; Xiao, Zhongdang

2018-05-20

Self-renewal is essential for the malignant biological behaviors of colorectal cancer stem cells. While the self-renewal molecular mechanisms of colorectal cancer stem cells are not yet fully understood. Recently, miRNAs are reported to be relevant to the self-renewal ability of cancer stem cells. In this study, we first isolated colorectal cancer stem cell from colorectal cancer cell line HCT-116 by 1% low serum culture. Then we conducted a comprehensive analysis based on the miRNAs profiles data of both colorectal cancer stem cells and normal cultured colorectal cancer cells. Pathway analysis revealed multiple pathways including Jak-STAT, TGF-beta, PI3K-Akt and MAPK signaling pathway that are correlated to colorectal cancer. Further, we constructed a miRNA-mRNA network, based on which, several miRNA/mRNA pairs were ranked according to their impact index to the self-renewal of colorectal cancer stem cells. Further biological experiment showed that up-regulation of miR-92a-3p led to cell cycle arrest and reduced colony formation. This work provides clues to find the new potential biomarkers for colorectal cancer stem cell diagnosis and select effective miRNAs for targeted therapy. Copyright © 2018 Elsevier B.V. All rights reserved.

Decoding of top-down cognitive processing for SSVEP-controlled BMI

PubMed Central

Min, Byoung-Kyong; Dähne, Sven; Ahn, Min-Hee; Noh, Yung-Kyun; Müller, Klaus-Robert

2016-01-01

We present a fast and accurate non-invasive brain-machine interface (BMI) based on demodulating steady-state visual evoked potentials (SSVEPs) in electroencephalography (EEG). Our study reports an SSVEP-BMI that, for the first time, decodes primarily based on top-down and not bottom-up visual information processing. The experimental setup presents a grid-shaped flickering line array that the participants observe while intentionally attending to a subset of flickering lines representing the shape of a letter. While the flickering pixels stimulate the participant’s visual cortex uniformly with equal probability, the participant’s intention groups the strokes and thus perceives a ‘letter Gestalt’. We observed decoding accuracy of 35.81% (up to 65.83%) with a regularized linear discriminant analysis; on average 2.05-fold, and up to 3.77-fold greater than chance levels in multi-class classification. Compared to the EEG signals, an electrooculogram (EOG) did not significantly contribute to decoding accuracies. Further analysis reveals that the top-down SSVEP paradigm shows the most focalised activation pattern around occipital visual areas; Granger causality analysis consistently revealed prefrontal top-down control over early visual processing. Taken together, the present paradigm provides the first neurophysiological evidence for the top-down SSVEP BMI paradigm, which potentially enables multi-class intentional control of EEG-BMIs without using gaze-shifting. PMID:27808125

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR)

PubMed Central

Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J.; Laclette, Juan P.; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

2015-01-01

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest. PMID:25989346

Decoding of top-down cognitive processing for SSVEP-controlled BMI

NASA Astrophysics Data System (ADS)

Min, Byoung-Kyong; Dähne, Sven; Ahn, Min-Hee; Noh, Yung-Kyun; Müller, Klaus-Robert

2016-11-01

We present a fast and accurate non-invasive brain-machine interface (BMI) based on demodulating steady-state visual evoked potentials (SSVEPs) in electroencephalography (EEG). Our study reports an SSVEP-BMI that, for the first time, decodes primarily based on top-down and not bottom-up visual information processing. The experimental setup presents a grid-shaped flickering line array that the participants observe while intentionally attending to a subset of flickering lines representing the shape of a letter. While the flickering pixels stimulate the participant’s visual cortex uniformly with equal probability, the participant’s intention groups the strokes and thus perceives a ‘letter Gestalt’. We observed decoding accuracy of 35.81% (up to 65.83%) with a regularized linear discriminant analysis; on average 2.05-fold, and up to 3.77-fold greater than chance levels in multi-class classification. Compared to the EEG signals, an electrooculogram (EOG) did not significantly contribute to decoding accuracies. Further analysis reveals that the top-down SSVEP paradigm shows the most focalised activation pattern around occipital visual areas; Granger causality analysis consistently revealed prefrontal top-down control over early visual processing. Taken together, the present paradigm provides the first neurophysiological evidence for the top-down SSVEP BMI paradigm, which potentially enables multi-class intentional control of EEG-BMIs without using gaze-shifting.

Engineering the anthocyanin regulatory complex of strawberry (Fragaria vesca)

PubMed Central

Lin-Wang, Kui; McGhie, Tony K.; Wang, Mindy; Liu, Yuhui; Warren, Benjamin; Storey, Roy; Espley, Richard V.; Allan, Andrew C.

2014-01-01

The woodland strawberry, Fragaria vesca is a model fruit for a number of rosaceous crops. We have engineered altered concentrations of anthocyanin in F. vesca, to determine the impact on plant growth and fruit quality. Anthocyanin concentrations were significantly increased by over-expression or decreased by knock-down of the R2R3 MYB activator, MYB10. In contrast, a potential bHLH partner for MYB10 (bHLH33) did not affect the anthocyanin pathway when knocked down using RNAi constructs. Metabolic analysis of fruits revealed that, of all the polyphenolics surveyed, only cyanidin, and pelargonidin glucoside, and coumaryl hexose were significantly affected by over-expression and knock down of MYB10. Using the F. vesca genome sequence, members of the MYB, bHLH, and WD40 families were examined. Global analysis of gene expression and targeted qPCR analysis of biosynthetic genes and regulators confirmed the effects of altering MYB10 expression, as well as the knock-down of bHLH33. Other members of the MYB transcription factor family were affected by the transgenes. Transient expression of strawberry genes in Nicotiana benthamiana revealed that MYB10 can auto-regulate itself, and potential repressors of MYB10. In tobacco, MYB10's activation of biosynthetic steps is inhibited by the strawberry repressor MYB1. PMID:25477896

Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile

USGS Publications Warehouse

Neilson, Julia W.; Quade, Jay; Ortiz, Marianyoly; Nelson, William M.; Legatzki, Antje; Tian, Fei; LaComb, Michelle; Betancourt, Julio L.; Wing, Rod A.; Soderlund, Carol A.; Maier, Raina M.

2012-01-01

Nearly half the earth's surface is occupied by dryland ecosystems, regions susceptible to reduced states of biological productivity caused by climate fluctuations. Of these regions, arid zones located at the interface between vegetated semiarid regions and biologically unproductive hyperarid zones are considered most vulnerable. The objective of this study was to conduct a deep diversity analysis of bacterial communities in unvegetated arid soils of the Atacama Desert, to characterize community structure and infer the functional potential of these communities based on observed phylogenetic associations. A 454-pyrotag analysis was conducted of three unvegetated arid sites located at the hyperarid-arid margin. The analysis revealed communities with unique bacterial diversity marked by high abundances of novel Actinobacteria and Chloroflexi and low levels of Acidobacteria and Proteobacteria, phyla that are dominant in many biomes. A 16S rRNA gene library of one site revealed the presence of clones with phylogenetic associations to chemoautotrophic taxa able to obtain energy through oxidation of nitrite, carbon monoxide, iron, or sulfur. Thus, soils at the hyperarid margin were found to harbor a wealth of novel bacteria and to support potentially viable communities with phylogenetic associations to non-phototrophic primary producers and bacteria capable of biogeochemical cycling.

Hepatitis B among immigrants from Myanmar: Genotypes and their clinical relevance.

PubMed

Schulz, Thomas R; Edwards, Rosalind; Thurnheer, M Christine; Yuen, Lilly; Littlejohn, Margaret; Revill, Peter; Chu, Melissa; Tanyeri, Firuz; Wade, Amanda; Biggs, Beverley-Ann; Sasadeusz, Joseph

2018-02-01

Hepatitis B virus (HBV) from 76 adult immigrants in Australia from Myanmar was characterized to determine the prevalence of different HBV genotypes and subgenotypes. A mutational analysis was then performed to determine the presence of clinically significant mutations and correlate them to clinical outcomes. Initial genotyping revealed 68 patients with genotype C (89.5%) and eight patients with genotype B (10.5%). Phylogenetic analysis revealed the large majority of the genotype C infections were of subgenotype C1 (67/68). Sequencing of the HBV polymerase gene (and overlapping surface gene) revealed no mutations associated with antiviral resistance. HBV surface gene mutations were detected in 10 patients with subgenotype C1. HBV BCP/PC sequencing was obtained for 71/76 (93%) patients. BCP and/or PC mutations were identified in 57/71 (80%) of PCR positive patients. Treatment had been commenced for 15/76 (18%) patients, a further 26 untreated patients were in a stage of disease where HBV treatment would be considered standard of care. It was identified that genotype C1 is the predominant sub-genotype in this population. Genotype C is known to be associated with increased risk of development of HCC. This highlights the need for screening for HCC given the potential for the development of liver cancer. It was also identified that people with HBV were potentially not receiving optimal therapy in a timely fashion. © 2017 Wiley Periodicals, Inc.

Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus.

PubMed

Guan, Tian-Pei; Teng, Jade L L; Yeong, Kai-Yan; You, Zhang-Qiang; Liu, Hao; Wong, Samson S Y; Lau, Susanna K P; Woo, Patrick C Y

2018-06-07

The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials. Copyright © 2018 Elsevier Inc. All rights reserved.

The use of available potential energy to evaluate the impact of satellite data on numerical model analysis during FGGE

NASA Technical Reports Server (NTRS)

Horn, Lyle H.; Koehler, Thomas L.; Whittaker, Linda M.

1988-01-01

To evaluate the effect of the FGGE satellite observing system, the following two data sets were compared by examining the available potential energy (APE) and extratropical cyclone activity within the entire global domain during the first Special Observing Period: (1) the complete FGGE IIIb set, which incorporates satellite soundings, and (2) a NOSAT set which incorporates only conventional data. The time series of the daily total APEs indicate that NOSAT values are larger than the FGGE values, although in the Northern Hemisphere the differences are negligible. Analyses of cyclone scale features revealed only minor differences between the Northern Hemisphere FGGE and NOSAT analyses. On the other hand, substantial differences were revealed in the two Southern Hemisphere analyses, where the satellite soundings apparently add detail to the FGGE set.

Computer based imaging and analysis of root gravitropism

NASA Technical Reports Server (NTRS)

Evans, M. L.; Ishikawa, H.

1997-01-01

Two key issues in studies of the nature of the gravitropic response in roots have been the determination of the precise pattern of differential elongation responsible for downward bending and the identification of the cells that show the initial motor response. The main approach for examining patterns of differential growth during root gravitropic curvature has been to apply markers to the root surface and photograph the root at regular intervals during gravitropic curvature. Although these studies have provided valuable information on the characteristics of the gravitropic motor response in roots, their labor intensive nature limits sample size and discourages both high frequency of sampling and depth of analysis of surface expansion data. In this brief review we describe the development of computer-based video analysis systems for automated measurement of root growth and shape change and discuss some key features of the root gravitropic response that have been revealed using this methodology. We summarize the capabilities of several new pieces of software designed to measure growth and shape changes in graviresponding roots and describe recent progress in developing analysis systems for studying the small, but experimentally popular, primary roots of Arabidopsis. A key finding revealed by such studies is that the initial gravitropic response of roots of maize and Arabidopsis occurs in the distal elongation zone (DEZ) near the root apical meristem, not in the main elongation zone. Another finding is that the initiation of rapid elongation in the DEZ following gravistimulation appears to be related to rapid membrane potential changes in this region of the root. These observations have provided the incentive for ongoing studies examining possible links between potential growth modifying factors (auxin, calcium, protons) and gravistimulated changes in membrane potential and growth patterns in the DEZ.

Genome-wide screening and identification of long noncoding RNAs and their interaction with protein coding RNAs in bladder urothelial cell carcinoma.

PubMed

Wang, Longxin; Fu, Dian; Qiu, Yongbin; Xing, Xiaoxiao; Xu, Feng; Han, Conghui; Xu, Xiaofeng; Wei, Zhifeng; Zhang, Zhengyu; Ge, Jingping; Cheng, Wen; Xie, Hai-Long

2014-07-10

To understand lncRNAs expression profiling and their potential functions in bladder cancer, we investigated the lncRNA and coding RNA expression on human bladder cancer and normal bladder tissues. Bioinformatic analysis revealed thousands of significantly differentially expressed lncRNAs and coding mRNA in bladder cancer relative to normal bladder tissue. Co-expression analysis revealed that 50% of lncRNAs and coding RNAs expressed in the same direction. A subset of lncRNAs might be involved in mTOR signaling, p53 signaling, cancer pathways. Our study provides a large scale of co-expression between lncRNA and coding RNAs in bladder cancer cells and lays biological basis for further investigation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

PubMed

Shah, Anup D; Inder, Kerry L; Shah, Alok K; Cristino, Alexandre S; McKie, Arthur B; Gabra, Hani; Davis, Melissa J; Hill, Michelle M

2016-10-07

Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

Quantitative analysis of single-molecule superresolution images

PubMed Central

Coltharp, Carla; Yang, Xinxing; Xiao, Jie

2014-01-01

This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10 – 50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images. PMID:25179006

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

PubMed

Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

2016-02-25

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. Copyright © 2016 Mehetre et al.

"Are You a Computer?" Opening Exchanges in Virtual Reference Shape the Potential for Teaching

ERIC Educational Resources Information Center

Dempsey, Paula R.

2016-01-01

Academic reference librarians frequently work with students who are not aware of their professional roles. In online interactions, a student might not even realize that the librarian is a person. The ways students initiate conversations reveal their understanding of the mutual roles involved in reference encounters. Conversation analysis of live…

Rooftop Solar Technical Potential for Low-to-Moderate Income Households in

Science.gov Websites

communities. A map of the United States, divided by county, is color-coded by the total solar technical of LMI households in the U.S. (approximately 43 percent), this analysis reveals two other important city governments, though to do so requires deployment on multi-family and renter-occupied buildings

Some newer marker phytoconstituents in methanolic extract of Moringa oleifera leaves and evaluation of its immunomodulatory and splenocytes proliferation potential in rats

PubMed Central

Jayanthi, M.; Garg, Satish K.; Yadav, Prashant; Bhatia, A. K.; Goel, Anjana

2015-01-01

Objectives: The present study was undertaken to unravel the newer marker phytoconstituents in methanolic extract of Moringa oleifera leaves (MOLE) and evaluation of its immunomodulatory and splenocytes proliferation potential in rats. Materials and Methods: Hot methanolic extract of MOLE was subjected to gas chromatography-mass spectrometry (GC-MS) analysis. Immunomodulatory potential was studied in four groups of rats following administration of MOLE at 62.5 and 125 mg/kg for 21 days, followed by immunization with Salmonella typhimurium “O” antigen and antibody titer determined using indirect enzyme-linked immunosorbent assay kit. Total lymphocytes and T- and B-lymphocytes count were determined in control and after MOLE administration (62.5 and 125 mg/kg) to rats for 42 days. Splenocytes (2 × 106 spleen cells/ml) from MOLE treated rats were harvested and stimulated using concanavalin A and optical density (OD) and stimulation index were determined. Splenocytes from healthy control rats were also collected and treated in vitro with different concentrations of MOLE (5, 10, 25, 50, and 100 µg/ml) and concanavalin A to determine effect of MOLE on OD and stimulation index. Results: GC-MS analysis revealed presence of 9,12,15-octadecatrienoic acid ethyl ester, 6-octadecenoic acid, cis-vaccenic acid and 2-octyl-cyclopropaneoctanal in MOLE. MOLE at 125 mg/kg increased the antibody titer by 50%. Although there was slight decline in lymphocytes count (total, B- and T-lymphocytes) in MOLE treated rats, percentage of T-lymphocytes was increased nonsignificantly. Ex vivo and in vitro studies revealed marked increase in OD and stimulation index indicating MOLE-induced splenocytes proliferation. Conclusion: GC-MS study revealed four new compounds in MOLE apart from promising its immunomodulatory potential based on humoral immune response, percentage increase in T-lymphocytes count, and induction of splenocytes proliferation. PMID:26600641

Attenuation of MUC4 potentiates the anticancer activity of auranofin via regulation of the Her2/Akt/FOXO3 pathway in ovarian cancer cells.

PubMed

Bae, Jun Sang; Lee, Jongsung; Park, Yoonkook; Park, Kyungmoon; Kim, Jung Ryul; Cho, Dong Hyu; Jang, Kyu Yun; Park, See-Hyoung

2017-10-01

Previously, we reported that auranofin induces apoptosis in SKOV3 cells via regulation of the IKKβ/FOXO3 pathway. In the present study, we reveal that the anticancer activity of auranofin in SKOV3 cells could be enhanced by the attenuation of MUC4 through the regulation of the Her2/Akt/FOXO3 pathway. Compared to the control-siRNA, siRNA transfection against MUC4 into SKOV3 cells accelerated the protein degradation of Her2. Under the same conditions, the expression level of phosphorylated Akt was also downregulated leading to an increase of FOXO3 in the nucleus. Notably, auranofin treatment in SKOV3 cells also resulted in the downregulation of the expression levels of both Her2 and phosphorylated Akt. Thus, Her2 was identified as the common molecular target protein by siRNA transfection against MUC4. Western blot analysis of total and nuclear fraction lysates from SKOV3 cells revealed that attenuation of MUC4 combined with auranofin treatment in SKOV3 cells synergistically activated FOXO3 translocation from the cytoplasm to the nucleus through the regulation of the Her2/Akt/FOXO3 pathway. Attenuation of MUC4 by siRNA transfection potentiated the antitumor effect of auranofin which was examined by performing in vitro assays such as WST-1, cell counting, colony formation, TUNEL and Annexin V staining. In addition, western blot analysis of the apoptosis‑related proteins such as PARP1, caspase-3, Bim extra large (EL), Bax and Bcl2 revealed that the attenuation of MUC4 by siRNA transfection potentiates the pro-apoptotic activity of auranofin in SKOV3 cells. Collectively, auranofin could regulate the Her2/Akt/FOXO3 signaling pathway in SKOV3 cells and be used as a potential antitumor agent considering the expression of MUC4 in ovarian cancer patients.

Dent and Flint maize diversity panels reveal important genetic potential for increasing biomass production.

PubMed

Rincent, R; Nicolas, S; Bouchet, S; Altmann, T; Brunel, D; Revilla, P; Malvar, R A; Moreno-Gonzalez, J; Campo, L; Melchinger, A E; Schipprack, W; Bauer, E; Schoen, C-C; Meyer, N; Ouzunova, M; Dubreuil, P; Giauffret, C; Madur, D; Combes, V; Dumas, F; Bauland, C; Jamin, P; Laborde, J; Flament, P; Moreau, L; Charcosset, A

2014-11-01

Genetic and phenotypic analysis of two complementary maize panels revealed an important variation for biomass yield. Flowering and biomass QTL were discovered by association mapping in both panels. The high whole plant biomass productivity of maize makes it a potential source of energy in animal feeding and biofuel production. The variability and the genetic determinism of traits related to biomass are poorly known. We analyzed two highly diverse panels of Dent and Flint lines representing complementary heterotic groups for Northern Europe. They were genotyped with the 50 k SNP-array and phenotyped as hybrids (crossed to a tester of the complementary pool) in a western European field trial network for traits related to flowering time, plant height, and biomass. The molecular information revealed to be a powerful tool for discovering different levels of structure and relatedness in both panels. This study revealed important variation and potential genetic progress for biomass production, even at constant precocity. Association mapping was run by combining genotypes and phenotypes in a mixed model with a random polygenic effect. This permitted the detection of significant associations, confirming height and flowering time quantitative trait loci (QTL) found in literature. Biomass yield QTL were detected in both panels but were unstable across the environments. Alternative kinship estimator only based on markers unlinked to the tested SNP increased the number of significant associations by around 40% with a satisfying control of the false positive rate. This study gave insights into the variability and the genetic architectures of biomass-related traits in Flint and Dent lines and suggests important potential of these two pools for breeding high biomass yielding hybrid varieties.

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

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

Raveh-Sadka, Tali; Thomas, Brian C.; Singh, Andrea

Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. Thus, spread of potential pathogens among hospitalized infants is of great concern. Here, we reconstructed hundreds of high-quality genomes of microorganisms that colonized co-hospitalized premature infants, assessed their metabolic potential, and tracked them over time to evaluate bacterial strain dispersal among infants. We compared microbial communities in infants who did and did not develop necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, our genome-resolved analysis revealed that strains colonizing each baby were typically distinct.more » In particular, no strain was common to all infants who developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to the spread of bacteria among infants. Furthermore, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.« less

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

DOE PAGES

Raveh-Sadka, Tali; Thomas, Brian C.; Singh, Andrea; ...

2015-03-03

Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. Thus, spread of potential pathogens among hospitalized infants is of great concern. Here, we reconstructed hundreds of high-quality genomes of microorganisms that colonized co-hospitalized premature infants, assessed their metabolic potential, and tracked them over time to evaluate bacterial strain dispersal among infants. We compared microbial communities in infants who did and did not develop necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, our genome-resolved analysis revealed that strains colonizing each baby were typically distinct.more » In particular, no strain was common to all infants who developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to the spread of bacteria among infants. Furthermore, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.« less

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

PubMed Central

Raveh-Sadka, Tali; Thomas, Brian C; Singh, Andrea; Firek, Brian; Brooks, Brandon; Castelle, Cindy J; Sharon, Itai; Baker, Robyn; Good, Misty; Morowitz, Michael J; Banfield, Jillian F

2015-01-01

Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. Thus, spread of potential pathogens among hospitalized infants is of great concern. Here, we reconstructed hundreds of high-quality genomes of microorganisms that colonized co-hospitalized premature infants, assessed their metabolic potential, and tracked them over time to evaluate bacterial strain dispersal among infants. We compared microbial communities in infants who did and did not develop necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, our genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants who developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to the spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales. DOI: http://dx.doi.org/10.7554/eLife.05477.001 PMID:25735037

Re-sequencing regions of the ovine Y chromosome in domestic and wild sheep reveals novel paternal haplotypes.

PubMed

Meadows, J R S; Kijas, J W

2009-02-01

The male-specific region of the ovine Y chromosome (MSY) remains poorly characterized, yet sequence variants from this region have the potential to reveal the wild progenitor of domestic sheep or examples of domestic and wild paternal introgression. The 5' promoter region of the sex-determining gene SRY was re-sequenced using a subset of wild sheep including bighorn (Ovis canadensis), thinhorn (Ovis dalli spp.), urial (Ovis vignei), argali (Ovis ammon), mouflon (Ovis musimon) and domestic sheep (Ovis aries). Seven novel SNPs (oY2-oY8) were revealed; these were polymorphic between but not within species. Re-sequencing and fragment analysis was applied to the MSY microsatellite SRYM18. It contains a complex compound repeat structure and sequencing of three novel size fragments revealed that a pentanucleotide element remained fixed, whilst a dinucleotide element displayed variability within species. Comparison of the sequence between species revealed that urial and argali sheep grouped more closely to the mouflon and domestic breeds than the pachyceriforms (bighorn and thinhorn). SNP and microsatellite data were combined to define six previously undetected haplotypes. Analysis revealed the mouflon as the only species to share a haplotype with domestic sheep, consistent with its status as a feral domesticate that has undergone male-mediated exchange with domestic animals. A comparison of the remaining wild species and domestic sheep revealed that O. aries is free from signatures of wild sheep introgression.

Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates.

PubMed

Hanafy, Radwa A; Couger, M B; Baker, Kristina; Murphy, Chelsea; O'Kane, Shannon D; Budd, Connie; French, Donald P; Hoff, Wouter D; Youssef, Noha

2016-09-01

Micrococcus luteus is a predominant member of skin microbiome. We here report on the genomic analysis of Micrococcus luteus strain O'Kane that was isolated from an elevator. The partial genome assembly of Micrococcus luteus strain O'Kane is 2.5 Mb with 2256 protein-coding genes and 62 RNA genes. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of glucose, galactose, fructose, mannose, alanine, aspartate, asparagine, glutamate, glutamine, glycine, serine, cysteine, methionine, arginine, proline, histidine, phenylalanine, and fatty acids. Genomic comparison to other M. luteus representatives identified the potential to degrade polyhydroxybutyrates, as well as several antibiotic resistance genes absent from other genomes.

Cost-benefit analysis and emission reduction of energy efficient lighting at the Universiti Tenaga Nasional.

PubMed

Ganandran, G S B; Mahlia, T M I; Ong, Hwai Chyuan; Rismanchi, B; Chong, W T

2014-01-01

This paper reports the result of an investigation on the potential energy saving of the lighting systems at selected buildings of the Universiti Tenaga Nasional. The scope of this project includes evaluation of the lighting system in the Library, Admin Building, College of Engineering, College of Information Technology, Apartments, and COE Food court of the university. The main objectives of this project are to design the proper retrofit scenario and to calculate the potential electricity saving, the payback period, and the potential environmental benefits. In this survey the policy for retrofitting the old lighting system with the new energy saving LEDs starts with 10% for the first year and continues constantly for 10 years until all the lighting systems have been replaced. The result of the life cycle analysis reveals that after four years, the selected buildings will bring profit for the investment.

Cost-Benefit Analysis and Emission Reduction of Energy Efficient Lighting at the Universiti Tenaga Nasional

PubMed Central

Ganandran, G. S. B.; Mahlia, T. M. I.; Ong, Hwai Chyuan; Rismanchi, B.; Chong, W. T.

2014-01-01

This paper reports the result of an investigation on the potential energy saving of the lighting systems at selected buildings of the Universiti Tenaga Nasional. The scope of this project includes evaluation of the lighting system in the Library, Admin Building, College of Engineering, College of Information Technology, Apartments, and COE Food court of the university. The main objectives of this project are to design the proper retrofit scenario and to calculate the potential electricity saving, the payback period, and the potential environmental benefits. In this survey the policy for retrofitting the old lighting system with the new energy saving LEDs starts with 10% for the first year and continues constantly for 10 years until all the lighting systems have been replaced. The result of the life cycle analysis reveals that after four years, the selected buildings will bring profit for the investment. PMID:25133258

Informed choice in direct-to-consumer genetic testing (DTCGT) websites: a content analysis of benefits, risks, and limitations.

PubMed

Singleton, Amanda; Erby, Lori Hamby; Foisie, Kathryn V; Kaphingst, Kimberly A

2012-06-01

An informed choice about health-related direct-to-consumer genetic testing (DTCGT) requires knowledge of potential benefits, risks, and limitations. To understand the information that potential consumers of DTCGT services are exposed to on company websites, we conducted a content analysis of 23 health-related DTCGT websites. Results revealed that benefit statements outweighed risk and limitation statements 6 to 1. The most frequently described benefits were: 1) disease prevention, 2) consumer education, 3) personalized medical recommendations, and 4) the ability to make health decisions. Thirty-five percent of websites also presented at least one risk of testing. Seventy-eight percent of websites mentioned at least one limitation of testing. Based on this information, potential consumers might get an inaccurate picture of genetic testing which could impact their ability to make an informed decision. Practices that enhance the presentation of balanced information on DTCGT company websites should be encouraged.

Chemical potential shift in organic field-effect transistors identified by soft X-ray operando nano-spectroscopy

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

Nagamura, Naoka, E-mail: NAGAMURA.Naoka@nims.go.jp; Kitada, Yuta; Honma, Itaru

2015-06-22

A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO{sub 2} (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift correspondingmore » to band bending by the field effect, resulting in p-type doping.« less

Selective depression of titanaugite in the ilmenite flotation with carboxymethyl starch

NASA Astrophysics Data System (ADS)

Meng, Qingyou; Yuan, Zhitao; Yu, Li; Xu, Yuankai; Du, Yusheng; Zhang, Chen

2018-05-01

In order to intensify the flotation separation of ilmenite from titanaugite, surface modification of mineral particles was carried out using carboxymethyl starch (CMS) by microflotation experiments, zeta potential measurements, Fourier transform infrared (FTIR) and atomic force microscopy (AFM) analysis. Microflotation results showed that CMS was a selective depressant, and it effectively enhanced the floatability difference between ilmenite and titanaugite in the pH range from 6.0 to 10.0. As it was revealed by the zeta potential, FTIR and AFM analysis, the CMS adsorption occurred onto mineral surfaces through chemisorption and hydrogen bonding, while CMS exhibited a stronger interaction with titanaugite than ilmenite. After that, the CMS adsorption impeded the adsorption of sodium oleate collector on titanaugite surfaces, giving rise to a concomitant decrease in the floatability of titanaugite. These findings exhibit great potential for CMS application in the selective flotation of ilmenite.

Memristive Model of the Barnacle Giant Muscle Fibers

NASA Astrophysics Data System (ADS)

Sah, Maheshwar Pd.; Kim, Hyongsuk; Eroglu, Abdullah; Chua, Leon

The generation of action potentials (oscillations) in biological systems is a complex, yet poorly understood nonlinear dynamical phenomenon involving ions. This paper reveals that the time-varying calcium ion and the time-varying potassium ion, which are essential for generating action potentials in Barnacle giant muscle fibers are in fact generic memristors in the perspective of electrical circuit theory. We will show that these two ions exhibit all the fingerprints of memristors from the equations of the Morris-Lecar model of the Barnacle giant muscle fibers. This paper also gives a textbook reference to understand the difference between memristor and nonlinear resistor via analysis of the potassium ion-channel memristor and calcium ion-channel nonlinear resistor. We will also present a comprehensive in-depth analysis of the generation of action potentials (oscillations) in memristive Morris-Lecar model using small-signal circuit model and the Hopf bifurcation theorem.

Structural, functional and pH sensitive release characteristics of water-soluble polysaccharide from the seeds of Albizia lebbeck L.

PubMed

Kumar Varma, Chekuri Ashok; Jayaram Kumar, K

2017-11-01

Plant polysaccharides, generally regarded as safe (GRAS), are gaining importance as excipients in drug delivery. Therefore, the current paper presents the studies on structural, functional and drug release study of water soluble polysaccharide (ALPS) from seeds of Albizia lebbeck L. High swelling, water holding capacity, foam stability and lower moisture content suggests its use as additive in food preparations. The apparent molecular weight of polysaccharide was found to be 1.98×10 2 kDa. Monosaccharide composition analysis indicated that ALPS consists of mannose (4.06%), rhamnose (22.79%), glucose (38.9%), galactose (17.84%) and xylose (16.42%). Micromeritic properties revealed that the polysaccharide possess potential for pharmaceutical applications. From the surface charge analysis, ALPS was found to be non-ionic polysaccharide. Morphological study reveals the polysaccharide with irregular particle shape and rough surface. Fourier transformed infrared spectroscopy (FTIR) study confirms the carbohydrate nature of polysaccharide. From the thermogravimetric analysis (TGA) data, the second mass loss (243-340°C) attributed to polysaccharide degradation. The drug release profile reveals the use of polysaccharide for the preparation of pH sensitive pharmaceutical dosage forms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

PubMed Central

Trojan, Daniela; Roux, Simon; Herbold, Craig; Rattei, Thomas; Woebken, Dagmar

2018-01-01

Summary Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large‐scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low‐ and high‐affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2, now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large‐scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment. PMID:29327410

Metagenomic analysis of bat guano samples revealed the presence of viruses potentially carried by insects, among others by Apis mellifera in Hungary.

PubMed

Zana, Brigitta; Kemenesi, Gábor; Urbán, Péter; Földes, Fanni; Görföl, Tamás; Estók, Péter; Boldogh, Sándor; Kurucz, Kornélia; Jakab, Ferenc

2018-03-01

The predominance of dietary viruses in bat guano samples had been described recently, suggesting a new opportunity to survey the prevalence and to detect new viruses of arthropods or even plant-infecting viruses circulating locally in the ecosystem. Here we describe the diversity of viruses belonging to the order Picornavirales in Hungarian insectivorous bat guano samples. The metagenomic analysis conducted on our samples has revealed the significant predominance of aphid lethal paralysis virus (ALPV) and Big Sioux River virus (BSRV) in Hungary for the first time. Phylogenetic analysis was used to clarify the relationship to previously identified ALPV strains infecting honey bees, showing that our strain possesses a close genetic relationship with the strains that have already been described as pathogenic to honey bees. Furthermore, studies have previously confirmed the ability of these viruses to replicate in adult honey bees; however, no signs related to these viruses have been revealed yet. With the identification of two recently described possibly honey bee infecting viruses for the first time in Hungary, our results might have importance for the health conditions of Hungarian honey bee colonies in the future.

The suitability of silicon carbide for photocatalytic water oxidation

NASA Astrophysics Data System (ADS)

Aslam, M.; Qamar, M. T.; Ahmed, Ikram; Rehman, Ateeq Ur; Ali, Shahid; Ismail, I. M. I.; Hameed, Abdul

2018-04-01

Silicon carbide (SiC), owing to its extraordinary chemical stability and refractory properties, is widely used in the manufacturing industry. Despite the semiconducting nature and morphology-tuned band gap, its efficacy as photocatalysts has not been thoroughly investigated. The current study reports the synthesis, characterization and the evaluation of the capability of silicon carbide for hydrogen generation from water splitting. The optical characterization of the as-synthesized powder exposed the formation of multi-wavelength absorbing entities in synthetic process. The structural analysis by XRD and the fine microstructure analysis by HRTEM revealed the cubic 3C-SiC (β-SiC) and hexagonal α-polymorphs (2H-SiC and 6H-SiC) as major and minor phases, respectively. The Mott-Schottky analysis verified the n-type nature of the material with the flat band potential of - 0.7 V. In the electrochemical evaluation, the sharp increase in the peak currents in various potential ranges, under illumination, revealed the plausible potential of the material for the oxidation of water and generation of hydrogen. The generation of hydrogen and oxygen, as a consequence of water splitting in the actual photocatalytic experiments, was observed and measured. A significant increase in the yield of hydrogen was noticed in the presence of methanol as h + scavenger, whereas a retarding effect was offered by the Fe3+ entities that served as e - scavengers. The combined effect of both methanol and Fe3+ ions in the photocatalytic process was also investigated. Besides hydrogen gas, the other evolved gasses such as methane and carbon monoxide were also measured to estimate the mechanism of the process.

Piloting the membranolytic activities of peptides with a self-organizing map.

PubMed

Lin, Yen-Chu; Hiss, Jan A; Schneider, Petra; Thelesklaf, Peter; Lim, Yi Fan; Pillong, Max; Koehler, Fabian M; Dittrich, Petra S; Halin, Cornelia; Wessler, Silja; Schneider, Gisbert

2014-10-13

Antimicrobial peptides (AMPs) show remarkable selectivity toward lipid membranes and possess promising antibiotic potential. Their modes of action are diverse and not fully understood, and innovative peptide design strategies are needed to generate AMPs with improved properties. We present a de novo peptide design approach that resulted in new AMPs possessing low-nanomolar membranolytic activities. Thermal analysis revealed an entropy-driven mechanism of action. The study demonstrates sustained potential of advanced computational methods for designing peptides with the desired activity. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Network Analysis Reveals the Recognition Mechanism for Mannose-binding Lectins

NASA Astrophysics Data System (ADS)

Zhao, Yunjie; Jian, Yiren; Zeng, Chen; Computational Biophysics Lab Team

The specific carbohydrate binding of mannose-binding lectin (MBL) protein in plants makes it a very useful molecular tool for cancer cell detection and other applications. The biological states of most MBL proteins are dimeric. Using dynamics network analysis on molecular dynamics (MD) simulations on the model protein of MBL, we elucidate the short- and long-range driving forces behind the dimer formation. The results are further supported by sequence coevolution analysis. We propose a general framework for deciphering the recognition mechanism underlying protein-protein interactions that may have potential applications in signaling pathways.

NREL Reveals Potential for Capturing Waste Heat via Nanotubes | News | NREL

Science.gov Websites

Reveals Potential for Capturing Waste Heat via Nanotubes News Release: NREL Reveals Potential for Capturing Waste Heat via Nanotubes April 4, 2016 A finely tuned carbon nanotube thin film has the potential to act as a thermoelectric power generator that captures and uses waste heat, according to

Central Atlantic regional ecological test site: A prototype regional environmental information system

NASA Technical Reports Server (NTRS)

Alexander, R. H. (Principal Investigator)

1973-01-01

The author has identified the following significant results. A comparison of photomorphic regions from an uncontrolled ERTS-1 mosaic of CARETS to land use areas on a map published in the National Atlas revealed close correlations in non-urban regions. Such regional scale analysis of ERTS-1 data has the potential for providing an economical sampling strategy for selecting sites for more detailed field measurements if other environmental variables can be correlated with patterns on ERTS-1 imagery. ERTS-1 imagery has also revealed for the first time the appearance of CARETS during the winter months. Investigators have identified extensive areas of conifers, which have previously been indistinguishable from deciduous vegetation. Imagery has also shown very clearly the extent of snow cover at a particular time over the region. The evaluation of ERTS-1 imagery used for the land use mapping of the shore zone of CARETS, has shown that the presence or absence of elements of an hierarchal system of shoreline landforms can help identify areas of potential rapid change. Changes in land use class distributions on the Barrier Islands signify the environmental response to natural and man-caused processes. Both environmental vulnerability and sensitivity can be estimated from the repetitive ERTS-1 coverage of long reaches of the CARETS coast. Results indicate potential applications to land use planning, management, and regional environmental quality analysis.

Analysis of Complete Genomes of Propionibacterium acnes Reveals a Novel Plasmid and Increased Pseudogenes in an Acne Associated Strain

PubMed Central

Fitz-Gibbon, Sorel; Tomida, Shuta; Li, Huiying

2013-01-01

The human skin harbors a diverse community of bacteria, including the Gram-positive, anaerobic bacterium Propionibacterium acnes. P. acnes has historically been linked to the pathogenesis of acne vulgaris, a common skin disease affecting over 80% of all adolescents in the US. To gain insight into potential P. acnes pathogenic mechanisms, we previously sequenced the complete genome of a P. acnes strain HL096PA1 that is highly associated with acne. In this study, we compared its genome to the first published complete genome KPA171202. HL096PA1 harbors a linear plasmid, pIMPLE-HL096PA1. This is the first described P. acnes plasmid. We also observed a five-fold increase of pseudogenes in HL096PA1, several of which encode proteins in carbohydrate transport and metabolism. In addition, our analysis revealed a few island-like genomic regions that are unique to HL096PA1 and a large genomic inversion spanning the ribosomal operons. Together, these findings offer a basis for understanding P. acnes virulent properties, host adaptation mechanisms, and its potential role in acne pathogenesis at the strain level. Furthermore, the plasmid identified in HL096PA1 may potentially provide a new opportunity for P. acnes genetic manipulation and targeted therapy against specific disease-associated strains. PMID:23762865

The tryptophan-derived endogenous arylhydrocarbon receptor ligand 6-formylindolo[3,2-b]carbazole (FICZ) is a nanomolar UVA-photosensitizer in epidermal keratinocytes

PubMed Central

Williams, Joshua D.; Cabello, Christopher M.; Qiao, Shuxi; Wondrak, Georg T.

2014-01-01

Endogenous UVA-chromophores may act as sensitizers of oxidative stress underlying cutaneous photoaging and photocarcinogenesis, but the molecular identity of non-DNA key chromophores displaying UVA-driven photodyamic activity in human skin remains largely undefined. Here we report that 6-formylindolo[3,2-b]carbazole (FICZ), a tryptophan photoproduct and endogenous high affinity aryl hydrocarbon receptor (AhR) agonist, acts as a nanomolar photosensitizer potentiating UVA-induced oxidative stress irrespective of AhR ligand activity. In human HaCaT and primary epidermal keratinocytes, photodynamic induction of apoptosis was elicited by the combined action of solar simulated UVA and FICZ, whereas exposure to the isolated action of UVA or FICZ did not impair viability. In a human epidermal tissue reconstruct, FICZ/UVA-cotreatment caused pronounced phototoxicity inducing keratinocyte cell death, and FICZ photodynamic activity was also substantiated in a murine skin exposure model. Array analysis revealed pronounced potentiation of cellular heat shock, ER stress, and oxidative stress response gene expression observed only upon FICZ/UVA-cotreatment. FICZ photosensitization caused intracellular oxidative stress, and comet analysis revealed introduction of formamidopyrimidine-DNA glycosylase (FPG)-sensitive oxidative DNA lesions suppressible by antioxidant cotreatment. Taken together, our data demonstrate that the endogenous AhR ligand FICZ displays nanomolar photodynamic activity representing a molecular mechanism of UVA-induced photooxidative stress potentially operative in human skin. PMID:25431849

Mathematical Modeling of Herpes Simplex Virus Distribution in Solid Tumors: Implications for Cancer Gene Therapy

PubMed Central

Mok, Wilson; Stylianopoulos, Triantafyllos; Boucher, Yves; Jain, Rakesh K.

2010-01-01

Purpose Although oncolytic viral vectors show promise for the treatment of various cancers, ineffective initial distribution and propagation throughout the tumor mass often limit the therapeutic response. A mathematical model is developed to describe the spread of herpes simplex virus from the initial injection site. Experimental Design The tumor is modeled as a sphere of radius R. The model incorporates reversible binding, interstitial diffusion, viral degradation, and internalization and physiologic parameters. Three species are considered as follows: free interstitial virus, virus bound to cell surfaces, and internalized virus. Results This analysis reveals that both rapid binding and internalization as well as hindered diffusion contain the virus to the initial injection volume, with negligible spread to the surrounding tissue. Unfortunately, increasing the dose to saturate receptors and promote diffusion throughout the tumor is not a viable option: the concentration necessary would likely compromise safety. However, targeted modifications to the virus that decrease the binding affinity have the potential to increase the number of infected cells by 1.5-fold or more. An increase in the effective diffusion coefficient can result in similar gains. Conclusions This analysis suggests criteria by which the potential response of a tumor to oncolytic herpes simplex virus therapy can be assessed. Furthermore, it reveals the potential of modifications to the vector delivery method, physicochemical properties of the virus, and tumor extracellular matrix composition to enhance efficacy. PMID:19318482

Stochastic resonance energy harvesting for a rotating shaft subject to random and periodic vibrations: influence of potential function asymmetry and frequency sweep

NASA Astrophysics Data System (ADS)

Kim, Hongjip; Che Tai, Wei; Zhou, Shengxi; Zuo, Lei

2017-11-01

Stochastic resonance is referred to as a physical phenomenon that is manifest in nonlinear systems whereby a weak periodic signal can be significantly amplified with the aid of inherent noise or vice versa. In this paper, stochastic resonance is considered to harvest energy from two typical vibrations in rotating shafts: random whirl vibration and periodic stick-slip vibration. Stick-slip vibrations impose a constant offset in centrifugal force and distort the potential function of the harvester, leading to potential function asymmetry. A numerical analysis based on a finite element method was conducted to investigate stochastic resonance with potential function asymmetry. Simulation results revealed that a harvester with symmetric potential function generates seven times higher power than that with asymmetric potential function. Furthermore, a frequency-sweep analysis also showed that stochastic resonance has hysteretic behavior, resulting in frequency difference between up-sweep and down-sweep excitations. An electromagnetic energy harvesting system was constructed to experimentally verify the numerical analysis. In contrast to traditional stochastic resonance harvesters, the proposed harvester uses magnetic force to compensate the offset in the centrifugal force. System identification was performed to obtain the parameters needed in the numerical analysis. With the identified parameters, the numerical simulations showed good agreement with the experiment results with around 10% error, which verified the effect of potential function asymmetry and frequency sweep excitation condition on stochastic resonance. Finally, attributed to compensating the centrifugal force offset, the proposed harvester generated nearly three times more open-circuit output voltage than its traditional counterpart.

A proteomic analysis identifies candidate early biomarkers to predict ovarian hyperstimulation syndrome in polycystic ovarian syndrome patients.

PubMed

Wu, Lan; Sun, Yazhou; Wan, Jun; Luan, Ting; Cheng, Qing; Tan, Yong

2017-07-01

Ovarian hyperstimulation syndrome (OHSS) is a potentially life‑threatening, iatrogenic complication that occurs during assisted reproduction. Polycystic ovarian syndrome (PCOS) significantly increases the risk of OHSS during controlled ovarian stimulation. Therefore, a more effective early prediction technique is required in PCOS patients. Quantitative proteomic analysis of serum proteins indicates the potential diagnostic value for disease. In the present study, the authors revealed the differentially expressed proteins in OHSS patients with PCOS as new diagnostic biomarkers. The promising proteins obtained from liquid chromatography‑mass spectrometry were subjected to ELISA and western blotting assay for further confirmation. A total of 57 proteins were identified with significant difference, of which 29 proteins were upregulated and 28 proteins were downregulated in OHSS patients. Haptoglobin, fibrinogen and lipoprotein lipase were selected as candidate biomarkers. Receiver operating characteristic curve analysis demonstrated all three proteins may have potential as biomarkers to discriminate OHSS in PCOS patients. Haptoglobin, fibrinogen and lipoprotein lipase have never been reported as a predictive marker of OHSS in PCOS patients, and their potential roles in OHSS occurrence deserve further studies. The proteomic results reported in the present study may gain deeper insights into the pathophysiology of OHSS.

Determinants of marriage dissolution

NASA Astrophysics Data System (ADS)

Rahim, Mohd Amirul Rafiq Abu; Shafie, Siti Aishah Mohd; Hadi, Az'lina Abdul; Razali, Nornadiah Mohd; Azid @ Maarof, Nur Niswah Naslina

2015-10-01

Nowadays, the number of divorce cases among Muslim couples is very worrisome whereby the total cases reported in 2013 increased by half of the total cases reported in the previous year. The questions on the true key factors of dissolution of marriage continue to arise. Thus, the objective of this study is to reveal the factors that contribute to the dissolution of marriage. A total of 181 cases and ten potential determinants were included in this study. The potential determinants considered were age at marriage of husband and wife, educational level of husband and wife, employment status of husband and wife, income of husband and wife, the number of children and the presence at a counseling session. Logistic regression analysis was used to analyze the data. The findings revealed that four determinants, namely the income of husband and wife, number of children and the presence at a counselling session were significant in predicting the likelihood of divorce among Muslim couples.

A potential target for organophosphate insecticides leading to spermatotoxicity.

PubMed

Suzuki, Himiko; Tomizawa, Motohiro; Ito, Yuki; Abe, Keisuke; Noro, Yuki; Kamijima, Michihiro

2013-10-16

Organophosphate (OP) insecticides as an anticholinesterase also act on the diverse serine hydrolase targets, thereby revealing secondary or unexpected toxic effects including male reproductive toxicity. The present investigation detects a possible target molecule(s) for OP-induced spermatotoxicity (sperm deformity, underdevelopment, and reduced motility) from a chemical standpoint. The activity-based protein profiling (ABPP) approach with a phosphonofluoridate fluorescent probe pinpointed the molecular target for fenitrothion (FNT, a major OP insecticide) oxon (bioactive metabolite of FNT) in the mouse testicular membrane proteome, i.e., FNT oxon phosphorylates the fatty acid amide hydrolase (FAAH), which plays pivotal roles in spermatogenesis and sperm motility acquirement. Subsequently, mice were treated orally with vehicle or FNT for 10 days, and FAAH activity in testis or epididymis cauda was markedly reduced by the subacute exposure. ABPP analysis revealed that FAAH was selectively inhibited among the FNT-treated testicular membrane proteome. Accordingly, FAAH is a potential target for OP-elicited spermatotoxicity.

Identification of volatile organic compounds in suburban Bangkok, Thailand and their potential for ozone formation

NASA Astrophysics Data System (ADS)

Suthawaree, Jeeranut; Tajima, Yosuke; Khunchornyakong, Alisa; Kato, Shungo; Sharp, Alice; Kajii, Yoshizumi

2012-02-01

Measurement of Volatile Organic Compound (VOC) was carried out in suburban Bangkok during July 2-8, 2008. Analysis was performed using GC-FID and GC-MS. High mixing ratios of VOCs detected during the morning and evening are most likely due to vehicular emissions. Averaged VOC mixing ratios revealed distinct difference between mixing ratios of weekdays and weekend, which the latter were found to be lower. The most abundance species were propane and toluene. Ratios of benzene over toluene suggested that additional toluene mixing ratios was owing to industrial emission, which was particularly larger during weekdays. Comparison between C2Cl4 and CH3Cl mixing ratios obtained for suburban Tokyo reveal a relatively lower influence of biomass burning than suburban Bangkok. Elucidating by Ozone Formation Potential, toluene was found to contribute the most to O3 production followed by ethylene, m-,p-xylene, and propylene.

Exome sequencing supports a de novo mutational paradigm for schizophrenia

PubMed Central

Xu, Bin; Roos, J. Louw; Dexheimer, Phillip; Boone, Braden; Plummer, Brooks; Levy, Shawn; Gogos, Joseph A.; Karayiorgou, Maria

2011-01-01

Despite high heritability, a large fraction of cases with schizophrenia do not have a family history of the disease (sporadic cases). Here, we examine the possibility that rare de novo protein-altering mutations contribute to the genetic component of schizophrenia by sequencing the exome of 53 sporadic cases, 22 unaffected controls and their parents. We identified 40 de novo mutations in 27 patients affecting 40 genes including a potentially disruptive mutation in DGCR2, a gene removed by the recurrent schizophrenia-predisposing 22q11.2 microdeletion. Comparison to rare inherited variants revealed that the identified de novo mutations show a large excess of nonsynonymous changes in cases, as well as a greater potential to affect protein structure and function. Our analysis reveals a major role of de novo mutations in schizophrenia and also a large mutational target, which together provide a plausible explanation for the high global incidence and persistence of the disease. PMID:21822266

Promoter analysis reveals cis-regulatory motifs associated with the expression of the WRKY transcription factor CrWRKY1 in Catharanthus roseus.

PubMed

Yang, Zhirong; Patra, Barunava; Li, Runzhi; Pattanaik, Sitakanta; Yuan, Ling

2013-12-01

WRKY transcription factors (TFs) are emerging as an important group of regulators of plant secondary metabolism. However, the cis-regulatory elements associated with their regulation have not been well characterized. We have previously demonstrated that CrWRKY1, a member of subgroup III of the WRKY TF family, regulates biosynthesis of terpenoid indole alkaloids in the ornamental and medicinal plant, Catharanthus roseus. Here, we report the isolation and functional characterization of the CrWRKY1 promoter. In silico analysis of the promoter sequence reveals the presence of several potential TF binding motifs, indicating the involvement of additional TFs in the regulation of the TIA pathway. The CrWRKY1 promoter can drive the expression of a β-glucuronidase (GUS) reporter gene in native (C. roseus protoplasts and transgenic hairy roots) and heterologous (transgenic tobacco seedlings) systems. Analysis of 5'- or 3'-end deletions indicates that the sequence located between positions -140 to -93 bp and -3 to +113 bp, relative to the transcription start site, is critical for promoter activity. Mutation analysis shows that two overlapping as-1 elements and a CT-rich motif contribute significantly to promoter activity. The CrWRKY1 promoter is induced in response to methyl jasmonate (MJ) treatment and the promoter region between -230 and -93 bp contains a putative MJ-responsive element. The CrWRKY1 promoter can potentially be used as a tool to isolate novel TFs involved in the regulation of the TIA pathway.

Meta-analyses of structural regional cerebral effects in type 1 and type 2 diabetes.

PubMed

Moulton, Calum D; Costafreda, Sergi G; Horton, Paul; Ismail, Khalida; Fu, Cynthia H Y

2015-12-01

Diabetes is associated with macrovascular and microvascular complications and is a major risk factor for neurological and psychiatric disorders, such as dementia and depression. Type 1 diabetes (T1DM) and type 2 diabetes (T2DM) have distinct etiologies and pathophysiological effects while sharing a common endpoint of persistent hyperglycemia. Neuroimaging studies in T1DM have revealed reductions in numerous regions, including the parahippocampal and occipital regions, while in T2DM there have been numerous reports of hippocampal atrophy. This meta-analysis aimed to identify consistent regional abnormalities in cerebral structures in T1DM and T2DM respectively, and also to examine the impact of potential confounds, including age, depression and vascular risk factors. Neuroimaging studies of both voxel-based morphometry (VBM) data and volumetric data were included. Ten T1DM studies (n = 613 patients) and 23 T2DM studies (n = 1364 patients) fulfilled inclusion criteria. The T1DM meta-analysis revealed reduced bilateral thalamus grey matter density in adults. The T2DM meta-analysis revealed reduced global brain volume and regional atrophy in the hippocampi, basal ganglia, and orbitofrontal and occipital lobes. Moreover, hippocampal atrophy in T2DM was not modified by hypertension, although there were more marked reductions in younger patients relative to healthy controls. In conclusion, T1DM and T2DM demonstrated distinct cerebral effects with generalised and specific target areas of grey matter reduction. Thalamic atrophy in T1DM may be a substrate of associated cognitive deficits. In T2DM, global cerebral atrophy may reflect atherosclerotic factors, while hippocampal atrophy was an independent effect providing a potential common neuropathological etiology for the comorbidity of T2DM with dementia and depression.

Surface chemistry of gold nanoparticles determines the biocorona composition impacting cellular uptake, toxicity and gene expression profiles in human endothelial cells.

PubMed

Chandran, Parwathy; Riviere, Jim E; Monteiro-Riviere, Nancy A

2017-05-01

This study investigated the role of nanoparticle size and surface chemistry on biocorona composition and its effect on uptake, toxicity and cellular responses in human umbilical vein endothelial cells (HUVEC), employing 40 and 80 nm gold nanoparticles (AuNP) with branched polyethyleneimine (BPEI), lipoic acid (LA) and polyethylene glycol (PEG) coatings. Proteomic analysis identified 59 hard corona proteins among the various AuNP, revealing largely surface chemistry-dependent signature adsorbomes exhibiting human serum albumin (HSA) abundance. Size distribution analysis revealed the relative instability and aggregation inducing potential of bare and corona-bound BPEI-AuNP, over LA- and PEG-AuNP. Circular dichroism analysis showed surface chemistry-dependent conformational changes of proteins binding to AuNP. Time-dependent uptake of bare, plasma corona (PC) and HSA corona-bound AuNP (HSA-AuNP) showed significant reduction in uptake with PC formation. Cell viability studies demonstrated dose-dependent toxicity of BPEI-AuNP. Transcriptional profiling studies revealed 126 genes, from 13 biological pathways, to be differentially regulated by 40 nm bare and PC-bound BPEI-AuNP (PC-BPEI-AuNP). Furthermore, PC formation relieved the toxicity of cationic BPEI-AuNP by modulating expression of genes involved in DNA damage and repair, heat shock response, mitochondrial energy metabolism, oxidative stress and antioxidant response, and ER stress and unfolded protein response cascades, which were aberrantly expressed in bare BPEI-AuNP-treated cells. NP surface chemistry is shown to play the dominant role over size in determining the biocorona composition, which in turn modulates cell uptake, and biological responses, consequently defining the potential safety and efficacy of nanoformulations.

Managing landscape connectivity for a fragmented area using spatial analysis model at town scale

NASA Astrophysics Data System (ADS)

Liu, Shiliang; Dong, Yuhong; Fu, Wei; Zhang, Zhaoling

2009-10-01

Urban growth has great effect on land uses of its suburbs. The habitat loss and fragmentation in those areas are a main threat to conservation of biodiversity. Enhancing landscape functional connectivity is usually an effective way to maintain high biodiversity level in disturbed area. Taking a small town in Beijing as an example, we designed potential landscape corridors based on identification of landscape element quality and "least-cost" path analysis. We described a general approach to establish the corridor network in such fragmented area at town scale. The results showed that landscape elements position has various effects on landscape suitability. Small forest patches and other green lands such as meadow, shrub, even farmland could be a potential stepping-stone or corridor for animal movements. Also, the analysis reveals that critical areas should be managed to facilitate the movement of dispersers among habitat patches.

Quantitative Proteomics Identifies Activation of Hallmark Pathways of Cancer in Patient Melanoma.

PubMed

Byrum, Stephanie D; Larson, Signe K; Avaritt, Nathan L; Moreland, Linley E; Mackintosh, Samuel G; Cheung, Wang L; Tackett, Alan J

2013-03-01

Molecular pathways regulating melanoma initiation and progression are potential targets of therapeutic development for this aggressive cancer. Identification and molecular analysis of these pathways in patients has been primarily restricted to targeted studies on individual proteins. Here, we report the most comprehensive analysis of formalin-fixed paraffin-embedded human melanoma tissues using quantitative proteomics. From 61 patient samples, we identified 171 proteins varying in abundance among benign nevi, primary melanoma, and metastatic melanoma. Seventy-three percent of these proteins were validated by immunohistochemistry staining of malignant melanoma tissues from the Human Protein Atlas database. Our results reveal that molecular pathways involved with tumor cell proliferation, motility, and apoptosis are mis-regulated in melanoma. These data provide the most comprehensive proteome resource on patient melanoma and reveal insight into the molecular mechanisms driving melanoma progression.

Online participation: a content analysis of differences in utilization of two online cancer communities by men and women, patients and family members.

PubMed

Ginossar, Tamar

2008-01-01

The Internet provides a new modality for health communication by facilitating the creation of virtual communities. These communities have the potential to influence health behavior beyond traditional FTF support groups. This study utilized content analysis of 1,424 e-mail messages posted to 2 online cancer communities to examine uses of these groups. Findings revealed (a) similarities in the content of communication in the 2 virtual communities, (b) gender differences in participation, and (c) differences in utilization of these online groups between patients and family members. These results are discussed in light of the diverse uses of online cancer communities that they reveal, the role of family members in support seeking and provision, and gender communication styles in health computer-mediated communication.

MiRNAs with Apoptosis Regulating Potential Are Differentially Expressed in Chronic Exercise-Induced Physiologically Hypertrophied Hearts

PubMed Central

Ramprasath, Tharmarajan; Kalpana, Krishnan

2015-01-01

Physiological cardiac hypertrophy is an adaptive mechanism, induced during chronic exercise. As it is reversible and not associated with cardiomyocyte death, it is considered as a natural tactic to prevent cardiac dysfunction and failure. Though, different studies revealed the importance of microRNAs (miRNAs) in pathological hypertrophy, their role during physiological hypertrophy is largely unexplored. Hence, this study is aimed at revealing the global expression profile of miRNAs during physiological cardiac hypertrophy. Chronic swimming protocol continuously for eight weeks resulted in induction of physiological hypertrophy in rats and histopathology revealed the absence of tissue damage, apoptosis or fibrosis. Subsequently, the total RNA was isolated and small RNA sequencing was executed. Analysis of small RNA reads revealed the differential expression of a large set of miRNAs during physiological hypertrophy. The expression profile of the significantly differentially expressed miRNAs was validated by qPCR. In silico prediction of target genes by miRanda, miRdB and TargetScan and subsequent qPCR analysis unraveled that miRNAs including miR-99b, miR-100, miR-19b, miR-10, miR-208a, miR-133, miR-191a, miR-22, miR-30e and miR-181a are targeting the genes that primarily regulate cell proliferation and cell death. Gene ontology and pathway mapping showed that the differentially expressed miRNAs and their target genes were mapped to apoptosis and cell death pathways principally via PI3K/Akt/mTOR and MAPK signaling. In summary, our data indicates that regulation of these miRNAs with apoptosis regulating potential can be one of the major key factors in determining pathological or physiological hypertrophy by controlling fibrosis, apoptosis and cell death mechanisms. PMID:25793527

Probing lipid membrane electrostatics

NASA Astrophysics Data System (ADS)

Yang, Yi

The electrostatic properties of lipid bilayer membranes play a significant role in many biological processes. Atomic force microscopy (AFM) is highly sensitive to membrane surface potential in electrolyte solutions. With fully characterized probe tips, AFM can perform quantitative electrostatic analysis of lipid membranes. Electrostatic interactions between Silicon nitride probes and supported zwitterionic dioleoylphosphatidylcholine (DOPC) bilayer with a variable fraction of anionic dioleoylphosphatidylserine (DOPS) were measured by AFM. Classical Gouy-Chapman theory was used to model the membrane electrostatics. The nonlinear Poisson-Boltzmann equation was numerically solved with finite element method to provide the potential distribution around the AFM tips. Theoretical tip-sample electrostatic interactions were calculated with the surface integral of both Maxwell and osmotic stress tensors on tip surface. The measured forces were interpreted with theoretical forces and the resulting surface charge densities of the membrane surfaces were in quantitative agreement with the Gouy-Chapman-Stern model of membrane charge regulation. It was demonstrated that the AFM can quantitatively detect membrane surface potential at a separation of several screening lengths, and that the AFM probe only perturbs the membrane surface potential by <2%. One important application of this technique is to estimate the dipole density of lipid membrane. Electrostatic analysis of DOPC lipid bilayers with the AFM reveals a repulsive force between the negatively charged probe tips and the zwitterionic lipid bilayers. This unexpected interaction has been analyzed quantitatively to reveal that the repulsion is due to a weak external field created by the internai membrane dipole moment. The analysis yields a dipole moment of 1.5 Debye per lipid with a dipole potential of +275 mV for supported DOPC membranes. This new ability to quantitatively measure the membrane dipole density in a noninvasive manner will be useful in identifying the biological effects of the dipole potential. Finally, heterogeneous model membranes were studied with fluid electric force microscopy (FEFM). Electrostatic mapping was demonstrated with 50 nm resolution. The capabilities of quantitative electrostatic measurement and lateral charge density mapping make AFM a unique and powerful probe of membrane electrostatics.

Variation in populations of Yarrow's spiny lizard, Sceloporus jarrovii, in the northern Madrean Archipelago region

Treesearch

George Middendorf; Jack Frankel; Douglas Ruby

2005-01-01

Population genetic analysis of Yarrow’s spiny lizard, Sceloporus jarrovii, suggests a metapopulational distribution pattern with potential divergence of genetically based traits. Comparing male pushup displays revealed populations east and west of the San Pedro River valley to be more similar among themselves than to those on the other side....

Sex Differences on "g" and Non-"g" Intellectual Performance Reveal Potential Sources of STEM Discrepancies

ERIC Educational Resources Information Center

Lemos, Gina C.; Abad, Francisco J.; Almeida, Leandro S.; Colom, Roberto

2013-01-01

The analysis of sex differences in cognitive abilities is largely confusing because these differences are masked by the pervasive influence of the general factor of intelligence (g). In this study a battery of five reasoning tests (abstract [AR], numerical [NR], verbal [VR], mechanical [MR], and spatial [SR]) was completed by a sample of 3233…

Comparative genomic analysis of full genome sequences of two closely related isolates of Clostridium perfringens reveals regions of genome plasticity with prevention potential

USDA-ARS?s Scientific Manuscript database

The spore-forming anaerobic Clostridium perfringens (CP) is the primary etiological agent of necrotic enteritis (NE) disease, one of priority enteric diseases in chickens which is responsible for annual losses of $6 billion in the US poultry industry. Our long term goal is to develop a recombinant v...

Diffusion profiling of tumor volumes using a histogram approach can predict proliferation and further microarchitectural features in medulloblastoma.

PubMed

Schob, Stefan; Beeskow, Anne; Dieckow, Julia; Meyer, Hans-Jonas; Krause, Matthias; Frydrychowicz, Clara; Hirsch, Franz-Wolfgang; Surov, Alexey

2018-05-31

Medulloblastomas are the most common central nervous system tumors in childhood. Treatment and prognosis strongly depend on histology and transcriptomic profiling. However, the proliferative potential also has prognostical value. Our study aimed to investigate correlations between histogram profiling of diffusion-weighted images and further microarchitectural features. Seven patients (age median 14.6 years, minimum 2 years, maximum 20 years; 5 male, 2 female) were included in this retrospective study. Using a Matlab-based analysis tool, histogram analysis of whole apparent diffusion coefficient (ADC) volumes was performed. ADC entropy revealed a strong inverse correlation with the expression of the proliferation marker Ki67 (r = - 0.962, p = 0.009) and with total nuclear area (r = - 0.888, p = 0.044). Furthermore, ADC percentiles, most of all ADCp90, showed significant correlations with Ki67 expression (r = 0.902, p = 0.036). Diffusion histogram profiling of medulloblastomas provides valuable in vivo information which potentially can be used for risk stratification and prognostication. First of all, entropy revealed to be the most promising imaging biomarker. However, further studies are warranted.

Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets.

PubMed

Ali, Amjad; Naz, Anam; Soares, Siomar C; Bakhtiar, Marriam; Tiwari, Sandeep; Hassan, Syed S; Hanan, Fazal; Ramos, Rommel; Pereira, Ulisses; Barh, Debmalya; Figueiredo, Henrique César Pereira; Ussery, David W; Miyoshi, Anderson; Silva, Artur; Azevedo, Vasco

2015-01-01

Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (~70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed. Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan-genome approach; the predicted conserved gene families (1,193) constitute ~77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all of the H. pylori genomes been analyzed.

The APP intracellular domain (AICD) potentiates ER stress-induced apoptosis.

PubMed

Kögel, Donat; Concannon, Caoimhín G; Müller, Thorsten; König, Hildegard; Bonner, Caroline; Poeschel, Simone; Chang, Steffi; Egensperger, Rupert; Prehn, Jochen H M

2012-09-01

Here we employed human SHEP neuroblastoma cells either stably or inducibly expressing the amyloid precursor protein (APP) intracellular domain (AICD) to investigate its ability to modulate stress-induced cell death. Analysis of effector caspase activation revealed that AICD overexpression was specifically associated with an increased sensitivity to apoptosis induced by the 2 endoplasmic reticulum (ER) stressors thapsigargin and tunicamycin, but not by staurosporine (STS). Basal and ER stress-induced expression of Bip/Grp78 and C/EBP-homologous protein/GADD153 were not altered by AICD implying that AICD potentiated cell death downstream or independent of the conserved unfolded protein response (UPR). Interestingly, quantitative polymerase chain reaction analysis and reporter gene assays revealed that AICD significantly downregulated messenger RNA levels of the Alzheimer's disease susceptibility gene ApoJ/clusterin, indicating transcriptional repression. Knockdown of ApoJ/clusterin mimicked the effect of AICD on ER stress-induced apoptosis, but had no discernible effect on staurosporine-induced cell death. Our data suggest that altered levels of AICD may abolish the prosurvival function of ApoJ/clusterin and increase the susceptibility of neurons to ER stress-mediated cell death, a pathway that may contribute to the pathogenesis of Alzheimer's disease. Copyright © 2012 Elsevier Inc. All rights reserved.

Quantifying the Variability in Species' Vulnerability to Ocean Acidification

NASA Astrophysics Data System (ADS)

Kroeker, K. J.; Kordas, R. L.; Crim, R.; Gattuso, J.; Hendriks, I.; Singh, G. G.

2012-12-01

Ocean acidification represents a threat to marine species and ecosystems worldwide. As such, understanding the potential ecological impacts of acidification is a high priority for science, management, and policy. As research on the biological impacts of ocean acidification continues to expand at an exponential rate, a comprehensive understanding of the generalities and/or variability in organisms' responses and the corresponding levels of certainty of these potential responses is essential. Meta-analysis is a quantitative technique for summarizing the results of primary research studies and provides a transparent method to examine the generalities and/or variability in scientific results across numerous studies. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining the biological impacts of ocean acidification. Our results reveal decreased survival, calcification, growth, reproduction and development in response to acidification across a broad range of marine organisms, as well as significant trait-mediated variation among taxonomic groups and enhanced sensitivity among early life history stages. In addition, our results reveal a pronounced sensitivity of molluscs to acidification, especially among the larval stages, and enhanced vulnerability to acidification with concurrent exposure to increased seawater temperatures across a diversity of organisms.

Members of a new subgroup of Streptococcus anginosus harbor virulence related genes previously observed in Streptococcus pyogenes.

PubMed

Babbar, Anshu; Kumar, Venkatesan Naveen; Bergmann, René; Barrantes, Israel; Pieper, Dietmar H; Itzek, Andreas; Nitsche-Schmitz, D Patric

2017-04-01

Conventionally categorized as commensals, the Streptococci of the species S. anginosus are facultative human pathogens that are difficult to diagnose and often overlooked. Furthermore, detailed investigation and diagnosis of S. anginosus infections is hampered by unexplored taxonomy and widely elusive molecular pathogenesis. To explore their pathogenic potential, S. anginosus isolates collected from patients of two geographical locations (Vellore, India and Leipzig, Germany) were subjected to multi-locus sequence analysis (MLSA). This analysis revealed the potential presence of a new distinct clade of the species S. anginosus, tentatively termed here as genomosubspecies vellorensis. A complementary PCR-based screening for S. pyogenes virulence factor as well as antibiotic resistance genes revealed not only the presence of superantigen- and extracellular DNase coding genes identical to corresponding genes of S. pyogenes, but also of erythromycin and tetracycline resistance genes in the genomes of the analyzed S. anginosus isolates, thus posing a matter of significant health concern. Identification of new pathogenic S. anginosus strains capable of causing difficult to treat infections may pose additional challenges to the diagnosis and treatment of Streptococcus based infections. Copyright © 2017 Elsevier GmbH. All rights reserved.

Unravelling the potential of a new uracil phosphoribosyltransferase (UPRT) from Arabidopsis thaliana in sensitizing HeLa cells towards 5-fluorouracil.

PubMed

Narayanan, Sharmila; Sanpui, Pallab; Sahoo, Lingaraj; Ghosh, Siddhartha Sankar

2016-10-01

In silico studies with uracil phosphoribosyltransferase from Arabidopsis thaliana (AtUPRT) revealed its lower binding energies for uracil and 5-fluorouracil (5-FU) as compared to those of bacterial UPRT indicating the prospective of AtUPRT in gene therapy implications. Hence, AtUPRT was cloned and stably expressed in cervical cancer cells (HeLa) to investigate the effect of prodrug 5-FU on these transfected cancer cells. The treatment of AtUPRT-expressing HeLa (HeLa-UPP) cells with 5-FU for 72h resulted in significant decrease in cell viability. Moreover, 5-FU was observed to induce apoptosis and perturb mitochondrial membrane potential in HeLa-UPP cells. While cell cycle analysis revealed significant S-phase arrest as a result of 5-FU treatment in HeLa-UPP cells, quantitative gene expression analysis demonstrated simultaneous upregulation of important cell cycle related genes, cyclin D1 and p21. The survival fractions of non-transfected, vector-transfected and AtUPRT-transfected HeLa cells, following 5-FU treatment, were calculated to be 0.425, 0.366 and 0.227, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

Transcriptome-wide identification of salt-responsive members of the WRKY gene family in Gossypium aridum.

PubMed

Fan, Xinqi; Guo, Qi; Xu, Peng; Gong, YuanYong; Shu, Hongmei; Yang, Yang; Ni, Wanchao; Zhang, Xianggui; Shen, Xinlian

2015-01-01

WRKY transcription factors are plant-specific, zinc finger-type transcription factors. The WRKY superfamily is involved in abiotic stress responses in many crops including cotton, a major fiber crop that is widely cultivated and consumed throughout the world. Salinity is an important abiotic stress that results in considerable yield losses. In this study, we identified 109 WRKY genes (GarWRKYs) in a salt-tolerant wild cotton species Gossypium aridum from transcriptome sequencing data to elucidate the roles of these factors in cotton salt tolerance. According to their structural features, the predicted members were divided into three groups (Groups I-III), as previously described for Arabidopsis. Furthermore, 28 salt-responsive GarWRKY genes were identified from digital gene expression data and subjected to real-time quantitative RT-PCR analysis. The expression patterns of most GarWRKY genes revealed by this analysis are in good agreement with those revealed by RNA-Seq analysis. RT-PCR analysis revealed that 27 GarWRKY genes were expressed in roots and one was exclusively expressed in roots. Analysis of gene orthology and motif compositions indicated that WRKY members from Arabidopsis, rice and soybean generally shared the similar motifs within the same subgroup, suggesting they have the similar function. Overexpression-GarWRKY17 and -GarWRKY104 in Arabidopsis revealed that they could positively regulate salt tolerance of transgenic Arabidopsis during different development stages. The comprehensive data generated in this study provide a platform for elucidating the functions of WRKY transcription factors in salt tolerance of G. aridum. In addition, GarWRKYs related to salt tolerance identified in this study will be potential candidates for genetic improvement of cultivated cotton salt stress tolerance.

Physical and electrochemical properties of ZnO films fabricated from highly cathodic electrodeposition potentials

NASA Astrophysics Data System (ADS)

Ismail, Abdul Hadi; Abdullah, Abdul Halim; Sulaiman, Yusran

2017-03-01

The physical and electrochemical properties of zinc oxide (ZnO) film electrode that were prepared electrochemically were studied. ZnO was electrodeposited on ITO glass substrate by applying three different highly cathodic potentials (-1.3 V, -1.5 V, -1.7 V) in a solution containing 70 mM of Zn(NO3)2.xH2O and 0.1 M KCl with bath temperatures of 70 °C and 80 °C. The presence of ZnO was asserted from XRD analysis where the corresponding peaks in the spectra were assigned. SEM images revealed the plate-like hexagonal morphology of ZnO which is in agreement with the XRD analysis. The areal capacitance of the ZnO was observed to increase when the applied electrodeposition potential is increased from -1.3 V to -1.5 V. However, the areal capacitance is found to decrease when the applied electrodeposition potential is further increased to -1.7 V. The resistance of charge transfer (Rct) of the ZnO decreased when the applied electrodeposition potential varies from -1.3 V to -1.7 V due to the decreased particle size of ZnO when more cathodic electrodeposition potential is applied.

Effect of land use land cover change on soil erosion potential in an agricultural watershed.

PubMed

Sharma, Arabinda; Tiwari, Kamlesh N; Bhadoria, P B S

2011-02-01

Universal soil loss equation (USLE) was used in conjunction with a geographic information system to determine the influence of land use and land cover change (LUCC) on soil erosion potential of a reservoir catchment during the period 1989 to 2004. Results showed that the mean soil erosion potential of the watershed was increased slightly from 12.11 t ha(-1) year(-1) in the year 1989 to 13.21 t ha(-1) year(-1) in the year 2004. Spatial analysis revealed that the disappearance of forest patches from relatively flat areas, increased in wasteland in steep slope, and intensification of cultivation practice in relatively more erosion-prone soil were the main factors contributing toward the increased soil erosion potential of the watershed during the study period. Results indicated that transition of other land use land cover (LUC) categories to cropland was the most detrimental to watershed in terms of soil loss while forest acted as the most effective barrier to soil loss. A p value of 0.5503 obtained for two-tailed paired t test between the mean erosion potential of microwatersheds in 1989 and 2004 also indicated towards a moderate change in soil erosion potential of the watershed over the studied period. This study revealed that the spatial location of LUC parcels with respect to terrain and associated soil properties should be an important consideration in soil erosion assessment process.

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.

PubMed

Hua, Zheng-Shuang; Han, Yu-Jiao; Chen, Lin-Xing; Liu, Jun; Hu, Min; Li, Sheng-Jin; Kuang, Jia-Liang; Chain, Patrick S G; Huang, Li-Nan; Shu, Wen-Sheng

2015-06-01

High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the 'divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.

H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle.

PubMed

Berry, Luke; Poudel, Saroj; Tokmina-Lukaszewska, Monika; Colman, Daniel R; Nguyen, Diep M N; Schut, Gerrit J; Adams, Michael W W; Peters, John W; Boyd, Eric S; Bothner, Brian

2018-01-01

Recent investigations into ferredoxin-dependent transhydrogenases, a class of enzymes responsible for electron transport, have highlighted the biological importance of flavin-based electron bifurcation (FBEB). FBEB generates biomolecules with very low reduction potential by coupling the oxidation of an electron donor with intermediate potential to the reduction of high and low potential molecules. Bifurcating systems can generate biomolecules with very low reduction potentials, such as reduced ferredoxin (Fd), from species such as NADPH. Metabolic systems that use bifurcation are more efficient and confer a competitive advantage for the organisms that harbor them. Structural models are now available for two NADH-dependent ferredoxin-NADP + oxidoreductase (Nfn) complexes. These models, together with spectroscopic studies, have provided considerable insight into the catalytic process of FBEB. However, much about the mechanism and regulation of these multi-subunit proteins remains unclear. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and statistical coupling analysis (SCA), we identified specific pathways of communication within the model FBEB system, Nfn from Pyrococus furiosus, under conditions at each step of the catalytic cycle. HDX-MS revealed evidence for allosteric coupling across protein subunits upon nucleotide and ferredoxin binding. SCA uncovered a network of co-evolving residues that can provide connectivity across the complex. Together, the HDX-MS and SCA data show that protein allostery occurs across the ensemble of iron‑sulfur cofactors and ligand binding sites using specific pathways that connect domains allowing them to function as dynamically coordinated units. Copyright © 2017 Elsevier B.V. All rights reserved.

Computer-assisted image analysis of human cilia and Chlamydomonas flagella reveals both similarities and differences in axoneme structure.

PubMed

O'Toole, Eileen T; Giddings, Thomas H; Porter, Mary E; Ostrowski, Lawrence E

2012-08-01

In the past decade, investigations from several different fields have revealed the critical role of cilia in human health and disease. Because of the highly conserved nature of the basic axonemal structure, many different model systems have proven useful for the study of ciliopathies, especially the unicellular, biflagellate green alga Chlamydomonas reinhardtii. Although the basic axonemal structure of cilia and flagella is highly conserved, these organelles often perform specialized functions unique to the cell or tissue in which they are found. These differences in function are likely reflected in differences in structural organization. In this work, we directly compare the structure of isolated axonemes from human cilia and Chlamydomonas flagella to identify similarities and differences that potentially play key roles in determining their functionality. Using transmission electron microscopy and 2D image averaging techniques, our analysis has confirmed the overall structural similarity between these two species, but also revealed clear differences in the structure of the outer dynein arms, the central pair projections, and the radial spokes. We also show how the application of 2D image averaging can clarify the underlying structural defects associated with primary ciliary dyskinesia (PCD). Overall, our results document the remarkable similarity between these two structures separated evolutionarily by over a billion years, while highlighting several significant differences, and demonstrate the potential of 2D image averaging to improve the diagnosis and understanding of PCD. Copyright © 2012 Wiley Periodicals, Inc.

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.

PubMed

Zhou, Xinrui; Zheng, Jie; Ivan, Fransiskus Xaverius; Yin, Rui; Ranganathan, Shoba; Chow, Vincent T K; Kwoh, Chee-Keong

2018-05-09

Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013, and raised more grave concerns with its increased potential to spread among humans. Experimental studies have revealed several host and virulence markers, indicating differential host binding preferences which can help estimate the potential of causing a pandemic. Here we systematically investigate the sequence pattern and structural characteristics of novel influenza A/H7N9 using computational approaches. The sequence analysis highlighted mutations in protein functional domains of influenza viruses. Molecular docking and molecular dynamics simulation revealed that the hemagglutinin (HA) of A/Taiwan/1/2017(H7N9) strain enhanced the binding with both avian and human receptor analogs, compared with the previous A/Shanghai/02/2013(H7N9) strain. The Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) calculation revealed the change of residue-ligand interaction energy and detected the residues with conspicuous binding preference. The results are novel and specific to the emerging influenza A/Taiwan/1/2017(H7N9) strain compared with A/Shanghai/02/2013(H7N9). Its enhanced ability to bind human receptor analogs, which are abundant in the human upper respiratory tract, may be responsible for the recent outbreak. Residues showing binding preference were detected, which could facilitate monitoring the circulating influenza viruses.

Psychometric properties of the Portuguese version of place attachment scale for youth in residential care.

PubMed

Magalhães, Eunice; Calheiros, María M

2015-01-01

Although the significant scientific advances on place attachment literature, no instruments exist specifically developed or adapted to residential care. 410 adolescents (11 - 18 years old) participated in this study. The place attachment scale evaluates five dimensions: Place identity, Place dependence, Institutional bonding, Caregivers bonding and Friend bonding. Data analysis included descriptive statistics, content validity, construct validity (Confirmatory Factor Analysis), concurrent validity with correlations with satisfaction with life and with institution, and reliability evidences. The relationship with individual characteristics and placement length was also verified. Content validity analysis revealed that more than half of the panellists perceive all the items as relevant to assess the construct in residential care. The structure with five dimensions revealed good fit statistics and concurrent validity evidences were found, with significant correlations with satisfaction with life and with the institution. Acceptable values of internal consistence and specific gender differences were found. The preliminary psychometric properties of this scale suggest it potential to be used with youth in care.

Proteomics Analysis Reveals Distinct Corona Composition on Magnetic Nanoparticles with Different Surface Coatings: Implications for Interactions with Primary Human Macrophages

PubMed Central

Vogt, Carmen; Pernemalm, Maria; Kohonen, Pekka; Laurent, Sophie; Hultenby, Kjell; Vahter, Marie; Lehtiö, Janne; Toprak, Muhammet S.; Fadeel, Bengt

2015-01-01

Superparamagnetic iron oxide nanoparticles (SPIONs) have emerged as promising contrast agents for magnetic resonance imaging. The influence of different surface coatings on the biocompatibility of SPIONs has been addressed, but the potential impact of the so-called corona of adsorbed proteins on the surface of SPIONs on their biological behavior is less well studied. Here, we determined the composition of the plasma protein corona on silica-coated versus dextran-coated SPIONs using mass spectrometry-based proteomics approaches. Notably, gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed distinct protein corona compositions for the two different SPIONs. Relaxivity of silica-coated SPIONs was modulated by the presence of a protein corona. Moreover, the viability of primary human monocyte-derived macrophages was influenced by the protein corona on silica-coated, but not dextran-coated SPIONs, and the protein corona promoted cellular uptake of silica-coated SPIONs, but did not affect internalization of dextran-coated SPIONs. PMID:26444829

Proteomics Analysis Reveals Distinct Corona Composition on Magnetic Nanoparticles with Different Surface Coatings: Implications for Interactions with Primary Human Macrophages.

PubMed

Vogt, Carmen; Pernemalm, Maria; Kohonen, Pekka; Laurent, Sophie; Hultenby, Kjell; Vahter, Marie; Lehtiö, Janne; Toprak, Muhammet S; Fadeel, Bengt

2015-01-01

Superparamagnetic iron oxide nanoparticles (SPIONs) have emerged as promising contrast agents for magnetic resonance imaging. The influence of different surface coatings on the biocompatibility of SPIONs has been addressed, but the potential impact of the so-called corona of adsorbed proteins on the surface of SPIONs on their biological behavior is less well studied. Here, we determined the composition of the plasma protein corona on silica-coated versus dextran-coated SPIONs using mass spectrometry-based proteomics approaches. Notably, gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed distinct protein corona compositions for the two different SPIONs. Relaxivity of silica-coated SPIONs was modulated by the presence of a protein corona. Moreover, the viability of primary human monocyte-derived macrophages was influenced by the protein corona on silica-coated, but not dextran-coated SPIONs, and the protein corona promoted cellular uptake of silica-coated SPIONs, but did not affect internalization of dextran-coated SPIONs.

Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles.

PubMed

Rattanachomsri, Ukrit; Kanokratana, Pattanop; Eurwilaichitr, Lily; Igarashi, Yasuo; Champreda, Verawat

2011-01-01

Sugarcane bagasse is an important lignocellulosic by-product with potential for conversion to biofuels and chemicals in biorefinery. As a step towards an understanding of microbial diversity and the processes existing in bagasse collection sites, the microbial community in industrial bagasse feedstock piles was investigated. Molecular biodiversity analysis of 16S rDNA sequences revealed the presence of a complex bacterial community. A diverse group of mainly aerobic and facultative anaerobic bacteria was identified reflecting the aerobic and high temperature microenvironmental conditions under the pile surface. The major bacterial taxa present were identified as Firmicutes, Alpha- and Gammaproteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Analysis of the eukaryotic microbial assemblage based on an internal transcribed spacer revealed the predominance of diverse cellulolytic and hemicellulolytic ascomycota. A microbial interaction model is proposed, focusing on lignocellulose degradation and methane metabolism. The insights into the microbial community in this study provide a basis for efficient utilization of bagasse in lignocellulosic biomass-based industries.

Genetic Variation and Population Differentiation in a Medical Herb Houttuynia cordata in China Revealed by Inter-Simple Sequence Repeats (ISSRs)

PubMed Central

Wei, Lin; Wu, Xian-Jin

2012-01-01

Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included. PMID:22942696

Genetic variation and population differentiation in a medical herb Houttuynia cordata in China revealed by inter-simple sequence repeats (ISSRs).

PubMed

Wei, Lin; Wu, Xian-Jin

2012-01-01

Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included.

Rheological properties in relation to molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2018-07-15

Quinoa starch granules are small (~0.5 - 3μm) with potentials for some food and other applications. To better exploit it as a new starch resource, this study investigates the steady shear and dynamic oscillatory properties of 9 quinoa starches varying in composition and structure. Steady shear analysis shows that the flow curves could be well described by 4 selected mathematic models. Temperature sweep analysis reveals that the quinoa starch encounters a 4-stage process including 2 phase transitions. Structure-function relationship analysis showed that composition as well as unit and internal chain length distribution of amylopectin have significant impact on the rheological properties (e.g., G' at 90°C) of quinoa starch. The roles of some individual unit chains and super-long unit chains of amylopectin in determining the rheological properties of quinoa starch were revealed. This study may stimulate further interest in understanding the structural basis of starch rheology. Copyright © 2018 Elsevier B.V. All rights reserved.

A First Survey on the Abundance of Plastics Fragments and Particles on Two Sandy Beaches in Kuching, Sarawak, Malaysia

NASA Astrophysics Data System (ADS)

Noik, V. James; Mohd Tuah, P.

2015-04-01

Plastic fragments and particles as an emerging environmental contaminant and pollutant are gaining scientific attention in the recent decades due to the potential threats on biota. This study aims to elucidate the presence, abundance and temporal change of plastic fragments and particles from two selected beaches, namely Santubong and Trombol in Kuching on two sampling times. Morphological and polymer identification assessment on the recovered plastics was also conducted. Overall comparison statistical analysis revealed that the abundance of plastic fragments/debris on both of sampling stations were insignificantly different (p>0.05). Likewise, statistical analysis on the temporal changes on the abundance yielded no significant difference for most of the sampling sites on each respective station, except STB-S2. Morphological studies revealed physical features of plastic fragments and debris were diverse in shapes, sizes, colors and surface fatigues. FTIR fingerprinting analysis shows that polypropylene and polyethylene were the dominant plastic polymers debris on both beaches.

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation

PubMed Central

Beaton, E. D.; Stevenson, Bradley S.; King-Sharp, Karen J.; Stamps, Blake W.; Nunn, Heather S.; Stuart, Marilyne

2016-01-01

Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth’s biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the differential historical events that have influenced the current bacterial composition. Categorizing the study site into smaller regions of interest of more closely spaced fractures, or of potentially hydraulically connected fractures, might improve the resolution of an analysis to reveal environmental influences that have shaped these bacterial communities. PMID:27999569

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation.

PubMed

Beaton, E D; Stevenson, Bradley S; King-Sharp, Karen J; Stamps, Blake W; Nunn, Heather S; Stuart, Marilyne

2016-01-01

Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth's biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the differential historical events that have influenced the current bacterial composition. Categorizing the study site into smaller regions of interest of more closely spaced fractures, or of potentially hydraulically connected fractures, might improve the resolution of an analysis to reveal environmental influences that have shaped these bacterial communities.

Analysis of the potential geochemical reactions in the Enceladus' hydrothermal environment

NASA Astrophysics Data System (ADS)

Ramirez-Cabañas, A. K.; Flandes, A.

2017-12-01

Enceladus is the sixth largest moon of Saturn and differs from its other moons, because of its cryovolcanic geysers that emanate from its south pole. The instruments of the Cassini spacecraft reveal different compounds in the gases and the dust of the geysers, such as salts (sodium chloride, sodium bicarbonate and/or sodium carbonate), as well as silica traces (Postberg et al., 2008, 2009) that could be the result of a hydrothermal environment (Hsu et al., 2014, Sekine et al., 2014). By means of a thermodynamic analysis, we propose and evaluate potential geochemical reactions that could happen from the interaction between the nucleus surface and the inner ocean of Enceladus. These reactions may well lead to the origin of the compounds found in the geysers. From this analysis, we propose that, at least, two minerals must be present in the condritic nucleus of Enceladus: olivines (fayalite and fosterite) and feldspar (orthoclase and albite). Subsequently, taking as reference the hydrothermal processes that take place on Earth, we propose the different stages of a potential hydrothermal scenario for Enceladus.

Bioindicator role of tintinnid (Protozoa: Ciliophora) for water quality monitoring in Kalpakkam, Tamil Nadu, south east coast of India.

PubMed

Rakshit, Dibyendu; Sahu, Gouri; Mohanty, Ajit Kumar; Satpathy, Kamala Kanta; Jonathan, M P; Murugan, K; Sarkar, Santosh Kumar

2017-01-15

The feasibility of a potential bioindicator based on functional groups of microzooplankton tintinnids for bioassessments of water quality status was studied during southwest monsoon (June to September) along the coastal waters of Kalpakkam, India during 2012-2015. The work highlights the following features (1) tintinnid community composed of 28 species belonging to 11 genera and 9 families, revealed significant differences among the four study sites (2) maximum numerical abundance (2224±90ind. l -1 ) and species diversity (H'=2.66) of tintinnid were recorded towards Bay of Bengal whereas minimum abundance (720±35ind. l -1 ) and diversity (H'=1.74) were encountered in the backwater sites, (3) multivariate analyses [RELATE, Biota-environment (BIOENV) and canonical analysis of principal coordinates (CAP)] reveal that chl a, nitrate and phosphate were the potential causative factors for tintinnid distribution. Based on the results, we suggest that tintinnids may be used as a potential bioindicator of water quality status in marine ecosystem. Copyright © 2016 Elsevier Ltd. All rights reserved.

Adsorption Analysis of Lactoferrin to Titanium, Stainless Steel, Zirconia, and Polymethyl Methacrylate Using the Quartz Crystal Microbalance Method

PubMed Central

Yoshida, Eiji; Hayakawa, Tohru

2016-01-01

It is postulated that biofilm formation in the oral cavity causes some oral diseases. Lactoferrin is an antibacterial protein in saliva and an important defense factor against biofilm development. We analyzed the adsorbed amount of lactoferrin and the dissociation constant (K d) of lactoferrin to the surface of different dental materials using an equilibrium analysis technique in a 27 MHz quartz crystal microbalance (QCM) measurement. Four different materials, titanium (Ti), stainless steel (SUS), zirconia (ZrO2) and polymethyl methacrylate (PMMA), were evaluated. These materials were coated onto QCM sensors and the surfaces characterized by atomic force microscopic observation, measurements of surface roughness, contact angles of water, and zeta potential. QCM measurements revealed that Ti and SUS showed a greater amount of lactoferrin adsorption than ZrO2 and PMMA. Surface roughness and zeta potential influenced the lactoferrin adsorption. On the contrary, the K d value analysis indicated that the adsorbed lactoferrin bound less tightly to the Ti and SUS surfaces than to the ZrO2 and PMMA surfaces. The hydrophobic interaction between lactoferrin and ZrO2 and PMMA is presumed to participate in better binding of lactoferrin to ZrO2 and PMMA surfaces. It was revealed that lactoferrin adsorption behavior was influenced by the characteristics of the material surface. PMID:26998486

Titanium-35niobium alloy as a potential material for biomedical implants: In vitro study.

PubMed

de Andrade, Dennia Perez; de Vasconcellos, Luana Marotta Reis; Carvalho, Isabel Chaves Silva; Forte, Lilibeth Ferraz de Brito Penna; de Souza Santos, Evelyn Luzia; Prado, Renata Falchete do; Santos, Dalcy Roberto Dos; Cairo, Carlos Alberto Alves; Carvalho, Yasmin Rodarte

2015-11-01

Research on new titanium alloys and different surface topographies aims to improve osseointegration. The objective of this study is to analyze the behavior of osteogenic cells cultivated on porous and dense samples of titanium-niobium alloys, and to compare them with the behavior of such type of cells on commercial pure titanium. Samples prepared using powder metallurgy were characterized using scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD), and metallographic and profilometer analyses. Osteogenic cells from newborn rat calvaria were plated over different groups: dense or porous samples composed of Ti or Ti-35niobium (Nb). Cell adhesion, cell proliferation, MTT assay, cell morphology, protein total content, alkaline phosphatase activity, and mineralization nodules were assessed. Results from XRD and EDS analysis confirmed the presence of Ti and Nb in the test alloy. Metallographic analysis revealed interconnected pores, with pore size ranging from 138 to 150μm. The profilometer analysis detected the greatest rugosity within the dense alloy samples. In vitro tests revealed similar biocompatibility between Ti-35Nb and Ti; furthermore, it was possible to verify that the association of porous surface topography and the Ti-35Nb alloy positively influenced mineralized matrix formation. We propose that the Ti-35Nb alloy with porous topography constitutes a biocompatible material with great potential for use in biomedical implants. Copyright © 2015 Elsevier B.V. All rights reserved.

An isobolographic analysis of the antinociceptive effect of xylopic acid in combination with morphine or diclofenac

PubMed Central

Woode, Eric; Ameyaw, Elvis Ofori; Abotsi, Wonder Kofi Mensah; Boakye-Gyasi, Eric

2015-01-01

Background: A common practice of managing pain globally is the combination of analgesics and this is aimed at facilitating patient compliance, simplifying prescription, and improving efficacy without increasing adverse effects. Fruit extracts of Xylopia aethiopica are used traditionally in the management of pain disorders and xylopic acid (XA) present in the fruit extract have been shown to possess analgesic properties in animals. There is the likelihood of concomitant use of XA and the commonly used analgesics in traditional settings. This study, therefore, evaluated the pharmacologic interaction between XA/morphine and xylopic/diclofenac combinations. Methods: The formalin test and acetic acid writhing test were used to study the antinociceptive activity of XA, morphine, and diclofenac. The isobolographic analysis was used to study the antinociceptive interactions between XA co-administered with morphine or diclofenac. Results: Results obtained revealed that XA (10–100 mg/kg), morphine (1–10 mg/kg), and diclofenac (1–10 mg/kg) produced dose-related antinociception with different potencies in the formalin and acetic acid writhing tests. Isobolographic analysis of XA/morphine and XA/diclofenac combinations revealed potentiation of their antinociceptive effects. The degree of potentiation calculated as interaction index showed synergism for both combinations in all the nociceptive tests. Conclusion: In conclusion, the present study demonstrated synergism for the co-administration of XA with morphine or diclofenac. PMID:26692735

High content analysis provides mechanistic insights on the pathways of toxicity induced by amine-modified polystyrene nanoparticles.

PubMed

Anguissola, Sergio; Garry, David; Salvati, Anna; O'Brien, Peter J; Dawson, Kenneth A

2014-01-01

The fast-paced development of nanotechnology needs the support of effective safety testing. We have developed a screening platform measuring simultaneously several cellular parameters for exposure to various concentrations of nanoparticles (NPs). Cell lines representative of different organ cell types, including lung, endothelium, liver, kidney, macrophages, glia, and neuronal cells were exposed to 50 nm amine-modified polystyrene (PS-NH2) NPs previously reported to induce apoptosis and to 50 nm sulphonated and carboxyl-modified polystyrene NPs that were reported to be silent. All cell lines apart from Raw 264.7 executed apoptosis in response to PS-NH2 NPs, showing specific sequences of EC50 thresholds; lysosomal acidification was the most sensitive parameter. Loss of mitochondrial membrane potential and plasma membrane integrity measured by High Content Analysis resulted comparably sensitive to the equivalent OECD-recommended assays, allowing increased output. Analysis of the acidic compartments revealed good cerrelation between size/fluorescence intensity and dose of PS-NH2 NPs applied; moreover steatosis and phospholipidosis were observed, consistent with the lysosomal alterations revealed by Lysotracker green; similar responses were observed when comparing astrocytoma cells with primary astrocytes. We have established a platform providing mechanistic insights on the response to exposure to nanoparticles. Such platform holds great potential for in vitro screening of nanomaterials in highthroughput format.

Secretome Analysis of the Pine Wood Nematode Bursaphelenchus xylophilus Reveals the Tangled Roots of Parasitism and Its Potential for Molecular Mimicry.

PubMed

Shinya, Ryoji; Morisaka, Hironobu; Kikuchi, Taisei; Takeuchi, Yuko; Ueda, Mitsuyoshi; Futai, Kazuyoshi

2013-01-01

Since it was first introduced into Asia from North America in the early 20(th) century, the pine wood nematode Bursaphelenchus xylophilus has caused the devastating forest disease called pine wilt. The emerging pathogen spread to parts of Europe and has since been found as the causal agent of pine wilt disease in Portugal and Spain. In 2011, the entire genome sequence of B. xylophilus was determined, and it allowed us to perform a more detailed analysis of B. xylophilus parasitism. Here, we identified 1,515 proteins secreted by B. xylophilus using a highly sensitive proteomics method combined with the available genomic sequence. The catalogue of secreted proteins contained proteins involved in nutrient uptake, migration, and evasion from host defenses. A comparative functional analysis of the secretome profiles among parasitic nematodes revealed a marked expansion of secreted peptidases and peptidase inhibitors in B. xylophilus via gene duplication and horizontal gene transfer from fungi and bacteria. Furthermore, we showed that B. xylophilus secreted the potential host mimicry proteins that closely resemble the host pine's proteins. These proteins could have been acquired by host-parasite co-evolution and might mimic the host defense systems in susceptible pine trees during infection. This study contributes to an understanding of their unique parasitism and its tangled roots, and provides new perspectives on the evolution of plant parasitism among nematodes.

Discovery of novel xylosides in co-culture of basidiomycetes Trametes versicolor and Ganoderma applanatum by integrated metabolomics and bioinformatics

NASA Astrophysics Data System (ADS)

Yao, Lu; Zhu, Li-Ping; Xu, Xiao-Yan; Tan, Ling-Ling; Sadilek, Martin; Fan, Huan; Hu, Bo; Shen, Xiao-Ting; Yang, Jie; Qiao, Bin; Yang, Song

2016-09-01

Transcriptomic analysis of cultured fungi suggests that many genes for secondary metabolite synthesis are presumably silent under standard laboratory condition. In order to investigate the expression of silent genes in symbiotic systems, 136 fungi-fungi symbiotic systems were built up by co-culturing seventeen basidiomycetes, among which the co-culture of Trametes versicolor and Ganoderma applanatum demonstrated the strongest coloration of confrontation zones. Metabolomics study of this co-culture discovered that sixty-two features were either newly synthesized or highly produced in the co-culture compared with individual cultures. Molecular network analysis highlighted a subnetwork including two novel xylosides (compounds 2 and 3). Compound 2 was further identified as N-(4-methoxyphenyl)formamide 2-O-β-D-xyloside and was revealed to have the potential to enhance the cell viability of human immortalized bronchial epithelial cell line of Beas-2B. Moreover, bioinformatics and transcriptional analysis of T. versicolor revealed a potential candidate gene (GI: 636605689) encoding xylosyltransferases for xylosylation. Additionally, 3-phenyllactic acid and orsellinic acid were detected for the first time in G. applanatum, which may be ascribed to response against T.versicolor stress. In general, the described co-culture platform provides a powerful tool to discover novel metabolites and help gain insights into the mechanism of silent gene activation in fungal defense.

Discovery of novel xylosides in co-culture of basidiomycetes Trametes versicolor and Ganoderma applanatum by integrated metabolomics and bioinformatics

PubMed Central

Yao, Lu; Zhu, Li-Ping; Xu, Xiao-Yan; Tan, Ling-Ling; Sadilek, Martin; Fan, Huan; Hu, Bo; Shen, Xiao-Ting; Yang, Jie; Qiao, Bin; Yang, Song

2016-01-01

Transcriptomic analysis of cultured fungi suggests that many genes for secondary metabolite synthesis are presumably silent under standard laboratory condition. In order to investigate the expression of silent genes in symbiotic systems, 136 fungi-fungi symbiotic systems were built up by co-culturing seventeen basidiomycetes, among which the co-culture of Trametes versicolor and Ganoderma applanatum demonstrated the strongest coloration of confrontation zones. Metabolomics study of this co-culture discovered that sixty-two features were either newly synthesized or highly produced in the co-culture compared with individual cultures. Molecular network analysis highlighted a subnetwork including two novel xylosides (compounds 2 and 3). Compound 2 was further identified as N-(4-methoxyphenyl)formamide 2-O-β-D-xyloside and was revealed to have the potential to enhance the cell viability of human immortalized bronchial epithelial cell line of Beas-2B. Moreover, bioinformatics and transcriptional analysis of T. versicolor revealed a potential candidate gene (GI: 636605689) encoding xylosyltransferases for xylosylation. Additionally, 3-phenyllactic acid and orsellinic acid were detected for the first time in G. applanatum, which may be ascribed to response against T.versicolor stress. In general, the described co-culture platform provides a powerful tool to discover novel metabolites and help gain insights into the mechanism of silent gene activation in fungal defense. PMID:27616058

Look Who's Talking - The Role of the IARPC Collaborations Website in Supporting Mutli-Institution Dialog on Arctic Research Imperatives

NASA Astrophysics Data System (ADS)

Starkweather, S.; Stephenson, S. N.; Rohde, J. A.; Bowden, S.

2015-12-01

The IARPC Collaborations website (www.iarpccollaborations.org) was developed to support collaborative implementation of the Interagency Arctic Research Policy Committee's (IARPC) 5-Year Plan for Arctic Research. The Plan describes an ambitious agenda for advancing understanding of the changing Arctic, a challenge that requires innovative approaches to integrate disparate research activities. IARPC was created by Congress to address this integration with a mandate that includes developing interagency collaboration and outside partnerships, specifically those with the State of Alaska, indigenous communities, academia, industry and non-governmental organizations. The IARPC Collaborations website was introduced in October of 2014 as an innovative means to address IARPC's mandate. It is an open, social networking platform with member-driven content and features to support dialog and milestone tracking. In its first year, IARPC Collaborations has attracted more than 600 members. Member-supplied content added to the site includes more than 575 research planning documents and scientific presentations and 300 updates on research plans and resources; all content is tagged with descriptive keywords to expedite discovery and elucidate connectivity across members and topics. Applying a social network analysis to metadata from the site reveals the strength and nature of this connectivity. This analysis demonstrates that Collaboration Team phone meetings remain the dominant form of communication. Dialog on the site through comment forums has been slow to emerge despite its merits of persistence and transparency. While more than 80 members have used the comment features at least once, the strong centrality of the IARPC Secretariat to website dialog is apparent. An analysis of content keywords demonstrates the potential for improved dialog based on overlapping interests as revealed by trending topics like "sea ice prediction", "traditional knowledge" and "permafrost carbon". Less than one year into launch, this analysis of IARPC's experiment in collaborative integration reveals the enduring strengths of traditional collaboration tools like secretariat support and phone meetings; the full potential of IARPC's social networking tools remains to be seen.

Potential application of non-small cell lung cancer-associated autoantibodies to early cancer diagnosis

PubMed Central

Yao, Yibing; Fan, Yu; Wu, Jun; Wan, Haisu; Wang, Jing; Lam, Stephen; Lam, Wan L.; Girard, Luc; Gazdar, Adi F.; Wu, Zhihao; Zhou, Qinghua

2015-01-01

To identify a panel of tumor associated autoantibodies which can potentially be used as biomarkers for the early diagnosis of non-small cell lung cancer (NSCLC). Thirty-five unique and in-frame expressed phage proteins were isolated. Based on the gene expression profiling, four proteins were selected for further study. Both receiver operating characteristic curve analysis and leave-one-out method revealed that combined measurements of four antibodies produced have better predictive accuracies than any single marker alone. Leave-one-out validation also showed significant relevance with all stages of NSCLC patients. The panel of autoantibodies has a high potential for detecting early stage NSCLC. PMID:22713465

Artificial fingerprint recognition by using optical coherence tomography with autocorrelation analysis.

PubMed

Cheng, Yezeng; Larin, Kirill V

2006-12-20

Fingerprint recognition is one of the most widely used methods of biometrics. This method relies on the surface topography of a finger and, thus, is potentially vulnerable for spoofing by artificial dummies with embedded fingerprints. In this study, we applied the optical coherence tomography (OCT) technique to distinguish artificial materials commonly used for spoofing fingerprint scanning systems from the real skin. Several artificial fingerprint dummies made from household cement and liquid silicone rubber were prepared and tested using a commercial fingerprint reader and an OCT system. While the artificial fingerprints easily spoofed the commercial fingerprint reader, OCT images revealed the presence of them at all times. We also demonstrated that an autocorrelation analysis of the OCT images could be potentially used in automatic recognition systems.

Artificial fingerprint recognition by using optical coherence tomography with autocorrelation analysis

NASA Astrophysics Data System (ADS)

Cheng, Yezeng; Larin, Kirill V.

2006-12-01

Fingerprint recognition is one of the most widely used methods of biometrics. This method relies on the surface topography of a finger and, thus, is potentially vulnerable for spoofing by artificial dummies with embedded fingerprints. In this study, we applied the optical coherence tomography (OCT) technique to distinguish artificial materials commonly used for spoofing fingerprint scanning systems from the real skin. Several artificial fingerprint dummies made from household cement and liquid silicone rubber were prepared and tested using a commercial fingerprint reader and an OCT system. While the artificial fingerprints easily spoofed the commercial fingerprint reader, OCT images revealed the presence of them at all times. We also demonstrated that an autocorrelation analysis of the OCT images could be potentially used in automatic recognition systems.

Identification of potential biomarkers for post-traumatic complications released after trauma-hemorrhage from murine Kupffer cells and its investigation in lung and liver.

PubMed

Schultze, Cornelia; Hildebrand, Frank; Noack, Sandra; Krettek, Christian; Zeckey, Christian; Neunaber, Claudia

2016-11-01

Early diagnosis of complications after severe trauma by specific biomarkers remains difficult. Identify potential new biomarkers for early diagnosis of post-traumatic complications. Mice underwent pressure-controlled hemorrhage or sham procedure. Four hours later, genome-wide expression of isolated Kupffer cells was compared with controls using Affymetrix-Genechip-Expression-Analysis and real-time-PCR. Expression analysis and real-time-PCR revealed a significant increase of gene expression of Cxcl10, Il4ra, Csf2rb2, Lcn2, and Gbp5. Cxcl10, Il4ra, Csf2rb2, Lcn2, and Gbp5 might represent new biomarkers for early diagnosis of post-traumatic complications, if they are linked to the development of post-traumatic complications.

Spanish adaptation of the Creative Potential and Practised Creativity scale (CPPC-17) in the workplace and inside the organization.

PubMed

Boada-Grau, Joan; Sánchez-García, José-Carlos; Prizmic-Kuzmica, Aldo-Javier; Vigil-Colet, Andreu

2014-01-01

This study follows the theoretical framework put forward by Hinton on creative potential and practised creativity. The objective was to adapt the 17-item Creative Potential and Practised Creativity scale into Spanish and examine its psychometric properties. The study sample was made up of 975 Spanish employees (48.5% men and 51.5% women). After performing a confirmatory factor analysis, the findings revealed a three-factor structure: Creative potential, Practised creativity and Perception of organizational support. Furthermore, appropriate reliability was found for all three factors as well as initial evidence of construct validity in relation to certain external correlates and a series of scales measuring workaholism, irritation, burnout and personality. The present scale may prove ideal for adequately identifying Creative potential, Practised creativity and Perceived organizational support.

A meta-analysis investigating factors underlying attrition rates in infant ERP studies.

PubMed

Stets, Manuela; Stahl, Daniel; Reid, Vincent M

2012-01-01

In this meta-analysis, we examined interrelationships between characteristics of infant event-related potential (ERP) studies and their attrition rates. One-hundred and forty-nine published studies provided information on 314 experimental groups of which 181 provided data on attrition. A random effects meta-analysis revealed a high average attrition rate of 49.2%. Additionally, we used meta-regression for 178 groups with attrition data to analyze which variables best explained attrition variance. Our main findings were that the nature of the stimuli-visual, auditory, or combined as well as if stimuli were animated-influenced exclusion rates from the final analysis and that infant age did not alter attrition rates.

A content analysis of smoking fetish videos on YouTube: regulatory implications for tobacco control.

PubMed

Kim, Kyongseok; Paek, Hye-Jin; Lynn, Jordan

2010-03-01

This study examined the prevalence, accessibility, and characteristics of eroticized smoking portrayal, also referred to as smoking fetish, on YouTube. The analysis of 200 smoking fetish videos revealed that the smoking fetish videos are prevalent and accessible to adolescents on the website. They featured explicit smoking behavior by sexy, young, and healthy females, with the content corresponding to PG-13 and R movie ratings. We discuss a potential impact of the prosmoking image on youth according to social cognitive theory, and implications for tobacco control.

Chemical phase analysis of seed mediated synthesized anisotropic silver nanoparticles

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

Bharti, Amardeep, E-mail: abharti@pu.ac.in; Goyal, Navdeep; Singh, Suman

Noble-metal nanoparticles are of great interest because of its broad applications almost in every stream (i.e. biology, chemistry and engineering) due to their unique size/shape dependant properties. In this paper, chemical phase of seed mediated synthesized anisotropic silver nanoparticle (AgNPs) has been investigated via fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). These nanaoparticles were synthesized by seed-growth method controlled by urea and dextrose results to highly stable 12-20 nm particle size revealed by zeta potential and transmission electron microscopy (TEM)

Algal Biomass Analysis by Laser-Based Analytical Techniques—A Review

PubMed Central

Pořízka, Pavel; Prochazková, Petra; Prochazka, David; Sládková, Lucia; Novotný, Jan; Petrilak, Michal; Brada, Michal; Samek, Ota; Pilát, Zdeněk; Zemánek, Pavel; Adam, Vojtěch; Kizek, René; Novotný, Karel; Kaiser, Jozef

2014-01-01

Algal biomass that is represented mainly by commercially grown algal strains has recently found many potential applications in various fields of interest. Its utilization has been found advantageous in the fields of bioremediation, biofuel production and the food industry. This paper reviews recent developments in the analysis of algal biomass with the main focus on the Laser-Induced Breakdown Spectroscopy, Raman spectroscopy, and partly Laser-Ablation Inductively Coupled Plasma techniques. The advantages of the selected laser-based analytical techniques are revealed and their fields of use are discussed in detail. PMID:25251409

To 3D or Not to 3D, That Is the Question: Do 3D Surface Analyses Improve the Ecomorphological Power of the Distal Femur in Placental Mammals?

PubMed Central

Gould, Francois D. H.

2014-01-01

Improvements in three-dimensional imaging technologies have renewed interest in the study of functional and ecological morphology. Quantitative approaches to shape analysis are used increasingly to study form-function relationships. These methods are computationally intensive, technically demanding, and time-consuming, which may limit sampling potential. There have been few side-by-side comparisons of the effectiveness of such approaches relative to more traditional analyses using linear measurements and ratios. Morphological variation in the distal femur of mammals has been shown to reflect differences in locomotor modes across clades. Thus I tested whether a geometric morphometric analysis of surface shape was superior to a multivariate analysis of ratios for describing ecomorphological patterns in distal femoral variation. A sample of 164 mammalian specimens from 44 genera was assembled. Each genus was assigned to one of six locomotor categories. The same hypotheses were tested using two methods. Six linear measurements of the distal femur were taken with calipers, from which four ratios were calculated. A 3D model was generated with a laser scanner, and analyzed using three dimensional geometric morphometrics. Locomotor category significantly predicted variation in distal femoral morphology in both analyses. Effect size was larger in the geometric morphometric analysis than in the analysis of ratios. Ordination reveals a similar pattern with arboreal and cursorial taxa as extremes on a continuum of morphologies in both analyses. Discriminant functions calculated from the geometric morphometric analysis were more accurate than those calculated from ratios. Both analysis of ratios and geometric morphometric surface analysis reveal similar, biologically meaningful relationships between distal femoral shape and locomotor mode. The functional signal from the morphology is slightly higher in the geometric morphometric analysis. The practical costs of conducting these sorts of analyses should be weighed against potentially slight increases in power when designing protocols for ecomorphological studies. PMID:24633081

Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection.

PubMed

Setliff, Ian; McDonnell, Wyatt J; Raju, Nagarajan; Bombardi, Robin G; Murji, Amyn A; Scheepers, Cathrine; Ziki, Rutendo; Mynhardt, Charissa; Shepherd, Bryan E; Mamchak, Alusha A; Garrett, Nigel; Karim, Salim Abdool; Mallal, Simon A; Crowe, James E; Morris, Lynn; Georgiev, Ivelin S

2018-06-13

Characterization of single antibody lineages within infected individuals has provided insights into the development of Env-specific antibodies. However, a systems-level understanding of the humoral response against HIV-1 is limited. Here, we interrogated the antibody repertoires of multiple HIV-infected donors from an infection-naive state through acute and chronic infection using next-generation sequencing. This analysis revealed the existence of "public" antibody clonotypes that were shared among multiple HIV-infected individuals. The HIV-1 reactivity for representative antibodies from an identified public clonotype shared by three donors was confirmed. Furthermore, a meta-analysis of publicly available antibody repertoire sequencing datasets revealed antibodies with high sequence identity to known HIV-reactive antibodies, even in repertoires that were reported to be HIV naive. The discovery of public antibody clonotypes in HIV-infected individuals represents an avenue of significant potential for better understanding antibody responses to HIV-1 infection, as well as for clonotype-specific vaccine development. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Soft J-tipped guide wire-induced cardiac perforation in a patient with right ventricular lipomatosis and wall thinning.

PubMed

Hiroshima, Yuki; Tajima, Katsushi; Shiono, Yousuke; Suzuki, Ikuko; Kohno, Kei; Kato, Yuichi; Shunji, Kawamura; Kato, Takeo

2012-01-01

Cardiac tamponade caused by perforation is a rare but potentially lethal complication of central venous catheter (CVC) insertion. We herein report a case of cardiac perforation associated with the use of a soft J-tipped guide wire. Twenty minutes after the insertion of a CVC, the patient developed unexpected cardiac arrest. An autopsy revealed 400 mL of pericardial blood. The right ventricular wall was 1 mm thick with about 10 myocyte layers, which is one-third that of the normal heart. A histological analysis revealed widespread fatty infiltration of the right ventricular wall (right ventricular lipomatosis).

Antibiofilm potential of flavonoids extracted from Moringa oleifera seed coat against Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans.

PubMed

Onsare, J G; Arora, D S

2015-02-01

The increased microbial drug resistance due to biofilms and the side effects associated with the use of conventional drugs is still a major concern in the medical fraternity. This work evaluates the antibiofilm potential of flavonoids extracted from Moringa oleifera seed coat (SC) in search for green and effective alternatives for overcoming menace of biofilms. The study evaluated the minimum inhibitory concentration (MIC) of flavonoids against respective test organisms, inhibition of initial cell attachment as well as disruption of preformed biofilms and metabolic activity of treated biofilms. Mutagenicity and cytotoxicity as well as characterization of the active component were also carried out. Although Pseudomonas aeruginosa showed the lowest MIC of 0.05 mg ml(-1), the action of flavonoids and gentamicin on initial cell attachment revealed a comparable effect against bacterial biofilms, i.e. Staphylococcus aureus and Pseudomonas aeruginosa with approx. 80% inhibition compared to Candida albicans. Disruption of the preformed biofilms revealed that susceptibility of P. aeruginosa began as early as 4 h of exposure to flavonoids with 88% growth inhibition at the end of 24-h incubation. Encouragingly, t-test analysis on the effect of the extract and the standard antibiotic against each organism indicated no significant variance at P < 0.05. A drastic low metabolic activity exhibited by the treated biofilms as compared to the untreated ones was further supportive of the antibiofilm potential of seed coat flavonoids. The bioactive component from M. oleifera seed coat has exhibited antibiofilm potential against the test organisms belonging to Gram positive, Gram negative and yeast. Antibiofilm potential and biosafety of plant-based flavonoids from M. oleifera seed coat reveal a prospective active principle that could be of use in biofilm-associated menace. © 2014 The Society for Applied Microbiology.

Electro-osmosis over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions

NASA Astrophysics Data System (ADS)

Ghosh, Uddipta; Chakraborty, Suman

2016-06-01

In this study, we attempt to bring out a generalized formulation for electro-osmotic flows over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions. To this end, we start with modified electro-chemical potential of the individual species and subsequently use it to derive modified Nernst-Planck equation accounting for the ionic fluxes generated because of the presence of non-electrostatic potential. We establish what we refer to as the Poisson-Helmholtz-Nernst-Planck equations, coupled with the Navier-Stokes equations, to describe the complete transport process. Our analysis shows that the presence of non-electrostatic interactions between the ions results in an excess body force on the fluid, and modifies the osmotic pressure as well, which has hitherto remained unexplored. We further apply our analysis to a simple geometry, in an effort to work out the Smoluchowski slip velocity for thin electrical double layer limits. To this end, we employ singular perturbation and develop a general framework for the asymptotic analysis. Our calculations reveal that the final expression for slip velocity remains the same as that without accounting for non-electrostatic interactions. However, the presence of non-electrostatic interactions along with ion specificity can significantly change the quantitative behavior of Smoluchowski slip velocity. We subsequently demonstrate that the presence of non-electrostatic interactions may significantly alter the effective interfacial potential, also termed as the "Zeta potential." Our analysis can potentially act as a guide towards the prediction and possibly quantitative determination of the implications associated with the existence of non-electrostatic potential, in an electrokinetic transport process.

Identification and evaluation of semiochemicals for the biological control of the beetle Omorgus suberosus (F.) (Coleoptera: Trogidae), a facultative predator of eggs of the sea turtle Lepidochelys olivacea (Eschscholtz).

PubMed

Cortez, Vieyle; Verdú, José R; Ortiz, Antonio J; Halffter, Gonzalo

2017-01-01

The beetle Omorgus suberosus (F.) is a facultative predator of eggs of the olive ridley turtle Lepidochelys olivacea (Eschscholtz). Laboratory and field investigations were conducted in order to characterize volatile attractants of O. suberosus and to explore the potential for application of these volatiles in a selective mass trapping method. Headspace sorptive extraction (HSSE) coupled to thermo-desorption gas chromatography-mass spectrometry (TD-GC-MS) analysis of the volatile constituents from beetles or turtle nests revealed 24 potential compounds. However, electroantennographic (EAG) measurements revealed antennal sensitivity only to indole, linoleic acid, trimethylamine, dimethyl sulphide, dimethyl disulphide and ammonia. Behavioural tests showed that these compounds are highly attractive to O. suberosus. Field trapping experiments revealed that indole and ammonia were more attractive than the other volatile compounds and showed similar attractiveness to that produced by conventional baits (chicken feathers). The use of a combined bait of indole and NH3 would therefore be the most effective trap design. The data presented are the first to demonstrate effective massive capture of O. suberosus using an attractant-based trapping method. These findings have potential for the development of an efficient mass trapping method for control of this beetle as part of efforts towards conservation of L. olivacea at La Escobilla in Oaxaca, Mexico.

Identification and evaluation of semiochemicals for the biological control of the beetle Omorgus suberosus (F.) (Coleoptera: Trogidae), a facultative predator of eggs of the sea turtle Lepidochelys olivacea (Eschscholtz)

PubMed Central

Cortez, Vieyle; Ortiz, Antonio J.; Halffter, Gonzalo

2017-01-01

The beetle Omorgus suberosus (F.) is a facultative predator of eggs of the olive ridley turtle Lepidochelys olivacea (Eschscholtz). Laboratory and field investigations were conducted in order to characterize volatile attractants of O. suberosus and to explore the potential for application of these volatiles in a selective mass trapping method. Headspace sorptive extraction (HSSE) coupled to thermo-desorption gas chromatography–mass spectrometry (TD-GC-MS) analysis of the volatile constituents from beetles or turtle nests revealed 24 potential compounds. However, electroantennographic (EAG) measurements revealed antennal sensitivity only to indole, linoleic acid, trimethylamine, dimethyl sulphide, dimethyl disulphide and ammonia. Behavioural tests showed that these compounds are highly attractive to O. suberosus. Field trapping experiments revealed that indole and ammonia were more attractive than the other volatile compounds and showed similar attractiveness to that produced by conventional baits (chicken feathers). The use of a combined bait of indole and NH3 would therefore be the most effective trap design. The data presented are the first to demonstrate effective massive capture of O. suberosus using an attractant-based trapping method. These findings have potential for the development of an efficient mass trapping method for control of this beetle as part of efforts towards conservation of L. olivacea at La Escobilla in Oaxaca, Mexico. PMID:28192472

Dangers resulting from DNA profiling of biological materials derived from patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT) with regard to forensic genetic analysis.

PubMed

Jacewicz, R; Lewandowski, K; Rupa-Matysek, J; Jędrzejczyk, M; Berent, J

The study documents the risk that comes with DNA analysis of materials derived from patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in forensic genetics. DNA chimerism was studied in 30 patients after allo-HSCT, based on techniques applied in contemporary forensic genetics, i.e. real-time PCR and multiplex PCR-STR with the use of autosomal DNA as well as Y-DNA markers. The results revealed that the DNA profile of the recipient's blood was identical with the donor's in the majority of cases. Therefore, blood analysis can lead to false conclusions in personal identification as well as kinship analysis. An investigation of buccal swabs revealed a mixture of DNA in the majority of recipients. Consequently, personal identification on the basis of stain analysis of the same origin may be impossible. The safest (but not ideal) material turned out to be the hair root. Its analysis based on autosomal DNA revealed 100% of the recipient's profile. However, an analysis based on Y-chromosome markers performed in female allo-HSCT recipients with male donors demonstrated the presence of donor DNA in hair cells - similarly to the blood and buccal swabs. In the light of potential risks arising from DNA profiling of biological materials derived from persons after allotransplantation in judicial aspects, certain procedures were proposed to eliminate such dangers. The basic procedures include abandoning the approach based exclusively on blood collection, both for kinship analysis and personal identification; asking persons who are to be tested about their history of allo-HSCT before sample collection and profile entry in the DNA database, and verification of DNA profiling based on hair follicles in uncertain cases.

The weapon potential of a microbe.

PubMed

Casadevall, Arturo; Pirofski, Liise-anne

2004-06-01

The designation of a microbe as a potential biological weapon poses the vexing question of how such a decision is made given the many pathogenic microbes that cause disease. Analysis of the properties of microbes that are currently considered biological weapons against humans revealed no obvious relationship to virulence, except that all are pathogenic for humans. Notably, the weapon potential of a microbe rather than its pathogenic properties or virulence appeared to be the major consideration when categorizing certain agents as biological weapons. In an effort to standardize the assessment of the risk that is posed by microbes as biological warfare agents using the basic principles of microbial communicability (defined here as a parameter of transmission) and virulence, a simple formula is proposed for estimating the weapon potential of a microbe.

Electronic zero-point fluctuation forces inside circuit components

PubMed Central

Leonhardt, Ulf

2018-01-01

One of the most intriguing manifestations of quantum zero-point fluctuations are the van der Waals and Casimir forces, often associated with vacuum fluctuations of the electromagnetic field. We study generalized fluctuation potentials acting on internal degrees of freedom of components in electrical circuits. These electronic Casimir-like potentials are induced by the zero-point current fluctuations of any general conductive circuit. For realistic examples of an electromechanical capacitor and a superconducting qubit, our results reveal the possibility of tunable forces between the capacitor plates, or the level shifts of the qubit, respectively. Our analysis suggests an alternative route toward the exploration of Casimir-like fluctuation potentials, namely, by characterizing and measuring them as a function of parameters of the environment. These tunable potentials may be useful for future nanoelectromechanical and quantum technologies. PMID:29719863

Analysis of penumbral eclipse data

NASA Technical Reports Server (NTRS)

Garrett, H. B.

1977-01-01

Two days of data from the ATS-6 1976 eclipse season were analyzed to determine the effects of varying photoelectron flux on spacecraft potential. Particular emphasis was placed on the variation in potential as the satellite entered the earth's penumbra. Measurements from the AE-C satellite of the solar UV radiation were used to construct a model of atmospheric attenuation. This model was found to be consistent with direct measurements of the variations in photoelectron flux as Injun 5 passed into eclipse. Applying the model to the ATS-6 data gave the time dependency of the solar illumination/photoelectron flux as the satellite was eclipsed. This relationship, when combined with the ATS-6 measurements of satellite potential, revealed a nearly linear relation between the solar illumination/photoelectron flux and the logarithm of the satellite potential.

Medication Incidents Involving Antiepileptic Drugs in Canadian Hospitals: A Multi-Incident Analysis.

PubMed

Cheng, Roger; Yang, Yu Daisy; Chan, Matthew; Patel, Tejal

2017-01-01

Medication errors involving antiepileptic drugs (AEDs) are not well studied but have the potential to cause significant harm. We investigated the occurrence of medication incidents in Canadian hospitals that involve AEDs, their severity and contributing factors by analyzing data from two national databases. Our multi-incident analysis revealed that while medication errors were rarely fatal, errors do occur of which some are serious. Medication incidents were most commonly caused by dose omissions, the dose or its frequency being incorrect and the wrong AED being given. Our analysis could augment quality-improvement initiatives by medication safety administrators to reduce AED medication incidents in hospitals.

Depression in female adolescents: an IPA analysis.

PubMed

Shaw, Samantha K; Dallos, Rudi; Shoebridge, Philip

2009-04-01

Six female adolescents participated in open-ended interviews regarding their experiences of depression. The transcripts of their interviews were explored using Interpretative Phenomenological Analysis (Smith, 1991). The analysis revealed three inter-connected super-ordinate themes which were: communication, hurt self, and difference. These themes centred on communication processes in participants' families and with peers, issues relating to shifts in identity through adolescence, and feelings of being damaged, distressed, and hurt. Amongst a range of potentially relevant perspectives, an attachment theory (Bowlby, 1969) orientation was found to be particularly relevant and helpful in interpreting the themes that captured these young women's experiences. Some implications for clinical practice are discussed.

An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome.

PubMed

Durand, Pierre M; Oelofse, Andries J; Coetzer, Theresa L

2006-11-04

The completed genome sequences of the malaria parasites P. falciparum, P. y. yoelii and P. vivax have revealed some unusual features. P. falciparum contains the most AT rich genome sequenced so far--over 90% in some regions. In comparison, P. y. yoelii is approximately 77% and P. vivax is approximately 55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in Plasmodium has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three Plasmodium species. Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in P. vivax, eight in P. y. yoelii and only six in P. falciparum. Further investigation of the six open reading frames in P. falciparum revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in P. y. yoelii and P. falciparum. One of the P. vivax open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene. There is a divergence in the frequencies of mobile genetic elements in the three Plasmodium species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the P. falciparum genome.

Molecular analysis of the bacterial microbiome in the forestomach fluid from the dromedary camel (Camelus dromedarius).

PubMed

Bhatt, Vaibhav D; Dande, Suchitra S; Patil, Nitin V; Joshi, Chaitanya G

2013-04-01

Rumen microorganisms play an important role in ruminant digestion and absorption of nutrients and have great potential applications in the field of rumen adjusting, food fermentation and biomass utilization etc. In order to investigate the composition of microorganisms in the rumen of camel (Camelus dromedarius), this study delves in the microbial diversity by culture-independent approach. It includes comparison of rumen samples investigated in the present study to other currently available metagenomes to reveal potential differences in rumen microbial systems. Pyrosequencing based metagenomics was applied to analyze phylogenetic and metabolic profiles by MG-RAST, a web based tool. Pyrosequencing of camel rumen sample yielded 8,979,755 nucleotides assembled to 41,905 sequence reads with an average read length of 214 nucleotides. Taxonomic analysis of metagenomic reads indicated Bacteroidetes (55.5 %), Firmicutes (22.7 %) and Proteobacteria (9.2 %) phyla as predominant camel rumen taxa. At a finer phylogenetic resolution, Bacteroides species dominated the camel rumen metagenome. Functional analysis revealed that clustering-based subsystem and carbohydrate metabolism were the most abundant SEED subsystem representing 17 and 13 % of camel metagenome, respectively. A high taxonomic and functional similarity of camel rumen was found with the cow metagenome which is not surprising given the fact that both are mammalian herbivores with similar digestive tract structures and functions. Combined pyrosequencing approach and subsystems-based annotations available in the SEED database allowed us access to understand the metabolic potential of these microbiomes. Altogether, these data suggest that agricultural and animal husbandry practices can impose significant selective pressures on the rumen microbiota regardless of rumen type. The present study provides a baseline for understanding the complexity of camel rumen microbial ecology while also highlighting striking similarities and differences when compared to other animal gastrointestinal environments.

Angiotensin-converting enzyme 2 is subject to post-transcriptional regulation by miR-421.

PubMed

Lambert, Daniel W; Lambert, Louise A; Clarke, Nicola E; Hooper, Nigel M; Porter, Karen E; Turner, Anthony J

2014-08-01

ACE2 (angiotensin converting enzyme 2) plays a critical role in the local tissue RAS (renin-angiotensin system) by hydrolysing the potent hypertensive and mitogenic peptide AngII (angiotensin II). Changes in the levels of ACE2 have been observed in a number of pathologies, including cardiovascular disease, but little is known of the mechanisms regulating its expression. In the present study, therefore, the potential role of miRNAs in the regulation of ACE2 expression in primary human cardiac myofibroblasts was examined. Putative miRNA-binding sites were identified in the 3'-UTR of the ACE2 transcript using online prediction algorithms. Two of these, miR-200b and miR-421, were selected for further analysis. A reporter system using the 3'-UTR of ACE2 fused to the coding region of firefly luciferase was used to determine the functionality of the identified binding sites in vitro. This identified miR-421, but not miR-200b, as a potential regulator of ACE2. The ability of miR-421, an miRNA implicated in the development of thrombosis, to down-regulate ACE2 expression was subsequently confirmed by Western blot analysis of both primary cardiac myofibroblasts and transformed cells transfected with a synthetic miR-421 precursor. Real-time PCR analysis of miR-421 revealed widespread expression in human tissues. miR-421 levels in cardiac myofibroblasts showed significant inter-patient variability, in keeping with the variability of ACE2 expression we have observed previously. In conclusion, the present study is the first to demonstrate that ACE2 may be subject to post-transcriptional regulation and reveals a novel potential therapeutic target, miR-421, which could be exploited to modulate ACE2 expression in disease.

Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass.

PubMed

Renan, Sharon; Greenbaum, Gili; Shahar, Naama; Templeton, Alan R; Bouskila, Amos; Bar-David, Shirli

2015-04-01

Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited. © 2015 John Wiley & Sons Ltd.

A novel approach to pharmaco-EEG for investigating analgesics: assessment of spectral indices in single-sweep evoked brain potentials.

PubMed

Gram, Mikkel; Graversen, Carina; Nielsen, Anders K; Arendt-Nielsen, Thomas; Mørch, Carsten D; Andresen, Trine; Drewes, Asbjørn M

2013-12-01

To compare results from analysis of averaged and single-sweep evoked brain potentials (EPs) by visual inspection and spectral analysis in order to identify an objective measure for the analgesic effect of buprenorphine and fentanyl. Twenty-two healthy males were included in a randomized study to assess the changes in EPs after 110 sweeps of painful electrical stimulation to the median nerve following treatment with buprenorphine, fentanyl or placebo patches. Bone pressure, cutaneous heat and electrical pain ratings were assessed. EPs and pain assessments were obtained before drug administration, 24, 48, 72 and 144 h after beginning of treatment. Features from EPs were extracted by three different approaches: (i) visual inspection of amplitude and latency of the main peaks in the average EPs, (ii) spectral distribution of the average EPs and (iii) spectral distribution of the EPs from single-sweeps. Visual inspection revealed no difference between active treatments and placebo (all P > 0.05). Spectral distribution of the averaged potentials showed a decrease in the beta (12-32 Hz) band for fentanyl (P = 0.036), which however did not correlate with pain ratings. Spectral distribution in the single-sweep EPs revealed significant increases in the theta, alpha and beta bands for buprenorphine (all P < 0.05) as well as theta band increase for fentanyl (P = 0.05). For buprenorphine, beta band activity correlated with bone pressure and cutaneous heat pain (both P = 0.04, r = 0.90). In conclusion single-sweep spectral band analysis increases the information on the response of the brain to opioids and may be used to identify the response to analgesics. © 2013 The Authors. British Journal of Clinical Pharmacology © 2013 The British Pharmacological Society.

Characterizing biomarkers in osteosarcoma metastasis based on an ego-network.

PubMed

Liu, Zhen; Song, Yan

2017-06-01

To characterize biomarkers that underlie osteosarcoma (OS) metastasis based on an ego-network. From the microarray data, we obtained 13,326 genes. By combining PPI data and microarray data, 10,520 shared genes were found and constructed into ego-networks. 17 significant ego-networks were identified with p < 0.05. In the pathway enrichment analysis, seven ego-networks were identified with the most significant pathway. These significant ego-modules were potential biomarkers that reveal the potential mechanisms in OS metastasis, which may contribute to understanding cancer prognoses and providing new perspectives in the treatment of cancer.

Minamata disease (organic mercury poisoning): neuroradiologic and electrophysiologic studies.

PubMed

Tokuomi, H; Uchino, M; Imamura, S; Yamanaga, H; Nakanishi, R; Ideta, T

1982-12-01

We studied 10 patients with Minamata disease (organic mercury poisoning) who have been followed for over 20 years. CT revealed a bilateral, symmetric, low-density area in the visual cortex and diffuse atrophy of the cerebellar hemispheres and vermis, especially the inferior vermis. Computerized quantitative analysis of the tremor of these patients showed a peculiar frequency of 7.075 Hz on postural tremor and 7.501 Hz on action tremor. On studies of short-latency somatosensory evoked potential, all patients showed a lack of the N20 component, the potential of the somatic sensory area.

Glutathione S-transferase-encoding gene as a potential probe for environmental bacterial isolates capable of degrading polycyclic aromatic hydrocarbons.

PubMed Central

Lloyd-Jones, G; Lau, P C

1997-01-01

Homologs of the glutathione S-transferase (GST)-encoding gene were identified in a collection of aromatic hydrocarbon-degrading Sphingomonas spp. isolated from New Zealand, Antarctica, and the United States by using PCR primers designed from the GST-encoding gene of Sphingomonas paucimobilis EPA505. Sequence analysis of PCR fragments generated from these isolates and of the GST gene amplified from DNA extracted from polycyclic aromatic hydrocarbon (PAH)-contaminated soil revealed a high degree of conservation, which may make the GST-encoding gene a potentially useful marker for PAH-degrading bacteria. PMID:9251217

Transcriptomic analysis reveals the potential of highly pathogenic PRRS virus to modulate immune system activation related to host-pathogen and damage associated signaling in infected porcine monocytes

USDA-ARS?s Scientific Manuscript database

One of the largest risks to the continued stability of the swine industry is by pathogens like porcine reproductive and respiratory syndrome virus (PRRSV) that can decimate production as it spreads among individuals. These infections can be low or highly pathogenic, and because it infects monocytic ...

Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus denitrificans Strain ISTOD1, Isolated from Wastewater

PubMed Central

Medhi, Kristina; Mishra, Arti

2018-01-01

ABSTRACT We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb, isolated from wastewater. It has been identified as a heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis revealed genes related to nitrogen and phosphorus removal, showing that the strain holds potential for bioremediation and biorefinery uses. PMID:29650568

Flow Cytometric Analysis of Hepatocytes from Normal, PFDA, and PH/DEN/ PB-Treated Rats

DTIC Science & Technology

1989-12-31

SUB-GROUP’ Perfluorodecanoic acid ( PFDA ); hepatocarcinogenesis; preneoplastic lesions; flow cytometry; imunotoxicitYyc3 1%&STRACT (Continue on...effects of perfluorodecanoic acid ( PFDA ). Flow cytometric evaluation of hepatocytes from PEDA-treated rats revealed an increase in size and granularity...was designed to generate preliminary information regarding the toxic and potential carcinogenic effects of perfluorodecanoic acid ( PFDA ) on rat

Investigating the sources and potential health risks of environmental contaminants in the soils and drinking waters from the rural clusters in Thiva area (Greece).

PubMed

Kelepertzis, Efstratios

2014-02-01

The present study investigates the possible influence of human activities on metal loadings of topsoil in a typical small rural city in central Greece and the chemical quality of tap water in surrounding villages. Furthermore, the study aimed to examine potential health risks of naturally enriched heavy metals to exposed population taking into account the soil and drinking water as exposure pathways. The mean concentrations of Ni, Cr, Co, Mn, Pb, Cu, Zn and Cd in the soil were 1777, 285, 99, 946, 30, 26, 78 and 0.67 mg/kg respectively. Combination of pollution indexes based on local reference background soils and statistical analyses (correlation analysis, cluster analysis and principal component analysis) revealed that anthropogenic activities have not modified the natural soil chemistry at least in a large scale. High Hazard Quotient (HQ) values for children were estimated for Ni, Cr and Co based on total metal concentrations for the soil ingestion route (9.26E-01, 9.75E-01 and 3.45E+00 respectively). However, evaluation of HQs based on published bioaccessible concentrations suggested that the population groups would not likely experience potential health risks as a result of exposure to contaminated soils. Concentrations of Cr(VI) in tap waters were within the allowable limits. However, the risk assessment model revealed that local residents (adults) of Eleonas and Neochori villages are at some carcinogenic risks considering lifetime ingestion of water (potential cancer risks 2.05E-04 and 1.29E-04 respectively). Despite the uncertainties accompanying these procedures and the great deal of debate regarding the human carcinogenicity of Cr(VI) by the oral route, results of this study drive attention to remediation measures that should include epidemiological studies for the local population. © 2013 Published by Elsevier Inc.

Antioxidant Activities, Metabolic Profiling, Proximate Analysis, Mineral Nutrient Composition of Salvadora persica Fruit Unravel a Potential Functional Food and a Natural Source of Pharmaceuticals.

PubMed

Kumari, Asha; Parida, Asish K; Rangani, Jaykumar; Panda, Ashok

2017-01-01

Salvadora persica is a medicinally important plant mainly used in oral hygiene. However, little attention has been given towards the nutritional prominence of this plant. This study encloses the proximate and mineral nutrient contents, amino acid composition, metabolite profiling and antioxidant potential of S. persica fruit. The ripen fruit contained substantial amount of sugars, mineral nutrients, carotenoids, polyphenols and flavonoids. The metabolic profiling of the fruit extract by GC-MS revealed a total of 22 metabolites comprising of sugars, sugar alcohols, organic acids, organic base, and aromatic silica compound. The identified metabolites have been previously reported to have potential antioxidant, antimicrobial, anti-hyperglycemic, and antitumor properties. The GC-MS analysis indicated high glucose and glucopyranose (247.62 and 42.90 mg g -1 FW respectively) contents in fruit of S. persica . The fruit extract demonstrated a significantly higher antioxidant and ROS scavenging properties along with high contents of mineral nutrients and essential amino acids. HPLC analysis revealed presence of essential and non-essential amino acid required for healthy body metabolism. The cysteine was found to be in highest amount (733.69 mg 100 g -1 DW) among all amino acids quantified. Specifically, compared to similar medicinal plants, previously reported as a source of non-conventional food and with some of the commercially important fruits, S. persica fruit appears to be a potential source of essential mineral nutrients, amino acids, vitamins (ascorbic acid and carotenoid) and pharmaceutically important metabolites contributing towards fulfilling the recommended daily requirement of these for a healthy human being. This is the first report establishing importance of S. persica fruit as nutraceuticals. The data presented here proposed that fruit of S. persica may be used as functional food or reinvigorating ingredient for processed food to reduce deficiency of nutrients among the vulnerable population group. The phytochemicals identified from S. persica fruit may be used as natural source for pharmaceutical preparations.

Antioxidant Activities, Metabolic Profiling, Proximate Analysis, Mineral Nutrient Composition of Salvadora persica Fruit Unravel a Potential Functional Food and a Natural Source of Pharmaceuticals

PubMed Central

Kumari, Asha; Parida, Asish K.; Rangani, Jaykumar; Panda, Ashok

2017-01-01

Salvadora persica is a medicinally important plant mainly used in oral hygiene. However, little attention has been given towards the nutritional prominence of this plant. This study encloses the proximate and mineral nutrient contents, amino acid composition, metabolite profiling and antioxidant potential of S. persica fruit. The ripen fruit contained substantial amount of sugars, mineral nutrients, carotenoids, polyphenols and flavonoids. The metabolic profiling of the fruit extract by GC-MS revealed a total of 22 metabolites comprising of sugars, sugar alcohols, organic acids, organic base, and aromatic silica compound. The identified metabolites have been previously reported to have potential antioxidant, antimicrobial, anti-hyperglycemic, and antitumor properties. The GC-MS analysis indicated high glucose and glucopyranose (247.62 and 42.90 mg g-1 FW respectively) contents in fruit of S. persica. The fruit extract demonstrated a significantly higher antioxidant and ROS scavenging properties along with high contents of mineral nutrients and essential amino acids. HPLC analysis revealed presence of essential and non-essential amino acid required for healthy body metabolism. The cysteine was found to be in highest amount (733.69 mg 100 g-1 DW) among all amino acids quantified. Specifically, compared to similar medicinal plants, previously reported as a source of non-conventional food and with some of the commercially important fruits, S. persica fruit appears to be a potential source of essential mineral nutrients, amino acids, vitamins (ascorbic acid and carotenoid) and pharmaceutically important metabolites contributing towards fulfilling the recommended daily requirement of these for a healthy human being. This is the first report establishing importance of S. persica fruit as nutraceuticals. The data presented here proposed that fruit of S. persica may be used as functional food or reinvigorating ingredient for processed food to reduce deficiency of nutrients among the vulnerable population group. The phytochemicals identified from S. persica fruit may be used as natural source for pharmaceutical preparations. PMID:28261096

Identification of potential transcriptomic markers in developing pediatric sepsis: a weighted gene co-expression network analysis and a case-control validation study.

PubMed

Li, Yiping; Li, Yanhong; Bai, Zhenjiang; Pan, Jian; Wang, Jian; Fang, Fang

2017-12-13

Sepsis represents a complex disease with the dysregulated inflammatory response and high mortality rate. The goal of this study was to identify potential transcriptomic markers in developing pediatric sepsis by a co-expression module analysis of the transcriptomic dataset. Using the R software and Bioconductor packages, we performed a weighted gene co-expression network analysis to identify co-expression modules significantly associated with pediatric sepsis. Functional interpretation (gene ontology and pathway analysis) and enrichment analysis with known transcription factors and microRNAs of the identified candidate modules were then performed. In modules significantly associated with sepsis, the intramodular analysis was further performed and "hub genes" were identified and validated by quantitative real-time PCR (qPCR) in this study. 15 co-expression modules in total were detected, and four modules ("midnight blue", "cyan", "brown", and "tan") were most significantly associated with pediatric sepsis and suggested as potential sepsis-associated modules. Gene ontology analysis and pathway analysis revealed that these four modules strongly associated with immune response. Three of the four sepsis-associated modules were also enriched with known transcription factors (false discovery rate-adjusted P < 0.05). Hub genes were identified in each of the four modules. Four of the identified hub genes (MYB proto-oncogene like 1, killer cell lectin like receptor G1, stomatin, and membrane spanning 4-domains A4A) were further validated to be differentially expressed between septic children and controls by qPCR. Four pediatric sepsis-associated co-expression modules were identified in this study. qPCR results suggest that hub genes in these modules are potential transcriptomic markers for pediatric sepsis diagnosis. These results provide novel insights into the pathogenesis of pediatric sepsis and promote the generation of diagnostic gene sets.

Tropomyosin 1: Multiple roles in the developing heart and in the formation of congenital heart defects.

PubMed

England, Jennifer; Granados-Riveron, Javier; Polo-Parada, Luis; Kuriakose, Diji; Moore, Christopher; Brook, J David; Rutland, Catrin S; Setchfield, Kerry; Gell, Christopher; Ghosh, Tushar K; Bu'Lock, Frances; Thornborough, Christopher; Ehler, Elisabeth; Loughna, Siobhan

2017-05-01

Tropomyosin 1 (TPM1) is an essential sarcomeric component, stabilising the thin filament and facilitating actin's interaction with myosin. A number of sarcomeric proteins, such as alpha myosin heavy chain, play crucial roles in cardiac development. Mutations in these genes have been linked to congenital heart defects (CHDs), occurring in approximately 1 in 145 live births. To date, TPM1 has not been associated with isolated CHDs. Analysis of 380 CHD cases revealed three novel mutations in the TPM1 gene; IVS1+2T>C, I130V, S229F and a polyadenylation signal site variant GATAAA/AATAAA. Analysis of IVS1+2T>C revealed aberrant pre-mRNA splicing. In addition, abnormal structural properties were found in hearts transfected with TPM1 carrying I130V and S229F mutations. Phenotypic analysis of TPM1 morpholino-treated embryos revealed roles for TPM1 in cardiac looping, atrial septation and ventricular trabeculae formation and increased apoptosis was seen within the heart. In addition, sarcomere assembly was affected and altered action potentials were exhibited. This study demonstrated that sarcomeric TPM1 plays vital roles in cardiogenesis and is a suitable candidate gene for screening individuals with isolated CHDs. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Proteomic characterization of EL4 lymphoma-derived tumors upon chemotherapy treatment reveals potential roles for lysosomes and caspase-6 during tumor cell death in vivo.

PubMed

Kramer, David A; Eldeeb, Mohamed A; Wuest, Melinda; Mercer, John; Fahlman, Richard P

2017-06-01

The murine mouse lymphoblastic lymphoma cell line (EL4) tumor model is an established in vivo apoptosis model for the investigation of novel cancer imaging agents and immunological treatments due to the rapid and significant response of the EL4 tumors to cyclophosphamide and etoposide combination chemotherapy. Despite the utility of this model system in cancer research, little is known regarding the molecular details of in vivo tumor cell death. Here, we report the first in-depth quantitative proteomic analysis of the changes that occur in these tumors upon cyclophosphamide and etoposide treatment in vivo. Using a label-free quantitative proteomic approach a total of 5838 proteins were identified in the treated and untreated tumors, of which 875 were determined to change in abundance with statistical significance. Initial analysis of the data reveals changes that may have been predicted, such as the downregulation of ribosomes, but demonstrates the robustness of the dataset. Analysis of the dataset also reveals the unexpected downregulation of caspase-3 and an upregulation of caspase-6 in addition to a global upregulation of lysosomal proteins in the bulk of the tumor. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

PubMed Central

Zagoskin, Maxim V.; Lazareva, Valentina I.; Grishanin, Andrey K.; Mukha, Dmitry V.

2014-01-01

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals. PMID:25215300

G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.

PubMed

Kaplan, Oktay I; Berber, Burak; Hekim, Nezih; Doluca, Osman

2016-11-02

Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation.

PubMed

Ni, Duan; Song, Kun; Zhang, Jian; Lu, Shaoyong

2017-10-26

Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras-NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras.

Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species

PubMed Central

Xie, Jianbo; Shi, Haowen; Du, Zhenglin; Wang, Tianshu; Liu, Xiaomeng; Chen, Sanfeng

2016-01-01

Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR. PMID:26856413

Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation

PubMed Central

Song, Kun; Zhang, Jian; Lu, Shaoyong

2017-01-01

Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras–NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras. PMID:29072601

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

Zhang, Qibin; Monroe, Matthew E.; Schepmoes, Athena A.

Non-enzymatic glycation of proteins is implicated in diabetes mellitus and its related complications. In this report, we extend our previous development and refinement of proteomics-based methods for the analysis of non-enzymatically glycated proteins to comprehensively identify glycated proteins in normal and diabetic human plasma and erythrocytes. Using immunodepletion, enrichment, and fractionation strategies, we identified 7749 unique glycated peptides, corresponding to 3742 unique glycated proteins. Semi-quantitative comparisons revealed a number of proteins with glycation levels significantly increased in diabetes relative to control samples and that erythrocyte proteins are more extensively glycated than plasma proteins. A glycation motif analysis revealed amino acidsmore » that are favored more than others in the protein primary structures in the vicinity of the glycation sites in both sample types. The glycated peptides and corresponding proteins reported here provide a foundation for the potential identification of novel markers for diabetes, glycemia, or diabetic complications.« less

Novel skeletal muscle ryanodine receptor mutation in a large Brazilian family with malignant hyperthermia.

PubMed

McWilliams, S; Nelson, T; Sudo, R T; Zapata-Sudo, G; Batti, M; Sambuughin, N

2002-07-01

Malignant hyperthermia (MH) is an autosomal dominant disorder that predisposes susceptible individuals to a potentially life-threatening crisis when exposed to commonly used anesthetics. Mutations in the skeletal muscle calcium release channel, ryanodine receptor (RYR1) are associated with MH in over 50% of affected families. Linkage analysis of the RYR1 gene region at 19q13 was performed in a large Brazilian family and a distinct disease co-segregating haplotype was revealed in the majority of members with diagnosis of MH. Subsequent sequencing of RYR1 mutational hot spots revealed a nucleotide substitution of C to T at position 7062, causing a novel amino acid change from Arg2355 to Cys associated with MH in the family. Haplotype analysis of the RYR1 gene area at 19q13 in the family with multiple MH members is an important tool in identification of genetic cause underlying this disease.

Biotransformation of Tributyltin chloride by Pseudomonas stutzeri strain DN2

PubMed Central

Khanolkar, Dnyanada S.; Naik, Milind Mohan; Dubey, Santosh Kumar

2014-01-01

A bacterial isolate capable of utilizing tributyltin chloride (TBTCl) as sole carbon source was isolated from estuarine sediments of west coast of India and identified as Pseudomonas stutzeri based on biochemical tests and Fatty acid methyl ester (FAME) analysis. This isolate was designated as strain DN2. Although this bacterial isolate could resist up to 3 mM TBTCl level, it showed maximum growth at 2 mM TBTCl in mineral salt medium (MSM). Pseudomonas stutzeri DN2 exposed to 2 mM TBTCl revealed significant alteration in cell morphology as elongation and shrinkage in cell size along with roughness of cell surface. FTIR and NMR analysis of TBTCl degradation product extracted using chloroform and purified using column chromatography clearly revealed biotransformation of TBTCl into Dibutyltin dichloride (DBTCl2) through debutylation process. Therefore, Pseudomonas stutzeri strain DN2 may be used as a potential bacterial strain for bioremediation of TBTCl contaminated aquatic environmental sites. PMID:25763027

Structural virology. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid.

PubMed

Gutsche, Irina; Desfosses, Ambroise; Effantin, Grégory; Ling, Wai Li; Haupt, Melina; Ruigrok, Rob W H; Sachse, Carsten; Schoehn, Guy

2015-05-08

Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the folded domain of the measles virus nucleoprotein encapsidating an RNA at a resolution of 4.3 angstroms. The resulting pseudoatomic model of the measles virus nucleocapsid offers important insights into the mechanism of the helical polymerization of nucleocapsids of negative-strand RNA viruses, in particular via the exchange subdomains of the nucleoprotein. The structure reveals the mode of the nucleoprotein-RNA interaction and explains why each nucleoprotein of measles virus binds six nucleotides, whereas the respiratory syncytial virus nucleoprotein binds seven. It provides a rational basis for further analysis of measles virus replication and transcription, and reveals potential targets for drug design. Copyright © 2015, American Association for the Advancement of Science.

A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions

PubMed Central

2013-01-01

Background Metabolomics has become increasingly popular in the study of disease phenotypes and molecular pathophysiology. One branch of metabolomics that encompasses the high-throughput screening of cellular metabolism is metabolic profiling. In the present study, the metabolic profiles of different tumour cells from colorectal carcinoma and breast adenocarcinoma were exposed to hypoxic and normoxic conditions and these have been compared to reveal the potential metabolic effects of hypoxia on the biochemistry of the tumour cells; this may contribute to their survival in oxygen compromised environments. In an attempt to analyse the complex interactions between metabolites beyond routine univariate and multivariate data analysis methods, correlation analysis has been integrated with a human metabolic reconstruction to reveal connections between pathways that are associated with normoxic or hypoxic oxygen environments. Results Correlation analysis has revealed statistically significant connections between metabolites, where differences in correlations between cells exposed to different oxygen levels have been highlighted as markers of hypoxic metabolism in cancer. Network mapping onto reconstructed human metabolic models is a novel addition to correlation analysis. Correlated metabolites have been mapped onto the Edinburgh human metabolic network (EHMN) with the aim of interlinking metabolites found to be regulated in a similar fashion in response to oxygen. This revealed novel pathways within the metabolic network that may be key to tumour cell survival at low oxygen. Results show that the metabolic responses to lowering oxygen availability can be conserved or specific to a particular cell line. Network-based correlation analysis identified conserved metabolites including malate, pyruvate, 2-oxoglutarate, glutamate and fructose-6-phosphate. In this way, this method has revealed metabolites not previously linked, or less well recognised, with respect to hypoxia before. Lactate fermentation is one of the key themes discussed in the field of hypoxia; however, malate, pyruvate, 2-oxoglutarate, glutamate and fructose-6-phosphate, which are connected by a single pathway, may provide a more significant marker of hypoxia in cancer. Conclusions Metabolic networks generated for each cell line were compared to identify conserved metabolite pathway responses to low oxygen environments. Furthermore, we believe this methodology will have general application within metabolomics. PMID:24153255

Evolutionarily Repurposed Networks Reveal the Well-Known Antifungal Drug Thiabendazole to Be a Novel Vascular Disrupting Agent

PubMed Central

Cha, Hye Ji; Byrom, Michelle; Mead, Paul E.; Ellington, Andrew D.; Wallingford, John B.; Marcotte, Edward M.

2012-01-01

Studies in diverse organisms have revealed a surprising depth to the evolutionary conservation of genetic modules. For example, a systematic analysis of such conserved modules has recently shown that genes in yeast that maintain cell walls have been repurposed in vertebrates to regulate vein and artery growth. We reasoned that by analyzing this particular module, we might identify small molecules targeting the yeast pathway that also act as angiogenesis inhibitors suitable for chemotherapy. This insight led to the finding that thiabendazole, an orally available antifungal drug in clinical use for 40 years, also potently inhibits angiogenesis in animal models and in human cells. Moreover, in vivo time-lapse imaging revealed that thiabendazole reversibly disassembles newly established blood vessels, marking it as vascular disrupting agent (VDA) and thus as a potential complementary therapeutic for use in combination with current anti-angiogenic therapies. Importantly, we also show that thiabendazole slows tumor growth and decreases vascular density in preclinical fibrosarcoma xenografts. Thus, an exploration of the evolutionary repurposing of gene networks has led directly to the identification of a potential new therapeutic application for an inexpensive drug that is already approved for clinical use in humans. PMID:22927795

Phycoremediation of Tannery Wastewater Using Microalgae Scenedesmus Species.

PubMed

Ajayan, Kayil Veedu; Selvaraju, Muthusamy; Unnikannan, Pachikaran; Sruthi, Palliyath

2015-01-01

A number of microalgae species are efficient in removing toxicants from wastewater. Many of these potential species are a promising, eco-friendly, and sustainable option for tertiary wastewater treatment with a possible advantage of improving the economics of microalgae cultivation for biofuel production. The present study deals with the phycoremediation of tannery wastewater (TWW) using Scenedesmus sp. isolated from a local habitat. The test species was grown in TWW under laboratory conditions and harvested on the 12th day. The results revealed that the algal biomass during the growth period not only reduced the pollution load of heavy metals (Cr-81.2-96%, Cu-73.2-98%, Pb-75-98% and Zn-65-98%) but also the nutrients (NO3 >44.3% and PO4 >95%). Fourier Transform Infrared (FTIR) spectrums of Scenedesmus sp. biomass revealed the involvement of hydroxyl amino, carboxylic and carbonyl groups. The scanning electron micrograph (SEM) and Energy Dispersive X-ray Spectroscopic analysis (EDS) revealed the surface texture, morphology and element distribution of the biosorbent. Furthermore, the wastewater generated during wet-blue tanning process can support dense population of Scenedesmus sp., making it a potential growth medium for biomass production of the test alga for phycoremediation of toxicants in tannery wastewaters.

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity.

PubMed

Stice, Shaun P; Stumpf, Spencer D; Gitaitis, Ron D; Kvitko, Brian H; Dutta, Bhabesh

2018-01-01

Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA) and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study.

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity

PubMed Central

Stice, Shaun P.; Stumpf, Spencer D.; Gitaitis, Ron D.; Kvitko, Brian H.; Dutta, Bhabesh

2018-01-01

Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA) and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study. PMID:29491851

Analyzing the genes related to Alzheimer's disease via a network and pathway-based approach.

PubMed

Hu, Yan-Shi; Xin, Juncai; Hu, Ying; Zhang, Lei; Wang, Ju

2017-04-27

Our understanding of the molecular mechanisms underlying Alzheimer's disease (AD) remains incomplete. Previous studies have revealed that genetic factors provide a significant contribution to the pathogenesis and development of AD. In the past years, numerous genes implicated in this disease have been identified via genetic association studies on candidate genes or at the genome-wide level. However, in many cases, the roles of these genes and their interactions in AD are still unclear. A comprehensive and systematic analysis focusing on the biological function and interactions of these genes in the context of AD will therefore provide valuable insights to understand the molecular features of the disease. In this study, we collected genes potentially associated with AD by screening publications on genetic association studies deposited in PubMed. The major biological themes linked with these genes were then revealed by function and biochemical pathway enrichment analysis, and the relation between the pathways was explored by pathway crosstalk analysis. Furthermore, the network features of these AD-related genes were analyzed in the context of human interactome and an AD-specific network was inferred using the Steiner minimal tree algorithm. We compiled 430 human genes reported to be associated with AD from 823 publications. Biological theme analysis indicated that the biological processes and biochemical pathways related to neurodevelopment, metabolism, cell growth and/or survival, and immunology were enriched in these genes. Pathway crosstalk analysis then revealed that the significantly enriched pathways could be grouped into three interlinked modules-neuronal and metabolic module, cell growth/survival and neuroendocrine pathway module, and immune response-related module-indicating an AD-specific immune-endocrine-neuronal regulatory network. Furthermore, an AD-specific protein network was inferred and novel genes potentially associated with AD were identified. By means of network and pathway-based methodology, we explored the pathogenetic mechanism underlying AD at a systems biology level. Results from our work could provide valuable clues for understanding the molecular mechanism underlying AD. In addition, the framework proposed in this study could be used to investigate the pathological molecular network and genes relevant to other complex diseases or phenotypes.

Spatial assessment of potential ecological risk of heavy metals in soils from informal e-waste recycling in Ghana.

PubMed

Kyere, Vincent Nartey; Greve, Klaus; Atiemo, Sampson Manukure; Ephraim, James

2017-01-01

The rapidly increasing annual global volume of e-waste, and of its inherently valuable fraction, has created an opportunity for individuals in Agbogbloshie, Accra, Ghana to make a living by using unconventional, uncontrolled, primitive and crude procedures to recycle and recover valuable metals from this waste. The current form of recycling procedures releases hazardous fractions, such as heavy metals, into the soil, posing a significant risk to the environment and human health. Using a handheld global positioning system, 132 soil samples based on 100 m grid intervals were collected and analysed for cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), lead (Pb) and zinc (Zn). Using geostatistical techniques and sediment quality guidelines, this research seeks to assess the potential risk these heavy metals posed to the proposed Korle Ecological Restoration Zone by informal e-waste processing site in Agbogbloshie, Accra, Ghana. Analysis of heavy metals revealed concentrations exceeded the regulatory limits of both Dutch and Canadian soil quality and guidance values, and that the ecological risk posed by the heavy metals extended beyond the main burning and dismantling sites of the informal recyclers to the school, residential, recreational, clinic, farm and worship areas. The heavy metals Cr, Cu, Pb and Zn had normal distribution, spatial variability, and spatial autocorrelation. Further analysis revealed the decreasing order of toxicity, Hg>Cd>Pb> Cu>Zn>Cr, of contributing significantly to the potential ecological risk in the study area.

Spatial assessment of potential ecological risk of heavy metals in soils from informal e-waste recycling in Ghana

PubMed Central

Greve, Klaus; Atiemo, Sampson Manukure

2017-01-01

The rapidly increasing annual global volume of e-waste, and of its inherently valuable fraction, has created an opportunity for individuals in Agbogbloshie, Accra, Ghana to make a living by using unconventional, uncontrolled, primitive and crude procedures to recycle and recover valuable metals from this waste. The current form of recycling procedures releases hazardous fractions, such as heavy metals, into the soil, posing a significant risk to the environment and human health. Using a handheld global positioning system, 132 soil samples based on 100 m grid intervals were collected and analysed for cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), lead (Pb) and zinc (Zn). Using geostatistical techniques and sediment quality guidelines, this research seeks to assess the potential risk these heavy metals posed to the proposed Korle Ecological Restoration Zone by informal e-waste processing site in Agbogbloshie, Accra, Ghana. Analysis of heavy metals revealed concentrations exceeded the regulatory limits of both Dutch and Canadian soil quality and guidance values, and that the ecological risk posed by the heavy metals extended beyond the main burning and dismantling sites of the informal recyclers to the school, residential, recreational, clinic, farm and worship areas. The heavy metals Cr, Cu, Pb and Zn had normal distribution, spatial variability, and spatial autocorrelation. Further analysis revealed the decreasing order of toxicity, Hg>Cd>Pb> Cu>Zn>Cr, of contributing significantly to the potential ecological risk in the study area. PMID:29056034

Perception of Climate Risk among Rural Farmers in Vietnam: Consistency within Households and with the Empirical Record.

PubMed

Cullen, Alison C; Anderson, C Leigh

2017-03-01

Rural farmers in Vietnamese communes perceive climate risk and potential impacts on livelihood within a complex context that may influence individual and household decisions. In a primary survey of 1,145 residents of the Thach Ha district of Ha Tinh province, we gathered data regarding perception about stability in climate, potential risks to livelihood, demographic characteristics, orientation toward risk, and interest in expanding economic activity. Temporal analysis of meteorological and economic indicator data forms an empirical basis for comparison with human perception. We ask the basic question: Are rural farmers' perceptions of climate consistent with the historical record and reproducible within households? We find that respondents do perceive climate anomalies, with some anchoring on recent extreme events as revealed by climate observational data, and further that spouses disproportionately share perceptions relative to randomly simulated pairings. To put climate-related risk perception in a larger context, we examine patterns across a range of risks to livelihood faced by farmers (livestock disease, pests, markets, health), using dimension reduction techniques. We find that our respondents distinguish among potential causes of low economic productivity, with substantial emphasis on climate-related impacts. They do not express uniform concern across risks, but rather average patterns reveal common modes and distinguish climate concern. Still, among those expressing concern about climate-related risks to livelihood we do not find an association with expressed intention to pursue changes in economic activity as a risk management response. © 2016 Society for Risk Analysis.

iTRAQ-based quantitative proteomic analysis reveals potential factors associated with the enhancement of phenazine-1-carboxamide production in Pseudomonas chlororaphis P3

PubMed Central

Jin, Xue-Jie; Peng, Hua-Song; Hu, Hong-Bo; Huang, Xian-Qing; Wang, Wei; Zhang, Xue-Hong

2016-01-01

Phenazine-1-carboxamide (PCN), a phenazine derivative, is strongly antagonistic to fungal phytopathogens. Pseudomonas chlororaphis HT66 is a PCN-producing, non-pathogenic biocontrol strain, and we obtained the mutant P. chlororaphis P3, which produces 4.7 times more PCN than the wild-type HT66 strain. To reveal the cause of PCN production enhancement in P3 and find potential factors related to PCN biosynthesis, an iTRAQ-based quantitative proteomic analysis was used to study the expression changes between the two strains. Of the 452 differentially expressed proteins, most were functionally mapped into PCN biosynthesis pathway or other related metabolisms. The upregulation of proteins, including PhzA/B, PhzD, PhzF, PhzG, and PhzH, involved in PCN biosynthesis was in agreement with the efficient production of PCN in P3. A number of proteins that function primarily in energy production, amino acid metabolism, and secondary metabolism played important roles in PCN biosynthesis. Notably, proteins involved in the uptake and conversion of phosphate, inorganic nitrogen sources, and iron improved the PCN production. Furthermore, the type VI secretion system may participate in the secretion or/and indirect biosynthetic regulation of PCN in P. chlororaphis. This study provides valuable clues to better understand the biosynthesis, excretion and regulation of PCN in Pseudomonas and also provides potential gene targets for further engineering high-yield strains. PMID:27273243

Sialylation potentials of the silkworm, Bombyx mori; B. mori possesses an active α2,6-sialyltransferase.

PubMed

Kajiura, Hiroyuki; Hamaguchi, Yuichi; Mizushima, Hiroki; Misaki, Ryo; Fujiyama, Kazuhito

2015-12-01

N-Glycosylation is an important post-translational modification in most secreted and membrane-bound proteins in eukaryotic cells. However, the insect N-glycosylation pathway and the potentials contributing to the N-glycan synthesis are still unclear because most of the studies on these subjects have focused on mammals and plants. Here, we identified Bombyx mori sialyltransferase (BmST), which is a Golgi-localized glycosyltransferase and which can modify N-glycans. BmST was ubiquitously expressed in different organs and in various stages of development and localized at the Golgi. Biochemical analysis using Sf9-expressed BmST revealed that BmST encoded α2,6-sialyltransferase and transferred N-acetylneuraminic acid (NeuAc) to the nonreducing terminus of Galβ1-R, but exhibited the highest activity toward GalNAcβ1,4-GlcNAc-R. Unlike human α2,6-sialyltransferase, BmST required the post-translational modification, especially N-glycosylation, for its full activity. N-Glycoprotein analysis of B. mori fifth instar larvae revealed that high-mannose-type structure was predominant and GlcNAc-linked and fucosylated structures were observed but endogenous galactosyl-, N-acetylgalactosaminyl- and sialyl-N-glycoproteins were undetectable under the standard analytical approach. These results indicate that B. mori genome encodes an α2,6-sialyltransferase, but further investigations of the sialylation potentials are necessary. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

NMR-based fecal metabolomics fingerprinting as predictors of earlier diagnosis in patients with colorectal cancer.

PubMed

Lin, Yan; Ma, Changchun; Liu, Chengkang; Wang, Zhening; Yang, Jurong; Liu, Xinmu; Shen, Zhiwei; Wu, Renhua

2016-05-17

Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its earlier detection for optimal disease management. A metabolomics based approach provides potential for noninvasive identification of biomarkers of colorectal carcinogenesis, as well as dissection of molecular pathways of pathophysiological conditions. Here, proton nuclear magnetic resonance spectroscopy (1HNMR) -based metabolomic approach was used to profile fecal metabolites of 68 CRC patients (stage I/II=20; stage III=25 and stage IV=23) and 32 healthy controls (HC). Pattern recognition through principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) was applied on 1H-NMR processed data for dimension reduction. OPLS-DA revealed that each stage of CRC could be clearly distinguished from HC based on their metabolomic profiles. Successive analyses identified distinct disturbances to fecal metabolites of CRC patients at various stages, compared with those in cancer free controls, including reduced levels of acetate, butyrate, propionate, glucose, glutamine, and elevated quantities of succinate, proline, alanine, dimethylglycine, valine, glutamate, leucine, isoleucine and lactate. These altered fecal metabolites potentially involved in the disruption of normal bacterial ecology, malabsorption of nutrients, increased glycolysis and glutaminolysis. Our findings revealed that the fecal metabolic profiles of healthy controls can be distinguished from CRC patients, even in the early stage (stage I/II), highlighting the potential utility of NMR-based fecal metabolomics fingerprinting as predictors of earlier diagnosis in CRC patients.

NMR-based fecal metabolomics fingerprinting as predictors of earlier diagnosis in patients with colorectal cancer

PubMed Central

Lin, Yan; Ma, Changchun; Liu, Chengkang; Wang, Zhening; Yang, Jurong; Liu, Xinmu; Shen, Zhiwei; Wu, Renhua

2016-01-01

Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its earlier detection for optimal disease management. A metabolomics based approach provides potential for noninvasive identification of biomarkers of colorectal carcinogenesis, as well as dissection of molecular pathways of pathophysiological conditions. Here, proton nuclear magnetic resonance spectroscopy (1HNMR) -based metabolomic approach was used to profile fecal metabolites of 68 CRC patients (stage I/II=20; stage III=25 and stage IV=23) and 32 healthy controls (HC). Pattern recognition through principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) was applied on 1H-NMR processed data for dimension reduction. OPLS-DA revealed that each stage of CRC could be clearly distinguished from HC based on their metabolomic profiles. Successive analyses identified distinct disturbances to fecal metabolites of CRC patients at various stages, compared with those in cancer free controls, including reduced levels of acetate, butyrate, propionate, glucose, glutamine, and elevated quantities of succinate, proline, alanine, dimethylglycine, valine, glutamate, leucine, isoleucine and lactate. These altered fecal metabolites potentially involved in the disruption of normal bacterial ecology, malabsorption of nutrients, increased glycolysis and glutaminolysis. Our findings revealed that the fecal metabolic profiles of healthy controls can be distinguished from CRC patients, even in the early stage (stage I/II), highlighting the potential utility of NMR-based fecal metabolomics fingerprinting as predictors of earlier diagnosis in CRC patients. PMID:27107423

Tentacle Transcriptome and Venom Proteome of the Pacific Sea Nettle, Chrysaora fuscescens (Cnidaria: Scyphozoa).

PubMed

Ponce, Dalia; Brinkman, Diane L; Potriquet, Jeremy; Mulvenna, Jason

2016-04-05

Jellyfish venoms are rich sources of toxins designed to capture prey or deter predators, but they can also elicit harmful effects in humans. In this study, an integrated transcriptomic and proteomic approach was used to identify putative toxins and their potential role in the venom of the scyphozoan jellyfish Chrysaora fuscescens. A de novo tentacle transcriptome, containing more than 23,000 contigs, was constructed and used in proteomic analysis of C. fuscescens venom to identify potential toxins. From a total of 163 proteins identified in the venom proteome, 27 were classified as putative toxins and grouped into six protein families: proteinases, venom allergens, C-type lectins, pore-forming toxins, glycoside hydrolases and enzyme inhibitors. Other putative toxins identified in the transcriptome, but not the proteome, included additional proteinases as well as lipases and deoxyribonucleases. Sequence analysis also revealed the presence of ShKT domains in two putative venom proteins from the proteome and an additional 15 from the transcriptome, suggesting potential ion channel blockade or modulatory activities. Comparison of these potential toxins to those from other cnidarians provided insight into their possible roles in C. fuscescens venom and an overview of the diversity of potential toxin families in cnidarian venoms.

The pleiotropic effects of fisetin and hesperetin on human acute promyelocytic leukemia cells are mediated through apoptosis, cell cycle arrest, and alterations in signaling networks.

PubMed

Adan, Aysun; Baran, Yusuf

2015-11-01

Fisetin and hesperetin, flavonoids from various plants, have several pharmaceutical activities including antioxidative, anti-inflammatory, and anticancer effects. However, studies elucidating the role and the mechanism(s) of action of fisetin and hesperetin in acute promyelocytic leukemia are absent. In this study, we investigated the mechanism of the antiproliferative and apoptotic actions exerted by fisetin and hesperetin on human HL60 acute promyelocytic leukemia cells. The viability of HL60 cells was evaluated using the MTT assay, apoptosis by annexin V/propidium iodide (PI) staining and cell cycle distribution using flow cytometry, and changes in caspase-3 enzyme activity and mitochondrial transmembrane potential. Moreover, we performed whole-genome microarray gene expression analysis to reveal genes affected by fisetin and hesperetin that can be important for developing of future targeted therapy. Based on data obtained from microarray analysis, we also described biological networks modulated after fisetin and hesperetin treatment by KEGG and IPA analysis. Fisetin and hesperetin treatment showed a concentration- and time-dependent inhibition of proliferation and induced G2/M arrest for both agents and G0/G1 arrest for hesperetin at only the highest concentrations. There was a disruption of mitochondrial membrane potential together with increased caspase-3 activity. Furthermore, fisetin- and hesperetin-triggered apoptosis was confirmed by annexin V/PI analysis. The microarray gene profiling analysis revealed some important biological pathways including mitogen-activated protein kinases (MAPK) and inhibitor of DNA binding (ID) signaling pathways altered by fisetin and hesperetin treatment as well as gave a list of genes modulated ≥2-fold involved in cell proliferation, cell division, and apoptosis. Altogether, data suggested that fisetin and hesperetin have anticancer properties and deserve further investigation.

Identification of biomarkers in human head and neck tumor cell lines that predict for in vitro sensitivity to gefitinib.

PubMed

Hickinson, D Mark; Marshall, Gayle B; Beran, Garry J; Varella-Garcia, Marileila; Mills, Elizabeth A; South, Marie C; Cassidy, Andrew M; Acheson, Kerry L; McWalter, Gael; McCormack, Rose M; Bunn, Paul A; French, Tim; Graham, Alex; Holloway, Brian R; Hirsch, Fred R; Speake, Georgina

2009-06-01

Potential biomarkers were identified for in vitro sensitivity to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor gefitinib in head and neck cancer. Gefitinib sensitivity was determined in cell lines, followed by transcript profiling coupled with a novel pathway analysis approach. Eleven cell lines were highly sensitive to gefitinib (inhibitor concentration required to give 50% growth inhibition [GI(50)] < 1 microM), three had intermediate sensitivity (GI(50) 1-7 microM), and six were resistant (GI(50) > 7 microM); an exploratory principal component analysis revealed a separation between the genomic profiles of sensitive and resistant cell lines. Subsequently, a hypothesis-driven analysis of Affymetrix data (Affymetrix, Inc., Santa Clara, CA, USA) revealed higher mRNA levels for E-cadherin (CDH1); transforming growth factor, alpha (TGF-alpha); amphiregulin (AREG); FLJ22662; EGFR; p21-activated kinase 6 (PAK6); glutathione S-transferase Pi (GSTP1); and ATP-binding cassette, subfamily C, member 5 (ABCC5) in sensitive versus resistant cell lines. A hypothesis-free analysis identified 46 gene transcripts that were strongly differentiated, seven of which had a known association with EGFR and head and neck cancer (human EGF receptor 3 [HER3], TGF-alpha, CDH1, EGFR, keratin 16 [KRT16], fibroblast growth factor 2 [FGF2], and cortactin [CTTN]). Polymerase chain reaction (PCR) and enzyme-linked immunoabsorbant assay analysis confirmed Affymetrix data, and EGFR gene mutation, amplification, and genomic gain correlated strongly with gefitinib sensitivity. We identified biomarkers that predict for in vitro responsiveness to gefitinib, seven of which have known association with EGFR and head and neck cancer. These in vitro predictive biomarkers may have potential utility in the clinic and warrant further investigation.

Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

DOE PAGES

Yu, Peiqiang

2006-01-01

Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advancedmore » synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in biological tissues at ultraspatial resolutions.« less

Proteomic analysis in type 2 diabetes patients before and after a very low calorie diet reveals potential disease state and intervention specific biomarkers.

PubMed

Sleddering, Maria A; Markvoort, Albert J; Dharuri, Harish K; Jeyakar, Skhandhan; Snel, Marieke; Juhasz, Peter; Lynch, Moira; Hines, Wade; Li, Xiaohong; Jazet, Ingrid M; Adourian, Aram; Hilbers, Peter A J; Smit, Johannes W A; Van Dijk, Ko Willems

2014-01-01

Very low calorie diets (VLCD) with and without exercise programs lead to major metabolic improvements in obese type 2 diabetes patients. The mechanisms underlying these improvements have so far not been elucidated fully. To further investigate the mechanisms of a VLCD with or without exercise and to uncover possible biomarkers associated with these interventions, blood samples were collected from 27 obese type 2 diabetes patients before and after a 16-week VLCD (Modifast ∼ 450 kcal/day). Thirteen of these patients followed an exercise program in addition to the VCLD. Plasma was obtained from 27 lean and 27 obese controls as well. Proteomic analysis was performed using mass spectrometry (MS) and targeted multiple reaction monitoring (MRM) and a large scale isobaric tags for relative and absolute quantitation (iTRAQ) approach. After the 16-week VLCD, there was a significant decrease in body weight and HbA1c in all patients, without differences between the two intervention groups. Targeted MRM analysis revealed differences in several proteins, which could be divided in diabetes-associated (fibrinogen, transthyretin), obesity-associated (complement C3), and diet-associated markers (apolipoproteins, especially apolipoprotein A-IV). To further investigate the effects of exercise, large scale iTRAQ analysis was performed. However, no proteins were found showing an exercise effect. Thus, in this study, specific proteins were found to be differentially expressed in type 2 diabetes patients versus controls and before and after a VLCD. These proteins are potential disease state and intervention specific biomarkers. Controlled-Trials.com ISRCTN76920690.

Proteomic Analysis in Type 2 Diabetes Patients before and after a Very Low Calorie Diet Reveals Potential Disease State and Intervention Specific Biomarkers

PubMed Central

Dharuri, Harish K.; Jeyakar, Skhandhan; Snel, Marieke; Juhasz, Peter; Lynch, Moira; Hines, Wade; Li, Xiaohong; Jazet, Ingrid M.; Adourian, Aram; Hilbers, Peter A. J.; Smit, Johannes W. A.; Van Dijk, Ko Willems

2014-01-01

Very low calorie diets (VLCD) with and without exercise programs lead to major metabolic improvements in obese type 2 diabetes patients. The mechanisms underlying these improvements have so far not been elucidated fully. To further investigate the mechanisms of a VLCD with or without exercise and to uncover possible biomarkers associated with these interventions, blood samples were collected from 27 obese type 2 diabetes patients before and after a 16-week VLCD (Modifast ∼450 kcal/day). Thirteen of these patients followed an exercise program in addition to the VCLD. Plasma was obtained from 27 lean and 27 obese controls as well. Proteomic analysis was performed using mass spectrometry (MS) and targeted multiple reaction monitoring (MRM) and a large scale isobaric tags for relative and absolute quantitation (iTRAQ) approach. After the 16-week VLCD, there was a significant decrease in body weight and HbA1c in all patients, without differences between the two intervention groups. Targeted MRM analysis revealed differences in several proteins, which could be divided in diabetes-associated (fibrinogen, transthyretin), obesity-associated (complement C3), and diet-associated markers (apolipoproteins, especially apolipoprotein A-IV). To further investigate the effects of exercise, large scale iTRAQ analysis was performed. However, no proteins were found showing an exercise effect. Thus, in this study, specific proteins were found to be differentially expressed in type 2 diabetes patients versus controls and before and after a VLCD. These proteins are potential disease state and intervention specific biomarkers. Trial Registration Controlled-Trials.com ISRCTN76920690 PMID:25415563

Synthesis of t-butyl 2-(4-hydroxy-3-methoxybenzylidene)hydrazine carboxylate: Experimental and theoretical investigations of its properties

NASA Astrophysics Data System (ADS)

Bhat, Muzzaffar A.; Lone, Shabir H.; Mir, Muzzaffar A.; Majid, Sheikh A.; Bhat, Haroon Mohi-ud-din; Butcher, Raymond J.; Srivastava, Sanjay K.

2018-07-01

A convenient and facile synthesis of t-butyl-2-(4-hydroxy-3-methoxybenzylidene)hydrazine carboxylate (1) was accomplished by refluxing t-butyl carbazate with an appropriate aldehyde in ethanol. The resulting compound was characterized using spectral data analysis augmented by X-ray. Single crystal analysis depicted that compound 1 crystallizes in a monoclinic crystal system with P 21/c space group having trans-geometry at the Cdbnd N bond. The structural and electronic properties of the title compound have been calculated using DFT/B3LYP/6-311G (d,p) level of theory. Theoretically obtained parameters were well compared to the experimentally obtained results which depicted excellent agreement. Molecular electrostatic potential surface, frontier orbital analysis and vibrational analysis were also carried out. HOMO-LUMO energy gap was calculated which allowed the calculation of relative reactivity descriptors like chemical hardness, chemical inertness, chemical potential, nucleophilicity and electrophilicity index of the synthesized product. Pass prediction was carried out which revealed that compound 1 can be highly active against Mcl-1 enzyme, with Pa of 0.544. Based on Pass, molecular docking of compound 1 was carried out against Mcl-1 protein. Compound 1 displayed a binding free energy of -5.22 kcal/mol and inhibition constant of 149.06 μM and 1 depicted only alkyl hydrophobic and mixed pi/alkyl hydrophobic interactions with Mcl-1 enzyme. In short, this study reveals the synthesis of a new schiff base, and unravels the structural, electronic and biological properties of the title compound, paving way for further research in the field of drug development.

The effects of abdominal lipectomy in metabolic syndrome components and insulin sensitivity in females: A systematic review and meta-analysis.

PubMed

Seretis, Konstantinos; Goulis, Dimitrios G; Koliakos, Georgios; Demiri, Efterpi

2015-12-01

Adipose tissue is an endocrine organ, which is implicated in the pathogenesis of obesity, metabolic syndrome and diabetes. Lipectomy offers a unique opportunity to permanently reduce the absolute number of fat cells, though its functional role remains unclear. This systematic and meta-analysis review aims to assess the effect of abdominal lipectomy on metabolic syndrome components and insulin sensitivity in women. A predetermined protocol, established according to the Cochrane Handbook's recommendations, was used. An electronic search in MEDLINE, Scopus, the Cochrane Library and CENTRAL electronic databases was conducted from inception to May 14, 2015. This search was supplemented by a review of reference lists of potentially eligible studies and a manual search of key journals in the field of plastic surgery. Eligible studies were prospective studies with ≥1month of follow-up that included females only who underwent abdominal lipectomy and reported on parameters of metabolic syndrome and insulin sensitivity. The systematic review included 11 studies with a total of 271 individuals. Conflicting results were revealed, though most studies showed no significant metabolic effects after lipectomy. The meta-analysis included 4 studies with 140 subjects. No significant changes were revealed between lipectomy and control groups. This meta-analysis provides evidence that abdominal lipectomy in females does not affect significantly the components of metabolic syndrome and insulin sensitivity. Further high quality studies are needed to elucidate the potential metabolic effects of abdominal lipectomy. Systematic review registration PROSPERO CRD42015017564 (www.crd.york.ac.uk/PROSPERO). Copyright © 2015 Elsevier Inc. All rights reserved.

Chapter 11. Community analysis-based methods

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

Cao, Y.; Wu, C.H.; Andersen, G.L.

2010-05-01

Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. Inmore » increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.« less

Word-wide meta-analysis of Quercus forests ectomycorrhizal fungal diversity reveals southwestern Mexico as a hotspot.

PubMed

García-Guzmán, Olimpia Mariana; Garibay-Orijel, Roberto; Hernández, Edith; Arellano-Torres, Elsa; Oyama, Ken

2017-11-01

Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis. The ITS DNA sequences of ECM root tips from 14 studies were included in the meta-analysis. In total, 1065 species of ECM fungi have been documented worldwide; however, 812 species have been only found at one site. Oak forests in Europe contain 416 species, Mexico 307, USA 285, and China 151. Species with wider distributions are Sebacinaceae sp. SH197130, Amanita subjunquillea, Cenococcum geophilum, Cortinarius decipiens, Russula hortensis, R. risigallina, R. subrubescens, Sebacinaceae sp. SH214607, Tomentella ferruginea, and T. lapida. The meta-analysis revealed (1) that Mexico is not only a hotspot for oak species but also for their ECM mycobionts. (2) There is a particularly high diversity of ECM Pezizales in oak seasonal forests from western USA to southwestern Mexico. (3) The oak forests in southwestern Mexico have the largest number of potential endemic species. (4) Globally, there is a high turnover of ECM fungal species associated with oaks, which indicates high levels of alpha and beta diversity in these communities.

Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India.

PubMed

Qumar, Shamsul; Majid, Mohammad; Kumar, Narender; Tiwari, Sumeet K; Semmler, Torsten; Devi, Savita; Baddam, Ramani; Hussain, Arif; Shaik, Sabiha; Ahmed, Niyaz

2017-01-01

Some life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in the livestock industry has led to an increased prevalence of multidrug-resistant bacteria with epidemic potential. Here, we present a functional molecular epidemiological analysis entailing the phenotypic and whole-genome sequence-based characterization of 11 H. pullorum isolates from broiler and free-range chickens sampled from retail wet markets in Hyderabad City, India. Antimicrobial susceptibility tests revealed all of the isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides, and macrolides. The isolates were also found to be extended-spectrum β-lactamase producers and were even resistant to clavulanic acid. Whole-genome sequencing and comparative genomic analysis of these isolates revealed the presence of five or six well-characterized antimicrobial resistance genes, including those encoding a resistance-nodulation-division efflux pump(s). Phylogenetic analysis combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates from free-range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n = 16), together with the genomes of 17 other Helicobacter species, revealed a high number (8,560) of H. pullorum-specific protein-encoding genes, with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain-specific gene content in isolates from free-range chickens (average, 34) compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1 to 9) and a significant presence of genomic islands (0 to 4) were observed in free-range and broiler chicken isolates. Taken together, these observations provide significant baseline data for functional molecular infection epidemiology of nonpyloric Helicobacter species such as H. pullorum by unraveling their evolution in chickens and their possible zoonotic transmission to humans. Globally, the poultry industry is expanding with an ever-growing consumer base for chicken meat. Given this, food-associated transmission of multidrug-resistant bacteria represents an important health care issue. Our study involves a critical baseline approach directed at genome sequence-based epidemiology and transmission dynamics of H. pullorum, a poultry pathogen having established zoonotic potential. We believe our studies would facilitate the development of surveillance systems that ensure the safety of food for humans and guide public health policies related to the use of antibiotics in animal feed in countries such as India. We sequenced 11 new genomes of H. pullorum as a part of this study. These genomes would provide much value in addition to the ongoing comparative genomic studies of helicobacters. Copyright © 2016 American Society for Microbiology.

Exercise training reinstates cortico-cortical sensorimotor functional connectivity following striatal lesioning: Development and application of a subregional-level analytic toolbox for perfusion autoradiographs of the rat brain

NASA Astrophysics Data System (ADS)

Peng, Yu-Hao; Heintz, Ryan; Wang, Zhuo; Guo, Yumei; Myers, Kalisa; Scremin, Oscar; Maarek, Jean-Michel; Holschneider, Daniel

2014-12-01

Current rodent connectome projects are revealing brain structural connectivity with unprecedented resolution and completeness. How subregional structural connectivity relates to subregional functional interactions is an emerging research topic. We describe a method for standardized, mesoscopic-level data sampling from autoradiographic coronal sections of the rat brain, and for correlation-based analysis and intuitive display of cortico-cortical functional connectivity (FC) on a flattened cortical map. A graphic user interface “Cx-2D” allows for the display of significant correlations of individual regions-of-interest, as well as graph theoretical metrics across the cortex. Cx-2D was tested on an autoradiographic data set of cerebral blood flow (CBF) of rats that had undergone bilateral striatal lesions, followed by 4 weeks of aerobic exercise training or no exercise. Effects of lesioning and exercise on cortico-cortical FC were examined during a locomotor challenge in this rat model of Parkinsonism. Subregional FC analysis revealed a rich functional reorganization of the brain in response to lesioning and exercise that was not apparent in a standard analysis focused on CBF of isolated brain regions. Lesioned rats showed diminished degree centrality of lateral primary motor cortex, as well as neighboring somatosensory cortex--changes that were substantially reversed in lesioned rats following exercise training. Seed analysis revealed that exercise increased positive correlations in motor and somatosensory cortex, with little effect in non-sensorimotor regions such as visual, auditory, and piriform cortex. The current analysis revealed that exercise partially reinstated sensorimotor FC lost following dopaminergic deafferentation. Cx-2D allows for standardized data sampling from images of brain slices, as well as analysis and display of cortico-cortical FC in the rat cerebral cortex with potential applications in a variety of autoradiographic and histologic studies.

Spectroscopic and molecular docking studies on N,N-di-tert-butoxycarbonyl (Boc)-2-amino pyridine: A potential bioactive agent for lung cancer treatment

NASA Astrophysics Data System (ADS)

Mohamed Asath, R.; Premkumar, R.; Mathavan, T.; Milton Franklin Benial, A.

2017-09-01

Potential energy surface scan was performed and the most stable molecular structure of the N,N-di-tert-butoxycarbonyl (Boc)-2-amino pyridine (DBAP) molecule was predicted. The most stable molecular structure of the molecule was optimized using B3LYP method with cc-pVTZ basis set. Anticancer activity of the DBAP molecule was evaluated by molecular docking analysis. The structural parameters and vibrational wavenumbers were calculated for the optimized molecular structure. The experimental and theoretical wavenumbers were assigned and compared. Ultraviolet-Visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated and Fukui function calculations were also carried out to investigate the reactive nature of the DBAP molecule. The natural bond orbital analysis was also performed to probe the intramolecular interactions and confirm the bioactivity of the DBAP molecule. The molecular docking analysis reveals the better inhibitory nature of the DBAP molecule against the epidermal growth factor receptor (EGFR) protein which causes lung cancer. Hence, the present study unveils the structural and bioactive nature of the title molecule. The DBAP molecule was identified as a potential inhibitor against the lung cancer which may be useful in further development of drug designing in the treatment of lung cancer.

Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: Dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer.

PubMed

Zhao, Qiang; Yue, Shengjie; Bilal, Muhammad; Hu, Hongbo; Wang, Wei; Zhang, Xuehong

2017-12-31

Bacteria belonging to the genera Sphingomonas and Sphingobium are known for their ability to catabolize aromatic compounds. In this study, we analyzed the whole genome sequences of 26 strains in the genera Sphingomonas and Sphingobium to gain insight into dissemination of bioremediation capabilities, biodegradation potential, central pathways and genome plasticity. Phylogenetic analysis revealed that both Sphingomonas sp. strain BHC-A and Sphingomonas paucimobilis EPA505 should be placed in the genus Sphingobium. The bph and xyl gene cluster was found in 6 polycyclic aromatic hydrocarbons-degrading strains. Transposase and IS coding genes were found in the 6 gene clusters, suggesting the mobility of bph and xyl gene clusters. β-ketoadipate and homogentisate pathways were the main central pathways in Sphingomonas and Sphingobium strains. A large number of oxygenase coding genes were predicted in the 26 genomes, indicating a huge biodegradation potential of the Sphingomonas and Sphingobium strains. Horizontal gene transfer related genes and prophages were predicted in the analyzed strains, suggesting the ongoing evolution and shaping of the genomes. Analysis of the 26 genomes in this work contributes to the understanding of dispersion of bioremediation capabilities, bioremediation potential and genome plasticity in strains belonging to the genera Sphingomonas and Sphingobium. Copyright © 2017 Elsevier B.V. All rights reserved.

Drug information, misinformation, and disinformation on social media: a content analysis study.

PubMed

Al Khaja, Khalid A J; AlKhaja, Alwaleed K; Sequeira, Reginald P

2018-05-24

Dissemination of misleading drug information through social media can be detrimental to the health of the public. This study, carried out in Bahrain, evaluated the truthfulness of 22 social media claims about drugs (72.7%), dietary supplements (22.7%), and toxic bisphenol-A (4.5%). They circulated on WhatsApp platform, as case studies. We categorized claims as objectively true, false, or potentially misleading. The content analysis revealed that "potentially misleading" claims were the most frequent messages (59.1%). They tend to exaggerate the efficacy or safety without sufficient evidence to substantiate claims. False claims (27.3%) were likely due to unfair competition or deception. Overall, 13.6% of the messages were objectively true claims that could withstand regulatory scrutiny. Majority of the drug-related messages on social media were potentially misleading or false claims that lacked credible evidence to support them. In the public interest, regulatory authorities should monitor such information disseminated via social media platforms.

The Functional Impact of Alternative Splicing in Cancer.

PubMed

Climente-González, Héctor; Porta-Pardo, Eduard; Godzik, Adam; Eyras, Eduardo

2017-08-29

Alternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis remain mostly unknown. We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein-protein interactions in cancer-related pathways. Moreover, there was a negative correlation between the number of these alternative splicing changes in a sample and the number of somatic mutations in drivers. We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer, and some of them could potentially be considered alternative splicing drivers (AS drivers). Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Informed choice in direct-to-consumer genetic testing (DTCGT) websites: a content analysis of benefits, risks, and limitations

PubMed Central

Singleton, Amanda; Erby, Lori Hamby; Foisie, Kathryn V.; Kaphingst, Kimberly

2012-01-01

An informed choice about health-related direct-to-consumer genetic testing (DTCGT) requires knowledge of potential benefits, risks, and limitations. To understand the information that potential consumers of DTCGT services are exposed to on company websites, we conducted a content analysis of 23 health-related DTCGT websites. Results revealed that benefit statements outweighed risk and limitation statements 6 to 1. The most frequently described benefits were 1) disease prevention, 2) consumer education, 3) personalized medical recommendations, and 4) the ability to make health decisions. Thirty-five percent of websites also presented at least one risk of testing. Seventy-eight percent of websites mentioned at least one limitation of testing. Based on this information, potential consumers might get an inaccurate picture of genetic testing which could impact their ability to make an informed decision. Practices that enhance the presentation of balanced information on DTCGT company websites should be encouraged. PMID:22194036

Profitable ultrasonic assisted microwave disintegration of sludge biomass: Modelling of biomethanation and energy parameter analysis.

PubMed

Kavitha, S; Rajesh Banu, J; Kumar, Gopalakrishnan; Kaliappan, S; Yeom, Ick Tae

2018-04-01

In this study, microwave irradiation has been employed to disintegrate the sludge biomass profitably by deagglomerating the sludge using a mechanical device, ultrasonicator. The outcomes of the study revealed that a specific energy input of 3.5 kJ/kg TS was found to be optimum for deagglomeration with limited cell lysis. A higher suspended solids (SS) reduction and biomass lysis efficiency of about 22.5% and 33.2% was achieved through ultrasonic assisted microwave disintegration (UMWD) when compared to microwave disintegration - MWD (15% and 20.9%). The results of biochemical methane potential (BMP) test were used to estimate biodegradability of samples. Among the samples subjected to BMP, UMWD showed better amenability towards anaerobic digestion with higher methane production potential of 0.3 L/g COD representing enhanced liquefaction potential of disaggregated sludge biomass. Economic analysis of the proposed method of sludge biomass pretreatment showed a net profit of 2.67 USD/Ton respectively. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T.

PubMed

Diken, Elif; Ozer, Tugba; Arikan, Muzaffer; Emrence, Zeliha; Oner, Ebru Toksoy; Ustek, Duran; Arga, Kazim Yalcin

2015-01-01

Halomonas smyrnensis AAD6T is a gram negative, aerobic, and moderately halophilic bacterium, and is known to produce high levels of levan with many potential uses in foods, feeds, cosmetics, pharmaceutical and chemical industries due to its outstanding properties. Here, the whole-genome analysis was performed to gain more insight about the biological mechanisms, and the whole-genome organization of the bacterium. Industrially crucial genes, including the levansucrase, were detected and the genome-scale metabolic model of H. smyrnensis AAD6T was reconstructed. The bacterium was found to have many potential applications in biotechnology not only being a levan producer, but also because of its capacity to produce Pel exopolysaccharide, polyhydroxyalkanoates, and osmoprotectants. The genomic information presented here will not only provide additional information to enhance our understanding of the genetic and metabolic network of halophilic bacteria, but also accelerate the research on systematical design of engineering strategies for biotechnology applications.

Conservation and variability of West Nile virus proteins.

PubMed

Koo, Qi Ying; Khan, Asif M; Jung, Keun-Ok; Ramdas, Shweta; Miotto, Olivo; Tan, Tin Wee; Brusic, Vladimir; Salmon, Jerome; August, J Thomas

2009-01-01

West Nile virus (WNV) has emerged globally as an increasingly important pathogen for humans and domestic animals. Studies of the evolutionary diversity of the virus over its known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relevance to the immune system. We describe a large-scale analysis of the entire WNV proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequences. This study, which used 2,746 WNV protein sequences collected from the NCBI GenPept database, focused on analysis of peptides of length 9 amino acids or more, which are immunologically relevant as potential T-cell epitopes. Entropy-based analysis of the diversity of WNV sequences, revealed the presence of numerous evolutionarily stable nonamer positions across the proteome (entropy value of < or = 1). The representation (frequency) of nonamers variant to the predominant peptide at these stable positions was, generally, low (< or = 10% of the WNV sequences analyzed). Eighty-eight fragments of length 9-29 amino acids, representing approximately 34% of the WNV polyprotein length, were identified to be identical and evolutionarily stable in all analyzed WNV sequences. Of the 88 completely conserved sequences, 67 are also present in other flaviviruses, and several have been associated with the functional and structural properties of viral proteins. Immunoinformatic analysis revealed that the majority (78/88) of conserved sequences are potentially immunogenic, while 44 contained experimentally confirmed human T-cell epitopes. This study identified a comprehensive catalogue of completely conserved WNV sequences, many of which are shared by other flaviviruses, and majority are potential epitopes. The complete conservation of these immunologically relevant sequences through the entire recorded WNV history suggests they will be valuable as components of peptide-specific vaccines or other therapeutic applications, for sequence-specific diagnosis of a wide-range of Flavivirus infections, and for studies of homologous sequences among other flaviviruses.

Lipid drug conjugate nanoparticle as a potential nanocarrier for the oral delivery of pemetrexed diacid: Formulation design, characterization, ex vivo, and in vivo assessment.

PubMed

Soni, Kriti; Mujtaba, Ali; Kohli, Kanchan

2017-10-01

The present work was to develop lipid drug conjugated (LDC) nanoparticles for the potential oral delivery of pemetrexed diacid (PTX) and evaluation of its in vitro, ex vivo and in vivo potentials. The LDC was prepared by salt formation of PTX with stearic acid and followed by cold homogenization technique to produce the LDC nanoparticles. FTIR analysis of LDC proved the presence of amide bond in LDC powder indicating the conjugation between drug and lipid. LDC nanoparticles was found to have particle size 121.9±1.85nm and zeta potential -51.6mV±1.23 and entrapment efficiency 81.0±0.89%. TEM images revealed spherical morphology and were in corroboration with particle size measurements. Ex vivo gut permeation studies revealed a very good enhancement in permeation of drug present in the LDC as compared to plain drug solution and were confirmed by CLSM. MTT assay conformed significant% toxicity at the end of 24h and 48h. Furthermore, the AUC 0-24 of PTX from the optimized LDC nanoparticels was found to be 4.22 folds higher than that from PTX suspension on oral administration. Thus, LDC has high potential for the oral delivery of PTX in cancer therapy and future prospects for the industrial purpose. Copyright © 2017 Elsevier B.V. All rights reserved.

Race and Older Mothers’ Differentiation: A Sequential Quantitative and Qualitative Analysis

PubMed Central

Sechrist, Jori; Suitor, J. Jill; Riffin, Catherine; Taylor-Watson, Kadari; Pillemer, Karl

2011-01-01

The goal of this paper is to demonstrate a process by which qualitative and quantitative approaches are combined to reveal patterns in the data that are unlikely to be detected and confirmed by either method alone. Specifically, we take a sequential approach to combining qualitative and quantitative data to explore race differences in how mothers differentiate among their adult children. We began with a standard multivariate analysis examining race differences in mothers’ differentiation among their adult children regarding emotional closeness and confiding. Finding no race differences in this analysis, we conducted an in-depth comparison of the Black and White mothers’ narratives to determine whether there were underlying patterns that we had been unable to detect in our first analysis. Using this method, we found that Black mothers were substantially more likely than White mothers to emphasize interpersonal relationships within the family when describing differences among their children. In our final step, we developed a measure of familism based on the qualitative data and conducted a multivariate analysis to confirm the patterns revealed by the in-depth comparison of the mother’s narratives. We conclude that using such a sequential mixed methods approach to data analysis has the potential to shed new light on complex family relations. PMID:21967639

Northeastern Brazilian margin: Regional tectonic evolution based on integrated analysis of seismic reflection and potential field data and modelling

NASA Astrophysics Data System (ADS)

Blaich, Olav A.; Tsikalas, Filippos; Faleide, Jan Inge

2008-10-01

Integration of regional seismic reflection and potential field data along the northeastern Brazilian margin, complemented by crustal-scale gravity modelling, is used to reveal and illustrate onshore-offshore crustal structure correlation, the character of the continent-ocean boundary, and the relationship of crustal structure to regional variation of potential field anomalies. The study reveals distinct along-margin structural and magmatic changes that are spatially related to a number of conjugate Brazil-West Africa transfer systems, governing the margin segmentation and evolution. Several conceptual tectonic models are invoked to explain the structural evolution of the different margin segments in a conjugate margin context. Furthermore, the constructed transects, the observed and modelled Moho relief, and the potential field anomalies indicate that the Recôncavo, Tucano and Jatobá rift system may reflect a polyphase deformation rifting-mode associated with a complex time-dependent thermal structure of the lithosphere. The constructed transects and available seismic reflection profiles, indicate that the northern part of the study area lacks major breakup-related magmatic activity, suggesting a rifted non-volcanic margin affinity. In contrast, the southern part of the study area is characterized by abrupt crustal thinning and evidence for breakup magmatic activity, suggesting that this region evolved, partially, with a rifted volcanic margin affinity and character.

Low-cost housing design and provision: A case study of Kenya

NASA Astrophysics Data System (ADS)

Kabo, Felichism W.

Shelter is as basic a human need as food and water. Today, many people in Third World countries live in sub-standard housing, or lack shelter altogether. Prior research addresses either one of two housing dimensions: broader provision processes, or specific aspects of design. This dissertation is an effort at addressing both dimensions, the underlying premise being that their inter-connectedness demands an integrative approach. More specifically, this dissertation is a combined strategy case study of housing design and provision in Kenya, a sub-Saharan African country with serious shelter problems. A majority of Kenya's urban population lives in slums or squatter settlements. This dissertation covers four major areas of housing design and provision in Kenya: building materials, user preferences for building materials and housing designs, interior layouts, and the organizational context of the housing sector. These four areas are theoretically unified by Canter's (1977) model of place. Each of the first three areas (housing design) relates to one or more of the three domains in the model. The fourth area (housing provision) pertains to the model's context and framework. The technical building materials research reveals the feasibility of making low-cost materials (soil-cements) with satisfactory engineering performance. The research in preference for building materials reveals that the two independent variables, soil and mix, have a significant effect on potential users' ratings. The housing preference study reveals that of the four independent variables, design and type had a significant effect on potential users' ratings, while materials and construction method did not have a significant effect. The interior layout studies reveal important associations between spatial configurations and a key space (the kitchen), and between configuration and conceptualizations of living, cooking, and sleeping spaces. The findings from the studies of preferences and interior layouts are then synthesized in the development of a low-cost housing prototype. Lastly, analysis of the organizational context reveals notable links between nominal housing-related responsibilities, and the potential power and influence of key organizations. The potential effects of the spatial context on housing organizations are also explored. Later, the key organizations are restructured to address shortcomings identified at the organizational and sectoral levels.

The Pathogenic Potential of a Microbe

PubMed Central

2017-01-01

ABSTRACT Virulence is a microbial property that is realized only in susceptible hosts. There is no absolute measurement for virulence, and consequently it is always measured relative to a standard, usually another microbe or host. This article introduces the concept of pathogenic potential, which provides a new approach to measuring the capacity of microbes for virulence. The pathogenic potential is proportional to the fraction of individuals who become symptomatic after infection with a defined inoculum and can include such attributes as mortality, communicability, and the time from infection to disease. The calculation of the pathogenic potential has significant advantages over the use of the lethal dose that kills 50% of infected individuals (LD50) and allows direct comparisons between individual microbes. An analysis of the pathogenic potential of several microbes for mice reveals a continuum, which in turn supports the view that there is no dividing line between pathogenic and nonpathogenic microbes. PMID:28251180

Combined Metabolomic Analysis of Plasma and Urine Reveals AHBA, Tryptophan and Serotonin Metabolism as Potential Risk Factors in Gestational Diabetes Mellitus (GDM)

PubMed Central

Leitner, Miriam; Fragner, Lena; Danner, Sarah; Holeschofsky, Nastassja; Leitner, Karoline; Tischler, Sonja; Doerfler, Hannes; Bachmann, Gert; Sun, Xiaoliang; Jaeger, Walter; Kautzky-Willer, Alexandra; Weckwerth, Wolfram

2017-01-01

Gestational diabetes mellitus during pregnancy has severe implications for the health of the mother and the fetus. Therefore, early prediction and an understanding of the physiology are an important part of prenatal care. Metabolite profiling is a long established method for the analysis and prediction of metabolic diseases. Here, we applied untargeted and targeted metabolomic protocols to analyze plasma and urine samples of pregnant women with and without GDM. Univariate and multivariate statistical analyses of metabolomic profiles revealed markers such as 2-hydroxybutanoic acid (AHBA), 3-hydroxybutanoic acid (BHBA), amino acids valine and alanine, the glucose-alanine-cycle, but also plant-derived compounds like sitosterin as different between control and GDM patients. PLS-DA and VIP analysis revealed tryptophan as a strong variable separating control and GDM. As tryptophan is biotransformed to serotonin we hypothesized whether serotonin metabolism might also be altered in GDM. To test this hypothesis we applied a method for the analysis of serotonin, metabolic intermediates and dopamine in urine by stable isotope dilution direct infusion electrospray ionization mass spectrometry (SID-MS). Indeed, serotonin and related metabolites differ significantly between control and GDM patients confirming the involvement of serotonin metabolism in GDM. Clustered correlation coefficient visualization of metabolite correlation networks revealed the different metabolic signatures between control and GDM patients. Eventually, the combination of selected blood plasma and urine sample metabolites improved the AUC prediction accuracy to 0.99. The detected GDM candidate biomarkers and the related systemic metabolic signatures are discussed in their pathophysiological context. Further studies with larger cohorts are necessary to underpin these observations. PMID:29312952

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

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

Hua, Zheng-Shuang; Han, Yu-Jiao; Chen, Lin-Xing

Here we report that high-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a ‘divide and conquer’ strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We reportmore » the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Finally, our study demonstrates the potential of the ‘divide and conquer’ strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.« less

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

DOE PAGES

Hua, Zheng-Shuang; Han, Yu-Jiao; Chen, Lin-Xing; ...

2014-11-07

Here we report that high-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a ‘divide and conquer’ strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We reportmore » the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Finally, our study demonstrates the potential of the ‘divide and conquer’ strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.« less

Network-Based Identification and Prioritization of Key Regulators of Coronary Artery Disease Loci

PubMed Central

Zhao, Yuqi; Chen, Jing; Freudenberg, Johannes M.; Meng, Qingying; Rajpal, Deepak K.; Yang, Xia

2017-01-01

Objective Recent genome-wide association studies of coronary artery disease (CAD) have revealed 58 genome-wide significant and 148 suggestive genetic loci. However, the molecular mechanisms through which they contribute to CAD and the clinical implications of these findings remain largely unknown. We aim to retrieve gene subnetworks of the 206 CAD loci and identify and prioritize candidate regulators to better understand the biological mechanisms underlying the genetic associations. Approach and Results We devised a new integrative genomics approach that incorporated (1) candidate genes from the top CAD loci, (2) the complete genetic association results from the 1000 genomes-based CAD genome-wide association studies from the Coronary Artery Disease Genome Wide Replication and Meta-Analysis Plus the Coronary Artery Disease consortium, (3) tissue-specific gene regulatory networks that depict the potential relationship and interactions between genes, and (4) tissue-specific gene expression patterns between CAD patients and controls. The networks and top-ranked regulators according to these data-driven criteria were further queried against literature, experimental evidence, and drug information to evaluate their disease relevance and potential as drug targets. Our analysis uncovered several potential novel regulators of CAD such as LUM and STAT3, which possess properties suitable as drug targets. We also revealed molecular relations and potential mechanisms through which the top CAD loci operate. Furthermore, we found that multiple CAD-relevant biological processes such as extracellular matrix, inflammatory and immune pathways, complement and coagulation cascades, and lipid metabolism interact in the CAD networks. Conclusions Our data-driven integrative genomics framework unraveled tissue-specific relations among the candidate genes of the CAD genome-wide association studies loci and prioritized novel network regulatory genes orchestrating biological processes relevant to CAD. PMID:26966275

Novel potential serological prostate cancer biomarkers using CT100+ cancer antigen microarray platform in a multi-cultural South African cohort

PubMed Central

Adeola, Henry A.; Smith, Muneerah; Kaestner, Lisa; Blackburn, Jonathan M.; Zerbini, Luiz F.

2016-01-01

There is a growing need for high throughput diagnostic tools for early diagnosis and treatment monitoring of prostate cancer (PCa) in Africa. The role of cancer-testis antigens (CTAs) in PCa in men of African descent is poorly researched. Hence, we aimed to elucidate the role of 123 Tumour Associated Antigens (TAAs) using antigen microarray platform in blood samples (N = 67) from a South African PCa, Benign prostatic hyperplasia (BPH) and disease control (DC) cohort. Linear (fold-over-cutoff) and differential expression quantitation of autoantibody signal intensities were performed. Molecular signatures of candidate PCa antigen biomarkers were identified and analyzed for ethnic group variation. Potential cancer diagnostic and immunotherapeutic inferences were drawn. We identified a total of 41 potential diagnostic/therapeutic antigen biomarkers for PCa. By linear quantitation, four antigens, GAGE1, ROPN1, SPANXA1 and PRKCZ were found to have higher autoantibody titres in PCa serum as compared with BPH where MAGEB1 and PRKCZ were highly expressed. Also, p53 S15A and p53 S46A were found highly expressed in the disease control group. Statistical analysis by differential expression revealed twenty-four antigens as upregulated in PCa samples, while 11 were downregulated in comparison to BPH and DC (FDR = 0.01). FGFR2, COL6A1and CALM1 were verifiable biomarkers of PCa analysis using urinary shotgun proteomics. Functional pathway annotation of identified biomarkers revealed similar enrichment both at genomic and proteomic level and ethnic variations were observed. Cancer antigen arrays are emerging useful in potential diagnostic and immunotherapeutic antigen biomarker discovery. PMID:26885621

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

PubMed

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

PubMed Central

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. PMID:27697855

Inhibition of epidermal growth factor receptor by ferulic acid and 4-vinylguaiacol in human breast cancer cells.

PubMed

Sudhagar, S; Sathya, S; Anuradha, R; Gokulapriya, G; Geetharani, Y; Lakshmi, B S

2018-02-01

To examine the potential of ferulic acid and 4-vinylguaiacol for inhibiting epidermal growth factor receptor (EGFR) in human breast cancer cells in vitro. Ferulic acid and 4-vinylguaiacol limit the EGF (epidermal growth factor)-induced breast cancer proliferation and new DNA synthesis. Western blot analysis revealed both ferulic acid and 4-vinylguaiacol exhibit sustained inhibition of EGFR activation through down-regulation of Tyr 1068 autophosphorylation. Molecular docking analysis shows ferulic acid forming hydrogen bond interaction with Lys 745 and Met 793 whereas, 4-vinylguaiacol forms two hydrogen bonds with Phe 856 and exhibits stronger hydrophobic interactions with multiple amino acid residues at the EGFR kinase domain. Ferulic acid and 4-vinylguaiacol could serve as a potential structure for the development of new small molecule therapeutics against EGFR.

Activity and Diversity of Methanotrophic Bacteria at Methane Seeps in Eastern Lake Constance Sediments ▿

PubMed Central

Deutzmann, Jörg S.; Wörner, Susanne; Schink, Bernhard

2011-01-01

The activity and community structure of aerobic methanotrophic communities were investigated at methane seeps (pockmarks) in the littoral and profundal zones of an oligotrophic freshwater lake (Lake Constance, Germany). Measurements of potential methane oxidation rates showed that sediments inside littoral pockmarks are hot spots of methane oxidation. Potential methane oxidation rates at littoral pockmark sites exceeded the rates of the surrounding sediment by 2 orders of magnitude. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the pmoA gene revealed major differences in the methanotrophic community composition between littoral pockmarks and the surrounding sediments. Clone library analysis confirmed that one distinct Methylobacter-related group dominates the community at littoral pockmarks. In profundal sediments, the differences between pockmarks and surrounding sediments were found to be less pronounced. PMID:21335392

Global metabolomics reveals potential urinary biomarkers of esophageal squamous cell carcinoma for diagnosis and staging

NASA Astrophysics Data System (ADS)

Xu, Jing; Chen, Yanhua; Zhang, Ruiping; He, Jiuming; Song, Yongmei; Wang, Jingbo; Wang, Huiqing; Wang, Luhua; Zhan, Qimin; Abliz, Zeper

2016-10-01

We performed a metabolomics study using liquid chromatography-mass spectrometry (LC-MS) combined with multivariate data analysis (MVDA) to discriminate global urine profiles in urine samples from esophageal squamous cell carcinoma (ESCC) patients and healthy controls (NC). Our work evaluated the feasibility of employing urine metabolomics for the diagnosis and staging of ESCC. The satisfactory classification between the healthy controls and ESCC patients was obtained using the MVDA model, and obvious classification of early-stage and advanced-stage patients was also observed. The results suggest that the combination of LC-MS analysis and MVDA may have potential applications for ESCC diagnosis and staging. We then conducted LC-MS/MS experiments to identify the potential biomarkers with large contributions to the discrimination. A total of 83 potential diagnostic biomarkers for ESCC were screened out, and 19 potential biomarkers were identified; the variations between the differences in staging using these potential biomarkers were further analyzed. These biomarkers may not be unique to ESCCs, but instead result from any malignant disease. To further elucidate the pathophysiology of ESCC, we studied related metabolic pathways and found that ESCC is associated with perturbations of fatty acid β-oxidation and the metabolism of amino acids, purines, and pyrimidines.

Identification of membrane-associated proteins with pathogenic potential expressed by Corynebacterium pseudotuberculosis grown in animal serum.

PubMed

Raynal, José Tadeu; Bastos, Bruno Lopes; Vilas-Boas, Priscilla Carolinne Bagano; Sousa, Thiago de Jesus; Costa-Silva, Marcos; de Sá, Maria da Conceição Aquino; Portela, Ricardo Wagner; Moura-Costa, Lília Ferreira; Azevedo, Vasco; Meyer, Roberto

2018-01-25

Previous works defining antigens that might be used as vaccine targets against Corynebacterium pseudotuberculosis, which is the causative agent of sheep and goat caseous lymphadenitis, have focused on secreted proteins produced in a chemically defined culture media. Considering that such antigens might not reflect the repertoire of proteins expressed during infection conditions, this experiment aimed to investigate the membrane-associated proteins with pathogenic potential expressed by C. pseudotuberculosis grown directly in animal serum. Its membrane-associated proteins have been extracted using an organic solvent enrichment methodology, followed by LC-MS/MS and bioinformatics analysis for protein identification and classification. The results revealed 22 membrane-associated proteins characterized as potentially pathogenic. An interaction network analysis indicated that the four potentially pathogenic proteins ciuA, fagA, OppA4 and OppCD were biologically connected within two distinct network pathways, which were both associated with the ABC Transporters KEGG pathway. These results suggest that C. pseudotuberculosis pathogenesis might be associated with the transport and uptake of nutrients; other seven identified potentially pathogenic membrane proteins also suggest that pathogenesis might involve events of bacterial resistance and adhesion. The proteins herein reported potentially reflect part of the protein repertoire expressed during real infection conditions and might be tested as vaccine antigens.

Screening, Characterization and In Vitro Evaluation of Probiotic Properties Among Lactic Acid Bacteria Through Comparative Analysis.

PubMed

Devi, Sundru Manjulata; Archer, Ann Catherine; Halami, Prakash M

2015-09-01

The present work aimed to identify probiotic bacteria from healthy human infant faecal and dairy samples. Subsequently, an assay was developed to evaluate the probiotic properties using comparative genetic approach for marker genes involved in adhesion to the intestinal epithelial layer. Several in vitro properties including tolerance to biological barriers (such as acid and bile), antimicrobial spectrum, resistance to simulated digestive fluids and cellular hydrophobicity were assessed. The potential probiotic cultures were rapidly characterized by morphological, physiological and molecular-based methods [such as RFLP, ITS, RAPD and (GTG)5]. Further analysis by 16S rDNA sequencing revealed that the selected isolates belong to Lactobacillus, Pediococcus and Enterococcus species. Two cultures of non-lactic, non-pathogenic Staphylococcus spp. were also isolated. The native isolates were able to survive under acidic, bile and simulated intestinal conditions. In addition, these cultures inhibited the growth of tested bacterial pathogens. Further, no correlation was observed between hydrophobicity and adhesion ability. Sequencing of probiotic marker genes such as bile salt hydrolase (bsh), fibronectin-binding protein (fbp) and mucin-binding protein (mub) for selected isolates revealed nucleotide variation. The probiotic binding domains were detected by several bioinformatic tools. The approach used in the study enabled the identification of potential probiotic domains responsible for adhesion of bacteria to intestinal epithelial layer, which may further assist in screening of novel probiotic bacteria. The rapid detection of binding domains will help in revealing the beneficial properties of the probiotic cultures. Further, studies will be performed to develop a novel probiotic product which will contribute in food and feed industry.

Adsorptive Removal of Toxic Chromium from Waste-Water Using Wheat Straw and Eupatorium adenophorum

PubMed Central

Song, Dagang; Pan, Kaiwen; Tariq, Akash; Azizullah, Azizullah; Sun, Feng; Li, Zilong; Xiong, Qinli

2016-01-01

Environmental pollution with heavy metals is a serious issue worldwide posing threats to humans, animals and plants and to the stability of overall ecosystem. Chromium (Cr) is one of most hazardous heavy metals with a high carcinogenic and recalcitrant nature. Aim of the present study was to select low-cost biosorbent using wheat straw and Eupatorium adenophorum through simple carbonization process, capable of removing Cr (VI) efficiently from wastewater. From studied plants a low cost adsorbent was prepared for removing Cr (VI) from aqueous solution following very simple carbonization method excluding activation process. Several factors such as pH, contact time, sorbent dosage and temperature were investigated for attaining ideal condition. For analysis of adsorption equilibrium isotherm data, Langmuir, Freundlich and Temkin models were used while pseudo-first-order, pseudo-second-order, external diffusion and intra-particle diffusion models were used for the analysis of kinetic data. The obtained results revealed that 99.9% of Cr (VI) removal was observed in the solution with a pH of 1.0. Among all the tested models Langmuir model fitted more closely according to the data obtained. Increase in adsorption capacity was observed with increasing temperature revealing endothermic nature of Cr (VI). The maximum Cr (VI) adsorption potential of E. adenophorum and wheat straw was 89.22 mg per 1 gram adsorbent at 308K. Kinetic data of absorption precisely followed pseudo-second-order model. Present study revealed highest potential of E. adenophorum and wheat straw for producing low cost adsorbent and to remove Cr (VI) from contaminated water. PMID:27911906

A Novel Bacteriophage Targeting Cronobacter sakazakii Is a Potential Biocontrol Agent in Foods

PubMed Central

Lee, Ju-Hoon; Bai, Jaewoo; Shin, Hakdong; Kim, Yeran; Park, Bookyung; Heu, Sunggi

2015-01-01

Cronobacter sakazakii is an important pathogen that causes high mortality in infants. Due to its occasional antibiotic resistance, a bacteriophage approach might be an alternative effective method for the control of this pathogen. To develop a novel biocontrol agent using bacteriophages, the C. sakazakii-infecting phage CR5 was newly isolated and characterized. Interestingly, this phage exhibited efficient and relatively durable host lysis activity. In addition, a specific gene knockout study and subsequent complementation experiment revealed that this phage infected the host strain using the bacterial flagella. The complete genome sequence analysis of phage CR5 showed that its genome contains 223,989 bp of DNA, including 231 predicted open reading frames (ORFs), and it has a G+C content of 50.06%. The annotated ORFs were classified into six functional groups (structure, packaging, host lysis, DNA manipulation, transcription, and additional functions); no gene was found to be related to virulence or toxin or lysogen formation, but >80% of the predicted ORFs are unknown. In addition, a phage proteomic analysis using SDS-PAGE and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) revealed that seven phage structural proteins are indeed present, supporting the ORF predictions. To verify the potential of this phage as a biocontrol agent against C. sakazakii, it was added to infant formula milk contaminated with a C. sakazakii clinical isolate or food isolate, revealing complete growth inhibition of the isolates by the addition of phage CR5 when the multiplicity of infection (MOI) was 105. PMID:26497465

Genomic analysis, cytokine expression, and microRNA profiling reveal biomarkers of human dietary zinc depletion and homeostasis.

PubMed

Ryu, Moon-Suhn; Langkamp-Henken, Bobbi; Chang, Shou-Mei; Shankar, Meena N; Cousins, Robert J

2011-12-27

Implementation of zinc interventions for subjects suspected of being zinc-deficient is a global need, but is limited due to the absence of reliable biomarkers. To discover molecular signatures of human zinc deficiency, a combination of transcriptome, cytokine, and microRNA analyses was applied to a dietary zinc depletion/repletion protocol with young male human subjects. Concomitant with a decrease in serum zinc concentration, changes in buccal and blood gene transcripts related to zinc homeostasis occurred with zinc depletion. Microarray analyses of whole blood RNA revealed zinc-responsive genes, particularly, those associated with cell cycle regulation and immunity. Responses of potential signature genes of dietary zinc depletion were further assessed by quantitative real-time PCR. The diagnostic properties of specific serum microRNAs for dietary zinc deficiency were identified by acute responses to zinc depletion, which were reversible by subsequent zinc repletion. Depression of immune-stimulated TNFα secretion by blood cells was observed after low zinc consumption and may serve as a functional biomarker. Our findings introduce numerous novel candidate biomarkers for dietary zinc status assessment using a variety of contemporary technologies and which identify changes that occur prior to or with greater sensitivity than the serum zinc concentration which represents the current zinc status assessment marker. In addition, the results of gene network analysis reveal potential clinical outcomes attributable to suboptimal zinc intake including immune function defects and predisposition to cancer. These demonstrate through a controlled depletion/repletion dietary protocol that the illusive zinc biomarker(s) can be identified and applied to assessment and intervention strategies.

Adsorptive Removal of Toxic Chromium from Waste-Water Using Wheat Straw and Eupatorium adenophorum.

PubMed

Song, Dagang; Pan, Kaiwen; Tariq, Akash; Azizullah, Azizullah; Sun, Feng; Li, Zilong; Xiong, Qinli

2016-01-01

Environmental pollution with heavy metals is a serious issue worldwide posing threats to humans, animals and plants and to the stability of overall ecosystem. Chromium (Cr) is one of most hazardous heavy metals with a high carcinogenic and recalcitrant nature. Aim of the present study was to select low-cost biosorbent using wheat straw and Eupatorium adenophorum through simple carbonization process, capable of removing Cr (VI) efficiently from wastewater. From studied plants a low cost adsorbent was prepared for removing Cr (VI) from aqueous solution following very simple carbonization method excluding activation process. Several factors such as pH, contact time, sorbent dosage and temperature were investigated for attaining ideal condition. For analysis of adsorption equilibrium isotherm data, Langmuir, Freundlich and Temkin models were used while pseudo-first-order, pseudo-second-order, external diffusion and intra-particle diffusion models were used for the analysis of kinetic data. The obtained results revealed that 99.9% of Cr (VI) removal was observed in the solution with a pH of 1.0. Among all the tested models Langmuir model fitted more closely according to the data obtained. Increase in adsorption capacity was observed with increasing temperature revealing endothermic nature of Cr (VI). The maximum Cr (VI) adsorption potential of E. adenophorum and wheat straw was 89.22 mg per 1 gram adsorbent at 308K. Kinetic data of absorption precisely followed pseudo-second-order model. Present study revealed highest potential of E. adenophorum and wheat straw for producing low cost adsorbent and to remove Cr (VI) from contaminated water.

Quantitative Proteomics Analysis Reveals Novel Insights into Mechanisms of Action of Long Noncoding RNA Hox Transcript Antisense Intergenic RNA (HOTAIR) in HeLa Cells*

PubMed Central

Zheng, Peng; Xiong, Qian; Wu, Ying; Chen, Ying; Chen, Zhuo; Fleming, Joy; Gao, Ding; Bi, Lijun; Ge, Feng

2015-01-01

Long noncoding RNAs (lncRNAs), which have emerged in recent years as a new and crucial layer of gene regulators, regulate various biological processes such as carcinogenesis and metastasis. HOTAIR (Hox transcript antisense intergenic RNA), a lncRNA overexpressed in most human cancers, has been shown to be an oncogenic lncRNA. Here, we explored the role of HOTAIR in HeLa cells and searched for proteins regulated by HOTAIR. To understand the mechanism of action of HOTAIR from a systems perspective, we employed a quantitative proteomic strategy to systematically identify potential targets of HOTAIR. The expression of 170 proteins was significantly dys-regulated after inhibition of HOTAIR, implying that they could be potential targets of HOTAIR. Analysis of this data at the systems level revealed major changes in proteins involved in diverse cellular components, including the cytoskeleton and the respiratory chain. Further functional studies on vimentin (VIM), a key protein involved in the cytoskeleton, revealed that HOTAIR exerts its effects on migration and invasion of HeLa cells, at least in part, through the regulation of VIM expression. Inhibition of HOTAIR leads to mitochondrial dysfunction and ultrastructural alterations, suggesting a novel role of HOTAIR in maintaining mitochondrial function in cancer cells. Our results provide novel insights into the mechanisms underlying the function of HOTAIR in cancer cells. We expect that the methods used in this study will become an integral part of functional studies of lncRNAs. PMID:25762744

Long-Term Coffee Consumption Is Associated with Decreased Incidence of New-Onset Hypertension: A Dose-Response Meta-Analysis.

PubMed

Grosso, Giuseppe; Micek, Agnieszka; Godos, Justyna; Pajak, Andrzej; Sciacca, Salvatore; Bes-Rastrollo, Maira; Galvano, Fabio; Martinez-Gonzalez, Miguel A

2017-08-17

To perform a dose-response meta-analysis of prospective cohort studies investigating the association between long-term coffee intake and risk of hypertension. An online systematic search of studies published up to November 2016 was performed. Linear and non-linear dose-response meta-analyses were conducted; potential evidence of heterogeneity, publication bias, and confounding effect of selected variables were investigated through sensitivity and meta-regression analyses. Seven cohorts including 205,349 individuals and 44,120 cases of hypertension were included. In the non-linear analysis, there was a 9% significant decreased risk of hypertension per seven cups of coffee a day, while, in the linear dose-response association, there was a 1% decreased risk of hypertension for each additional cup of coffee per day. Among subgroups, there were significant inverse associations for females, caffeinated coffee, and studies conducted in the US with longer follow-up. Analysis of potential confounders revealed that smoking-related variables weakened the strength of association between coffee consumption and risk of hypertension. Increased coffee consumption is associated with a modest decrease in risk of hypertension in prospective cohort studies. Smoking status is a potential effect modifier on the association between coffee consumption and risk of hypertension.

Analysis of Plasma-Sprayed Thermal Barrier Coatings With Homogeneous and Heterogeneous Bond Coats Under Spatially Uniform Cyclic Thermal Loading

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Pindera, Marek-Jerzy; Aboudi, Jacob

2003-01-01

This report summarizes the results of a numerical investigation into the spallation mechanism in plasma-sprayed thermal barrier coatings observed under spatially-uniform cyclic thermal loading. The analysis focuses on the evolution of local stress and inelastic strain fields in the vicinity of the rough top/bond coat interface during thermal cycling, and how these fields are influenced by the presence of an oxide film and spatially uniform and graded distributions of alumina particles in the metallic bond coat aimed at reducing the top/bond coat thermal expansion mismatch. The impact of these factors on the potential growth of a local horizontal delamination at the rough interface's crest is included. The analysis is conducted using the Higher-Order Theory for Functionally Graded Materials with creep/relaxation constituent modeling capabilities. For two-phase bond coat microstructures, both the actual and homogenized properties are employed in the analysis. The results reveal the important contributions of both the normal and shear stress components to the delamination growth potential in the presence of an oxide film, and suggest mixed-mode crack propagation. The use of bond coats with uniform or graded microstructures is shown to increase the potential for delamination growth by increasing the magnitude of the crack-tip shear stress component.

Comparative sequence analysis revealed altered chromosomal organization and a novel insertion sequence encoding DNA modification and potentially stress-related functions in an Escherichia coli O157:H7 foodborne isolate

USDA-ARS?s Scientific Manuscript database

We recently described the complete genome of enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain NADC 6564, an isolate of strain 86-24 linked to the 1986 disease outbreak. In the current study, we compared the chromosomal sequence of NADC 6564 to the well-characterized chromosomal sequences of ...

Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus denitrificans Strain ISTOD1, Isolated from Wastewater.

PubMed

Medhi, Kristina; Mishra, Arti; Thakur, Indu Shekhar

2018-04-12

We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb, isolated from wastewater. It has been identified as a heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis revealed genes related to nitrogen and phosphorus removal, showing that the strain holds potential for bioremediation and biorefinery uses. Copyright © 2018 Medhi et al.

Infrasound Signals from Ground-Motion Sources

DTIC Science & Technology

2008-09-01

signals as a basis for discriminants between underground nuclear tests ( UGT ) and earthquakes (EQ). In an earlier program, infrasound signals from... UGTs and EQs were collected at ranges of a few hundred kilometers, in the far-field. Analysis of these data revealed two parameters that had potential...well. To study the near-field signals, we are using computational techniques based on modeled ground motions from UGTs and EQs. One is the closed

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization

DOE PAGES

Kothari, Ankita; Charrier, Marimikel; Wu, Yu -Wei; ...

2016-09-22

The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulatedmore » genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. As a result, this study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.« less

Alpharetroviral Vector-mediated Gene Therapy for X-CGD: Functional Correction and Lack of Aberrant Splicing

PubMed Central

Kaufmann, Kerstin B.; Brendel, Christian; Suerth, Julia D.; Mueller-Kuller, Uta; Chen-Wichmann, Linping; Schwäble, Joachim; Pahujani, Shweta; Kunkel, Hana; Schambach, Axel; Baum, Christopher; Grez, Manuel

2013-01-01

Comparative integrome analysis has revealed that the most neutral integration pattern among retroviruses is attributed to alpharetroviruses. We chose X-linked chronic granulomatous disease (X-CGD) as model to evaluate the potential of self-inactivating (SIN) alpharetroviral vectors for gene therapy of monogenic diseases. Therefore, we combined the alpharetroviral vector backbone with the elongation factor-1α short promoter, both considered to possess a low genotoxic profile, to drive transgene (gp91phox) expression. Following efficient transduction transgene expression was sustained and provided functional correction of the CGD phenotype in a cell line model at low vector copy number. Further analysis in a murine X-CGD transplantation model revealed gene-marking of bone marrow cells and oxidase positive granulocytes in peripheral blood. Transduction of human X-CGD CD34+ cells provided functional correction up to wild-type levels and long-term expression upon transplantation into a humanized mouse model. In contrast to lentiviral vectors, no aberrantly spliced transcripts containing cellular exons fused to alpharetroviral sequences were found in transduced cells, implying that the safety profile of alpharetroviral vectors may extend beyond their neutral integration profile. Taken together, this highlights the potential of this SIN alpharetroviral system as a platform for new candidate vectors for future gene therapy of hematopoietic disorders. PMID:23207695

Effects of Perfluorooctanoic Acid on Metabolic Profiles in Brain and Liver of Mouse Revealed by a High-throughput Targeted Metabolomics Approach

NASA Astrophysics Data System (ADS)

Yu, Nanyang; Wei, Si; Li, Meiying; Yang, Jingping; Li, Kan; Jin, Ling; Xie, Yuwei; Giesy, John P.; Zhang, Xiaowei; Yu, Hongxia

2016-04-01

Perfluorooctanoic acid (PFOA), a perfluoroalkyl acid, can result in hepatotoxicity and neurobehavioral effects in animals. The metabolome, which serves as a connection among transcriptome, proteome and toxic effects, provides pathway-based insights into effects of PFOA. Since understanding of changes in the metabolic profile during hepatotoxicity and neurotoxicity were still incomplete, a high-throughput targeted metabolomics approach (278 metabolites) was used to investigate effects of exposure to PFOA for 28 d on brain and liver of male Balb/c mice. Results of multivariate statistical analysis indicated that PFOA caused alterations in metabolic pathways in exposed individuals. Pathway analysis suggested that PFOA affected metabolism of amino acids, lipids, carbohydrates and energetics. Ten and 18 metabolites were identified as potential unique biomarkers of exposure to PFOA in brain and liver, respectively. In brain, PFOA affected concentrations of neurotransmitters, including serotonin, dopamine, norepinephrine, and glutamate in brain, which provides novel insights into mechanisms of PFOA-induced neurobehavioral effects. In liver, profiles of lipids revealed involvement of β-oxidation and biosynthesis of saturated and unsaturated fatty acids in PFOA-induced hepatotoxicity, while alterations in metabolism of arachidonic acid suggesting potential of PFOA to cause inflammation response in liver. These results provide insight into the mechanism and biomarkers for PFOA-induced effects.

Evaluation of the TRPM2 channel as a biomarker in breast cancer using public databases analysis.

PubMed

Sumoza-Toledo, Adriana; Espinoza-Gabriel, Mario Iván; Montiel-Condado, Dvorak

Breast cancer is one of the most common malignancies affecting women. Recent investigations have revealed a major role of ion channels in cancer. The transient receptor potential melastatin-2 (TRPM2) is a plasma membrane and lysosomal channel with important roles in cell migration and cell death in immune cells and tumor cells. In this study, we investigated the prognostic value of TRPM2 channel in breast cancer, analyzing public databases compiled in Oncomine™ (Thermo Fisher, Ann Arbor, MI) and online Kaplan-Meier Plotter platforms. The results revealed that TRPM2 mRNA overexpression is significant in situ and invasive breast carcinoma compared to normal breast tissue. Furthermore, multi-gene validation using Oncomine™ showed that this channel is coexpressed with proteins related to cellular migration, transformation, and apoptosis. On the other hand, Kaplan-Meier analysis exhibited that low expression of TRPM2 could be used to predict poor outcome in ER- and HER2+ breast carcinoma patients. TRPM2 is a promising biomarker for aggressiveness of breast cancer, and a potential target for the development of new therapies. Copyright © 2016 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization

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

Kothari, Ankita; Charrier, Marimikel; Wu, Yu -Wei

The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulatedmore » genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. As a result, this study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.« less

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle.

PubMed

Zhang, Jiachao; Xu, Chuanbiao; Huo, Dongxue; Hu, Qisong; Peng, Qiannan

2017-02-08

Previous studies suggested a close relationship between ruminant gut microbes and the mammary gland. In this study, shotgun metagenomic sequencing was used to reveal the differences in the intestinal microbiome potentially related to milk components in Murrah buffaloes and Chinese Holstein cattle. A PCoA based on the weighted Unifrac distances showed an apparent clustering pattern in the structure of intestinal microbiota between buffalo and cattle. We could attribute the structural difference to the genera of Sutterella, Coprococcus and Dorea. A further analysis of microbial functional features revealed that the biosynthesis of amino acids (including lysine, valine, leucine and isoleucine), lipopolysaccharide biosynthesis and cofactor/vitamin biosynthesis were enriched in the buffalo. In contrast, dairy cattle had higher levels of pyruvate metabolism and carbon fixation in photosynthetic organisms. A further correlation analysis based on different milk components and the typical microbiome uncovered a significant positive correlation between milk protein and the microbial biosynthesis of amino acids, which was also positively correlated in the genera of Parabacteroides, Dorea and Sutterella. This study will expand our understanding of the intestinal microbiome of buffalo and cattle as representative ruminants, as well as provide new views about how to improve the production and nutritional qualities of animal milk.

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma.

PubMed

Lu, Haifeng; Ren, Zhigang; Li, Ang; Zhang, Hua; Jiang, Jianwen; Xu, Shaoyan; Luo, Qixia; Zhou, Kai; Sun, Xiaoli; Zheng, Shusen; Li, Lanjuan

2016-09-08

Liver carcinoma (LC) is a common malignancy worldwide, associated with high morbidity and mortality. Characterizing microbiome profiles of tongue coat may provide useful insights and potential diagnostic marker for LC patients. Herein, we are the first time to investigate tongue coat microbiome of LC patients with cirrhosis based on 16S ribosomal RNA (rRNA) gene sequencing. After strict inclusion and exclusion criteria, 35 early LC patients with cirrhosis and 25 matched healthy subjects were enrolled. Microbiome diversity of tongue coat in LC patients was significantly increased shown by Shannon, Simpson and Chao 1 indexes. Microbiome on tongue coat was significantly distinguished LC patients from healthy subjects by principal component analysis. Tongue coat microbial profiles represented 38 operational taxonomic units assigned to 23 different genera, distinguishing LC patients. Linear discriminant analysis (LDA) effect size (LEfSe) reveals significant microbial dysbiosis of tongue coats in LC patients. Strikingly, Oribacterium and Fusobacterium could distinguish LC patients from healthy subjects. LEfSe outputs show microbial gene functions related to categories of nickel/iron_transport, amino_acid_transport, energy produced system and metabolism between LC patients and healthy subjects. These findings firstly identify microbiota dysbiosis of tongue coat in LC patients, may providing novel and non-invasive potential diagnostic biomarker of LC.

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma

NASA Astrophysics Data System (ADS)

Lu, Haifeng; Ren, Zhigang; Li, Ang; Zhang, Hua; Jiang, Jianwen; Xu, Shaoyan; Luo, Qixia; Zhou, Kai; Sun, Xiaoli; Zheng, Shusen; Li, Lanjuan

2016-09-01

Liver carcinoma (LC) is a common malignancy worldwide, associated with high morbidity and mortality. Characterizing microbiome profiles of tongue coat may provide useful insights and potential diagnostic marker for LC patients. Herein, we are the first time to investigate tongue coat microbiome of LC patients with cirrhosis based on 16S ribosomal RNA (rRNA) gene sequencing. After strict inclusion and exclusion criteria, 35 early LC patients with cirrhosis and 25 matched healthy subjects were enrolled. Microbiome diversity of tongue coat in LC patients was significantly increased shown by Shannon, Simpson and Chao 1 indexes. Microbiome on tongue coat was significantly distinguished LC patients from healthy subjects by principal component analysis. Tongue coat microbial profiles represented 38 operational taxonomic units assigned to 23 different genera, distinguishing LC patients. Linear discriminant analysis (LDA) effect size (LEfSe) reveals significant microbial dysbiosis of tongue coats in LC patients. Strikingly, Oribacterium and Fusobacterium could distinguish LC patients from healthy subjects. LEfSe outputs show microbial gene functions related to categories of nickel/iron_transport, amino_acid_transport, energy produced system and metabolism between LC patients and healthy subjects. These findings firstly identify microbiota dysbiosis of tongue coat in LC patients, may providing novel and non-invasive potential diagnostic biomarker of LC.

Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis.

PubMed

Zheng, Wenning; Tan, Mui Fern; Old, Lesley A; Paterson, Ian C; Jakubovics, Nicholas S; Choo, Siew Woh

2017-06-07

Streptococcus gordonii and Streptococcus sanguinis are pioneer colonizers of dental plaque and important agents of bacterial infective endocarditis (IE). To gain a greater understanding of these two closely related species, we performed comparative analyses on 14 new S. gordonii and 5 S. sanguinis strains using various bioinformatics approaches. We revealed S. gordonii and S. sanguinis harbor open pan-genomes and share generally high sequence homology and number of core genes including virulence genes. However, we observed subtle differences in genomic islands and prophages between the species. Comparative pathogenomics analysis identified S. sanguinis strains have genes encoding IgA proteases, mitogenic factor deoxyribonucleases, nickel/cobalt uptake and cobalamin biosynthesis. On the contrary, genomic islands of S. gordonii strains contain additional copies of comCDE quorum-sensing system components involved in genetic competence. Two distinct polysaccharide locus architectures were identified, one of which was exclusively present in S. gordonii strains. The first evidence of genes encoding the CylA and CylB system by the α-haemolytic S. gordonii is presented. This study provides new insights into the genetic distinctions between S. gordonii and S. sanguinis, which yields understanding of tooth surfaces colonization and contributions to dental plaque formation, as well as their potential roles in the pathogenesis of IE.

Clinical application of plasma thermograms. Utility, practical approaches and considerations.

PubMed

Garbett, Nichola C; Mekmaysy, Chongkham S; DeLeeuw, Lynn; Chaires, Jonathan B

2015-04-01

Differential scanning calorimetry (DSC) studies of blood plasma are part of an emerging area of the clinical application of DSC to biofluid analysis. DSC analysis of plasma from healthy individuals and patients with various diseases has revealed changes in the thermal profiles of the major plasma proteins associated with the clinical status of the patient. The sensitivity of DSC to the concentration of proteins, their interactions with other proteins or ligands, or their covalent modification underlies the potential utility of DSC analysis. A growing body of literature has demonstrated the versatility and performance of clinical DSC analysis across a range of biofluids and in a number of disease settings. The principles, practice and challenges of DSC analysis of plasma are described in this article. Copyright © 2014 Elsevier Inc. All rights reserved.

Clinical application of plasma thermograms. Utility, practical approaches and considerations

PubMed Central

Garbett, Nichola C.; Mekmaysy, Chongkham S.; DeLeeuw, Lynn; Chaires, Jonathan B.

2014-01-01

Differential scanning calorimetry (DSC) studies of blood plasma are part of an emerging area of the clinical application of DSC to biofluid analysis. DSC analysis of plasma from healthy individuals and patients with various diseases has revealed changes in the thermal profiles of the major plasma proteins associated with the clinical status of the patient. The sensitivity of DSC to the concentration of proteins, their interactions with other proteins or ligands, or their covalent modifications underlies the potential utility of DSC analysis. A growing body of literature has demonstrated the versatility and performance of clinical DSC analysis across a range of biofluids and in a number of disease settings. The principles, practice and challenges of DSC analysis of plasma are described in this article. PMID:25448297

Microbial Metabolic Potential for Carbon Degradation and Nutrient (Nitrogen and Phosphorus) Acquisition in an Ombrotrophic Peatland

PubMed Central

Tfaily, Malak M.; Green, Stefan J.; Steinweg, J. Megan; Chanton, Patrick; Imvittaya, Aopeau; Chanton, Jeffrey P.; Cooper, William; Schadt, Christopher

2014-01-01

This study integrated metagenomic and nuclear magnetic resonance (NMR) spectroscopic approaches to investigate microbial metabolic potential for organic matter decomposition and nitrogen (N) and phosphorus (P) acquisition in soils of an ombrotrophic peatland in the Marcell Experimental Forest (MEF), Minnesota, USA. This analysis revealed vertical stratification in key enzymatic pathways and taxa containing these pathways. Metagenomic analyses revealed that genes encoding laccases and dioxygenases, involved in aromatic compound degradation, declined in relative abundance with depth, while the relative abundance of genes encoding metabolism of amino sugars and all four saccharide groups increased with depth in parallel with a 50% reduction in carbohydrate content. Most Cu-oxidases were closely related to genes from Proteobacteria and Acidobacteria, and type 4 laccase-like Cu-oxidase genes were >8 times more abundant than type 3 genes, suggesting an important and overlooked role for type 4 Cu-oxidase in phenolic compound degradation. Genes associated with sulfate reduction and methanogenesis were the most abundant anaerobic respiration genes in these systems, with low levels of detection observed for genes of denitrification and Fe(III) reduction. Fermentation genes increased in relative abundance with depth and were largely affiliated with Syntrophobacter. Methylocystaceae-like small-subunit (SSU) rRNA genes, pmoA, and mmoX genes were more abundant among methanotrophs. Genes encoding N2 fixation, P uptake, and P regulons were significantly enriched in the surface peat and in comparison to other ecosystems, indicating N and P limitation. Persistence of inorganic orthophosphate throughout the peat profile in this P-limiting environment indicates that P may be bound to recalcitrant organic compounds, thus limiting P bioavailability in the subsurface. Comparative metagenomic analysis revealed a high metabolic potential for P transport and starvation, N2 fixation, and oligosaccharide degradation at MEF relative to other wetland and soil environments, consistent with the nutrient-poor and carbohydrate-rich conditions found in this Sphagnum-dominated boreal peatland. PMID:24682299

Microbial metabolic potential for carbon degradation and nutrient (nitrogen and phosphorus) acquisition in an ombrotrophic peatland.

PubMed

Lin, Xueju; Tfaily, Malak M; Green, Stefan J; Steinweg, J Megan; Chanton, Patrick; Imvittaya, Aopeau; Chanton, Jeffrey P; Cooper, William; Schadt, Christopher; Kostka, Joel E

2014-06-01

This study integrated metagenomic and nuclear magnetic resonance (NMR) spectroscopic approaches to investigate microbial metabolic potential for organic matter decomposition and nitrogen (N) and phosphorus (P) acquisition in soils of an ombrotrophic peatland in the Marcell Experimental Forest (MEF), Minnesota, USA. This analysis revealed vertical stratification in key enzymatic pathways and taxa containing these pathways. Metagenomic analyses revealed that genes encoding laccases and dioxygenases, involved in aromatic compound degradation, declined in relative abundance with depth, while the relative abundance of genes encoding metabolism of amino sugars and all four saccharide groups increased with depth in parallel with a 50% reduction in carbohydrate content. Most Cu-oxidases were closely related to genes from Proteobacteria and Acidobacteria, and type 4 laccase-like Cu-oxidase genes were >8 times more abundant than type 3 genes, suggesting an important and overlooked role for type 4 Cu-oxidase in phenolic compound degradation. Genes associated with sulfate reduction and methanogenesis were the most abundant anaerobic respiration genes in these systems, with low levels of detection observed for genes of denitrification and Fe(III) reduction. Fermentation genes increased in relative abundance with depth and were largely affiliated with Syntrophobacter. Methylocystaceae-like small-subunit (SSU) rRNA genes, pmoA, and mmoX genes were more abundant among methanotrophs. Genes encoding N2 fixation, P uptake, and P regulons were significantly enriched in the surface peat and in comparison to other ecosystems, indicating N and P limitation. Persistence of inorganic orthophosphate throughout the peat profile in this P-limiting environment indicates that P may be bound to recalcitrant organic compounds, thus limiting P bioavailability in the subsurface. Comparative metagenomic analysis revealed a high metabolic potential for P transport and starvation, N2 fixation, and oligosaccharide degradation at MEF relative to other wetland and soil environments, consistent with the nutrient-poor and carbohydrate-rich conditions found in this Sphagnum-dominated boreal peatland.

Efficacy of hemostasis for epidural venous plexus and safety for neural structure using soft coagulation system in spinal surgery: a laboratory investigation using a porcine model.

PubMed

Nishida, Kotaro; Kakutani, Kenichiro; Maeno, Koichiro; Takada, Toru; Yurube, Takashi; Kuroda, Ryosuke; Kurosaka, Masahiro

2013-10-01

A laboratory investigation using porcine model. To clarify the effectiveness of the soft coagulation system for stopping bleeding from the epidural vein using different outputs and the safety in terms of tissue damage including spinal cord injury. Problems associated with coagulation using an electrosurgical device, such as carbonization of tissue or adhesion to the electrode, have been highlighted. So called "soft coagulation" has been developed to solve these problems. Its' utility as well as the safety of the neural structure in spine surgery has never been reported. A total of 3 animals and 45 spinal segments were used. Total laminectomy was performed to expose the dural tube and epidural venous plexus. Stable bleeding was induced by a 22 G needle puncture. Soft coagulation monopolar output (SCM), soft coagulation bipolar output (SCB), and conventional bipolar output (CB) were used as the coagulators. Valid hemostasis was defined as macroscopically complete bleeding stoppage by coagulation within 3 minutes. The neurological assessment was evaluated by somatosensory evoked potential. Histologic analysis was performed to determine the area of thermal damage. Valid hemostasis ratio was 75.0% of SCM group, 68.8% of SCB group, and 30.8% of CB group. Somatosensory evoked potential monitoring revealed that spinal cord injury was observed in 4 lesions (25%) of the SCM group. Neither bipolar groups (SCB and CB) showed any changes in waveform pattern. Histologic analysis revealed that severe thermal damages were observed in the epidural space of the SCM group. The usefulness of soft coagulation is revealed in terms of bleeding stoppage from epidural vessels and reduced soft-tissue damage compared with the conventional electric device. However, assessing the potential risk of severe neural tissue damage including spinal cord injury, a bipolar soft coagulation is strongly recommended for use in spine surgery.

Assessment of penetration potential of pH responsive double walled biodegradable nanogels coated with eucalyptus oil for the controlled delivery of 5-fluorouracil: In vitro and ex vivo studies.

PubMed

Sahu, Prashant; Kashaw, Sushil K; Jain, Sanyog; Sau, Samaresh; Iyer, Arun K

2017-05-10

Penetration enhancers coated biodegradable polymeric nanogels loaded with cytotoxic drugs applied via the topical route, can be a promising strategy for improving the chemotherapeutic efficiency of skin cancers. The major objective of proposed research was to investigate the in vitro and ex vivo chemotherapeutic potential of double walled PLGA-chitosan biodegradable nanogel entrapped with 5-fluororuacil (5-FU) coated with eucalyptus oil, topically applied onto the skin. 5-FU was first entrapped in PLGA core by solvent evaporation technique followed by coating with cationic chitosan for ionic interaction with anionic skin cancer cell membrane. A surface coating of eucalyptus oil (1%) was employed to improve the penetration efficacy of the nanogel into stratum corneum. The surface modified biodegradable double walled nanogel was characterized for particle size, charge and thermal properties followed by pH dependent in vitro analysis. Human keratinocyte (HaCaT) cell line was employed for the bio- and cyto-compatibility testing prior to the hemolysis assay and coagulation assessment. A porcine skin ex vivo screening was performed for assessing the penetration potential of the nanogels. DLS and TEM revealed a particle size about 170nm for the double walled nanogels. The nanogels also exhibited high thermal stability as analyzed by thermogravimetry (TG) and differential thermal analysis (DTA). The drug entrapment efficacy was about ~40%. The drug release showed sustained release pattern noted up to 24h. The low hemolysis of 2.39% with short prothrombin time (PT) and activated partial thromboplastin time (APTT) of 14.2 and 35.5s respectively, revealed high biocompatibility of the nanogels. The cellular uptake and localization was assessed by confocal microscopy. The cytotoxicity (MTT assay) on HaCaT cell line demonstrated high cytocompatibilty of the nanogels. An ex vivo evaluation using porcine skin displayed efficient and steady state flux of 5-FU from the biodegradable nanogles into the skin, while the histology of the porcine skin revealed enhanced penetration potential of eucalyptus oil coated PLGA-chitosan double walled nanogels. Taken together the in vivo and ex vivo results portend promising potential for the utility of the biodegradable nanogels for treating skin cancers. Copyright © 2017. Published by Elsevier B.V.

Application of Dempster-Shafer theory, spatial analysis and remote sensing for groundwater potentiality and nitrate pollution analysis in the semi-arid region of Khuzestan, Iran.

PubMed

Rahmati, Omid; Melesse, Assefa M

2016-10-15

Effective management and sustainable development of groundwater resources of arid and semi-arid environments require monitoring of groundwater quality and quantity. The aim of this paper is to develop a reasonable methodological framework for producing the suitability map for drinking water through the geographic information system, remote sensing and field surveys of the Andimeshk-Dezful, Khozestan province, Iran as a semi-arid region. This study investigated the delineation of groundwater potential zone based on Dempster-Shafer (DS) theory of evidence and evaluate its applicability for groundwater potentiality mapping. The study also analyzed the spatial distribution of groundwater nitrate concentration; and produced the suitability map for drinking water. The study has been carried out with the following steps: i) creation of maps of groundwater conditioning factors; ii) assessment of groundwater occurrence characteristics; iii) creation of groundwater potentiality map (GPM) and model validation; iv) collection and chemical analysis of water samples; v) assessment of groundwater nitrate pollution; and vi) creation of groundwater potentiality and quality map. The performance of the DS was also evaluated using the receiver operating characteristic (ROC) curve method and pumping test data to ensure its generalization ability, which eventually, the GPM showed 87.76% accuracy. The detailed analysis of groundwater potentiality and quality revealed that the 'non acceptable' areas covers an area of about 1479km(2) (60%). The study will provide significant information for groundwater management and exploitation in areas where groundwater is a major source of water and its exploration is critical to support drinking water need. Copyright © 2016 Elsevier B.V. All rights reserved.

Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer*

PubMed Central

Wu, Xinyan; Zahari, Muhammad Saddiq; Renuse, Santosh; Nirujogi, Raja Sekhar; Kim, Min-Sik; Manda, Srikanth S.; Stearns, Vered; Gabrielson, Edward; Sukumar, Saraswati; Pandey, Akhilesh

2015-01-01

Tamoxifen, an estrogen receptor-α (ER) antagonist, is an important agent for the treatment of breast cancer. However, this therapy is complicated by the fact that a substantial number of patients exhibit either de novo or acquired resistance. To characterize the signaling mechanisms underlying this resistance, we treated the MCF7 breast cancer cell line with tamoxifen for over six months and showed that this cell line acquired resistance to tamoxifen in vitro and in vivo. We performed SILAC-based quantitative phosphoproteomic profiling on the tamoxifen resistant and vehicle-treated sensitive cell lines to quantify the phosphorylation alterations associated with tamoxifen resistance. From >5600 unique phosphopeptides identified, 1529 peptides exhibited hyperphosphorylation and 409 peptides showed hypophosphorylation in the tamoxifen resistant cells. Gene set enrichment analysis revealed that focal adhesion pathway was one of the most enriched signaling pathways activated in tamoxifen resistant cells. Significantly, we showed that the focal adhesion kinase FAK2 was not only hyperphosphorylated but also transcriptionally up-regulated in tamoxifen resistant cells. FAK2 suppression by specific siRNA knockdown or a small molecule inhibitor repressed cellular proliferation in vitro and tumor formation in vivo. More importantly, our survival analysis revealed that high expression of FAK2 is significantly associated with shorter metastasis-free survival in estrogen receptor-positive breast cancer patients treated with tamoxifen. Our studies suggest that FAK2 is a potential therapeutic target for the management of hormone-refractory breast cancers. PMID:26330541

Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

PubMed Central

Inskeep, William P.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Rusch, Douglas B.; Tringe, Susannah G.; Macur, Richard E.; Jennings, Ryan deM.; Boyd, Eric S.; Spear, John R.; Roberto, Francisco F.

2013-01-01

Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40–45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP. PMID:23720654

Secretome Analysis of the Pine Wood Nematode Bursaphelenchus xylophilus Reveals the Tangled Roots of Parasitism and Its Potential for Molecular Mimicry

PubMed Central

Shinya, Ryoji; Takeuchi, Yuko; Ueda, Mitsuyoshi; Futai, Kazuyoshi

2013-01-01

Since it was first introduced into Asia from North America in the early 20th century, the pine wood nematode Bursaphelenchus xylophilus has caused the devastating forest disease called pine wilt. The emerging pathogen spread to parts of Europe and has since been found as the causal agent of pine wilt disease in Portugal and Spain. In 2011, the entire genome sequence of B. xylophilus was determined, and it allowed us to perform a more detailed analysis of B. xylophilus parasitism. Here, we identified 1,515 proteins secreted by B. xylophilus using a highly sensitive proteomics method combined with the available genomic sequence. The catalogue of secreted proteins contained proteins involved in nutrient uptake, migration, and evasion from host defenses. A comparative functional analysis of the secretome profiles among parasitic nematodes revealed a marked expansion of secreted peptidases and peptidase inhibitors in B. xylophilus via gene duplication and horizontal gene transfer from fungi and bacteria. Furthermore, we showed that B. xylophilus secreted the potential host mimicry proteins that closely resemble the host pine’s proteins. These proteins could have been acquired by host–parasite co-evolution and might mimic the host defense systems in susceptible pine trees during infection. This study contributes to an understanding of their unique parasitism and its tangled roots, and provides new perspectives on the evolution of plant parasitism among nematodes. PMID:23805310

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites.

PubMed

Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire; Mikaelyan, Aram; Nonoh, James O; Scheffrahn, Rudolf H; Sillam-Dussès, David; Brune, Andreas

2015-11-26

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Here, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among wood- and litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. Community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.

Copy number variants in patients with short stature

PubMed Central

van Duyvenvoorde, Hermine A; Lui, Julian C; Kant, Sarina G; Oostdijk, Wilma; Gijsbers, Antoinet CJ; Hoffer, Mariëtte JV; Karperien, Marcel; Walenkamp, Marie JE; Noordam, Cees; Voorhoeve, Paul G; Mericq, Verónica; Pereira, Alberto M; Claahsen-van de Grinten, Hedi L; van Gool, Sandy A; Breuning, Martijn H; Losekoot, Monique; Baron, Jeffrey; Ruivenkamp, Claudia AL; Wit, Jan M

2014-01-01

Height is a highly heritable and classic polygenic trait. Recent genome-wide association studies (GWAS) have revealed that at least 180 genetic variants influence adult height. However, these variants explain only about 10% of the phenotypic variation in height. Genetic analysis of short individuals can lead to the discovery of novel rare gene defects with a large effect on growth. In an effort to identify novel genes associated with short stature, genome-wide analysis for copy number variants (CNVs), using single-nucleotide polymorphism arrays, in 162 patients (149 families) with short stature was performed. Segregation analysis was performed if possible, and genes in CNVs were compared with information from GWAS, gene expression in rodents' growth plates and published information. CNVs were detected in 40 families. In six families, a known cause of short stature was found (SHOX deletion or duplication, IGF1R deletion), in two combined with a de novo potentially pathogenic CNV. Thirty-three families had one or more potentially pathogenic CNVs (n=40). In 24 of these families, segregation analysis could be performed, identifying three de novo CNVs and nine CNVs segregating with short stature. Four were located near loci associated with height in GWAS (ADAMTS17, TULP4, PRKG2/BMP3 and PAPPA). Besides six CNVs known to be causative for short stature, 40 CNVs with possible pathogenicity were identified. Segregation studies and bioinformatics analysis suggested various potential candidate genes. PMID:24065112

Long-range RNA pairings contribute to mutually exclusive splicing

PubMed Central

Yue, Yuan; Yang, Yun; Dai, Lanzhi; Cao, Guozheng; Chen, Ran; Hong, Weiling; Liu, Baoping; Shi, Yang; Meng, Yijun; Shi, Feng; Xiao, Mu; Jin, Yongfeng

2016-01-01

Mutually exclusive splicing is an important means of increasing the protein repertoire, by which the Down's syndrome cell adhesion molecule (Dscam) gene potentially generates 38,016 different isoforms in Drosophila melanogaster. However, the regulatory mechanisms remain obscure due to the complexity of the Dscam exon cluster. Here, we reveal a molecular model for the regulation of the mutually exclusive splicing of the serpent pre-mRNA based on competition between upstream and downstream RNA pairings. Such dual RNA pairings confer fine tuning of the inclusion of alternative exons. Moreover, we demonstrate that the splicing outcome of alternative exons is mediated in relative pairing strength-correlated mode. Combined comparative genomics analysis and experimental evidence revealed similar bidirectional structural architectures in exon clusters 4 and 9 of the Dscam gene. Our findings provide a novel mechanistic framework for the regulation of mutually exclusive splicing and may offer potentially applicable insights into long-range RNA–RNA interactions in gene regulatory networks. PMID:26554032

Long-range RNA pairings contribute to mutually exclusive splicing.

PubMed

Yue, Yuan; Yang, Yun; Dai, Lanzhi; Cao, Guozheng; Chen, Ran; Hong, Weiling; Liu, Baoping; Shi, Yang; Meng, Yijun; Shi, Feng; Xiao, Mu; Jin, Yongfeng

2016-01-01

Mutually exclusive splicing is an important means of increasing the protein repertoire, by which the Down's syndrome cell adhesion molecule (Dscam) gene potentially generates 38,016 different isoforms in Drosophila melanogaster. However, the regulatory mechanisms remain obscure due to the complexity of the Dscam exon cluster. Here, we reveal a molecular model for the regulation of the mutually exclusive splicing of the serpent pre-mRNA based on competition between upstream and downstream RNA pairings. Such dual RNA pairings confer fine tuning of the inclusion of alternative exons. Moreover, we demonstrate that the splicing outcome of alternative exons is mediated in relative pairing strength-correlated mode. Combined comparative genomics analysis and experimental evidence revealed similar bidirectional structural architectures in exon clusters 4 and 9 of the Dscam gene. Our findings provide a novel mechanistic framework for the regulation of mutually exclusive splicing and may offer potentially applicable insights into long-range RNA-RNA interactions in gene regulatory networks. © 2015 Yue et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Synthesis of nanoparticle emulsion collector HNP and its application in microfine chalcopyrite flotation

NASA Astrophysics Data System (ADS)

He, G. C.; Ding, J.; Huang, C. H.; Kang, Q.

2018-01-01

Hydrophobic polystyrene nanoparticles bearing thiazole groups named HNP were used as collectors to improve recovery of microfine chalcopyrite in flotation. HNP adsorbs onto microfine particles selectively, which were modified hydrophobically to induce flotation effectively. Particle size and scanning electron microscope analysis for HNP show that HNP is a spherical nano particles with small size, uniform distribution and good dispersion. Infrared spectrum analysis for HNP proved that functional monomer 2-mercapto styrene acrylic thiazole was bonded chemically onto styrene. Flotation test results indicate that HNP is the right collector of chalcopyrite. Especially, the recovery of chalcopyrite is higher than 95% in neutral and acid media. FTIR results reveal that the flotation selectivity of collector HNP is due to strong chemical absorption onto chalcopyrite surface. Zeta potential analysis shows that the zeta potential of chalcopyrite decreased more quickly after interaction with HNP with the increase of pulp pH value, confirming that collector HNP is an anionic collector. Scanning electron microscope conform that HNP has good selective adsorption on chalcopyrite.

Determinants of internet poker adoption.

PubMed

Philander, Kahlil S; Abarbanel, B Lillian

2014-09-01

In nearly all jurisdictions, adoption of a new form of gambling has been a controversial and contentious subject. Online gambling has been no different, though there are many aspects that affect online gambling that do not appear in the brick and mortar environment. This study seeks to identify whether demographic, economic, political, technological, and/or sociological determinants contribute to online poker gambling adoption. A theoretical discussion of these categories' importance to online poker is provided and exploratory empirical analysis is used to examine their potential validity. The analysis revealed support for all of the proposed categories of variables thought to be predictive of online gambling legality.

A Sensitivity Analysis of the Nocturnal Boundary-Layer Properties to Atmospheric Emissivity Formulations

NASA Astrophysics Data System (ADS)

Siqueira, Mario B.; Katul, Gabriel G.

2010-02-01

A one-dimensional model for the mean potential temperature within the nocturnal boundary layer (NBL) was used to assess the sensitivity of three NBL properties (height, thermal stratification strength, and near-surface cooling) to three widely used atmospheric emissivity formulations. The calculations revealed that the NBL height is robust to the choice of the emissivity function, though this is not the case for NBL Richardson number and near-surface cooling rate. Rather than endorse one formulation, our analysis highlights the importance of atmospheric emissivity in modelling the radiative properties of the NBL especially for clear-sky conditions.

Analysis of the interactions between He + ions and transition metal surfaces using co-axial impact collision ion scattering spectroscopy

NASA Astrophysics Data System (ADS)

Walker, M.; Brown, M. G.; Draxler, M.; Fishwick, L.; Dowsett, M. G.; McConville, C. F.

2011-01-01

The interactions between low energy He + ions and a series of transition metal surfaces have been studied using co-axial impact collision ion scattering spectroscopy (CAICISS). Experimental data were collected from the Ni(110), Cu(100), Pd(111), Pt(111) and Au(111) surfaces using ion beams with primary energies between 1.5 keV and 4.0 keV. The shadow cone radii deduced from the experimental surface peak positions were found to closely match theoretical predictions. Data analysis was performed using both the FAN and Kalypso simulation codes, revealing a consistent requirement for a reduction of 0.252 in the screening length correction in the Molière approximation within the Thomas-Fermi (TFM) interaction potential. The adjustments of the screening length in the TFM potential, predicted by O'Connor, and the uncorrected Ziegler-Biersack-Littmark (ZBL) potential both yielded inaccurate results for all of the surfaces and incident energies studied. We also provide evidence that, despite their different computational methodologies, the FAN and Kalypso simulation codes generate similar results given identical input parameters for the analysis of 180° backscattering spectra.

Runoff potentiality of a watershed through SCS and functional data analysis technique.

PubMed

Adham, M I; Shirazi, S M; Othman, F; Rahman, S; Yusop, Z; Ismail, Z

2014-01-01

Runoff potentiality of a watershed was assessed based on identifying curve number (CN), soil conservation service (SCS), and functional data analysis (FDA) techniques. Daily discrete rainfall data were collected from weather stations in the study area and analyzed through lowess method for smoothing curve. As runoff data represents a periodic pattern in each watershed, Fourier series was introduced to fit the smooth curve of eight watersheds. Seven terms of Fourier series were introduced for the watersheds 5 and 8, while 8 terms of Fourier series were used for the rest of the watersheds for the best fit of data. Bootstrapping smooth curve analysis reveals that watersheds 1, 2, 3, 6, 7, and 8 are with monthly mean runoffs of 29, 24, 22, 23, 26, and 27 mm, respectively, and these watersheds would likely contribute to surface runoff in the study area. The purpose of this study was to transform runoff data into a smooth curve for representing the surface runoff pattern and mean runoff of each watershed through statistical method. This study provides information of runoff potentiality of each watershed and also provides input data for hydrological modeling.

Linear and nonlinear analysis of kinetic Alfven waves in quantum magneto-plasmas with arbitrary temperature degeneracy

NASA Astrophysics Data System (ADS)

Sadiq, Nauman; Ahmad, Mushtaq; Farooq, M.; Jan, Qasim

2018-06-01

Linear and nonlinear kinetic Alfven waves (KAWs) are studied in collisionless, non-relativistic two fluid quantum magneto-plasmas by considering arbitrary temperature degeneracy. A general coupling parameter is applied to discuss the range of validity of the proposed model in nearly degenerate and nearly non-degenerate plasma limits. Linear analysis of KAWs shows an increase (decrease) in frequency with the increase in parameter ζ ( δ ) for the nearly non-degenerate (nearly degenerate) plasma limit. The energy integral equation in the form of Sagdeev potential is obtained by using the approach of the Lorentz transformation. The analysis reveals that the amplitude of the Sagdeev potential curves and soliton structures remains the same, but the potential depth and width of soliton structure change for both the limiting cases. It is further observed that only density hump structures are formed in the sub-alfvenic region for value Kz 2 > 1 . The effects of parameters ζ, δ on the nonlinear properties of KAWs are shown in graphical plots. New results for comparison with earlier work have also been highlighted. The significance of this work to astrophysical plasmas is also emphasized.

Runoff Potentiality of a Watershed through SCS and Functional Data Analysis Technique

PubMed Central

Adham, M. I.; Shirazi, S. M.; Othman, F.; Rahman, S.; Yusop, Z.; Ismail, Z.

2014-01-01

Runoff potentiality of a watershed was assessed based on identifying curve number (CN), soil conservation service (SCS), and functional data analysis (FDA) techniques. Daily discrete rainfall data were collected from weather stations in the study area and analyzed through lowess method for smoothing curve. As runoff data represents a periodic pattern in each watershed, Fourier series was introduced to fit the smooth curve of eight watersheds. Seven terms of Fourier series were introduced for the watersheds 5 and 8, while 8 terms of Fourier series were used for the rest of the watersheds for the best fit of data. Bootstrapping smooth curve analysis reveals that watersheds 1, 2, 3, 6, 7, and 8 are with monthly mean runoffs of 29, 24, 22, 23, 26, and 27 mm, respectively, and these watersheds would likely contribute to surface runoff in the study area. The purpose of this study was to transform runoff data into a smooth curve for representing the surface runoff pattern and mean runoff of each watershed through statistical method. This study provides information of runoff potentiality of each watershed and also provides input data for hydrological modeling. PMID:25152911

Bifurcation analysis of an automatic dynamic balancing mechanism for eccentric rotors

NASA Astrophysics Data System (ADS)

Green, K.; Champneys, A. R.; Lieven, N. J.

2006-04-01

We present a nonlinear bifurcation analysis of the dynamics of an automatic dynamic balancing mechanism for rotating machines. The principle of operation is to deploy two or more masses that are free to travel around a race at a fixed distance from the hub and, subsequently, balance any eccentricity in the rotor. Mathematically, we start from a Lagrangian description of the system. It is then shown how under isotropic conditions a change of coordinates into a rotating frame turns the problem into a regular autonomous dynamical system, amenable to a full nonlinear bifurcation analysis. Using numerical continuation techniques, curves are traced of steady states, limit cycles and their bifurcations as parameters are varied. These results are augmented by simulations of the system trajectories in phase space. Taking the case of a balancer with two free masses, broad trends are revealed on the existence of a stable, dynamically balanced steady-state solution for specific rotation speeds and eccentricities. However, the analysis also reveals other potentially attracting states—non-trivial steady states, limit cycles, and chaotic motion—which are not in balance. The transient effects which lead to these competing states, which in some cases coexist, are investigated.

Emotion processing in the visual brain: a MEG analysis.

PubMed

Peyk, Peter; Schupp, Harald T; Elbert, Thomas; Junghöfer, Markus

2008-06-01

Recent functional magnetic resonance imaging (fMRI) and event-related brain potential (ERP) studies provide empirical support for the notion that emotional cues guide selective attention. Extending this line of research, whole head magneto-encephalogram (MEG) was measured while participants viewed in separate experimental blocks a continuous stream of either pleasant and neutral or unpleasant and neutral pictures, presented for 330 ms each. Event-related magnetic fields (ERF) were analyzed after intersubject sensor coregistration, complemented by minimum norm estimates (MNE) to explore neural generator sources. Both streams of analysis converge by demonstrating the selective emotion processing in an early (120-170 ms) and a late time interval (220-310 ms). ERF analysis revealed that the polarity of the emotion difference fields was reversed across early and late intervals suggesting distinct patterns of activation in the visual processing stream. Source analysis revealed the amplified processing of emotional pictures in visual processing areas with more pronounced occipito-parieto-temporal activation in the early time interval, and a stronger engagement of more anterior, temporal, regions in the later interval. Confirming previous ERP studies showing facilitated emotion processing, the present data suggest that MEG provides a complementary look at the spread of activation in the visual processing stream.

Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama.

PubMed

Kim, Soo-Jin; Ka, Sojeong; Ha, Jung-Woo; Kim, Jaemin; Yoo, DongAhn; Kim, Kwondo; Lee, Hak-Kyo; Lim, Dajeong; Cho, Seoae; Hanotte, Olivier; Mwai, Okeyo Ally; Dessie, Tadelle; Kemp, Stephen; Oh, Sung Jong; Kim, Heebal

2017-05-12

Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied. We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N'Dama cattle. We analysed genetic variation patterns in N'Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N'Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N'Dama may engage in skeletal growth as well as immune systems. Our results imply that N'Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.

The Raman spectrum character of skin tumor induced by UVB

NASA Astrophysics Data System (ADS)

Wu, Shulian; Hu, Liangjun; Wang, Yunxia; Li, Yongzeng

2016-03-01

In our study, the skin canceration processes induced by UVB were analyzed from the perspective of tissue spectrum. A home-made Raman spectral system with a millimeter order excitation laser spot size combined with a multivariate statistical analysis for monitoring the skin changed irradiated by UVB was studied and the discrimination were evaluated. Raman scattering signals of the SCC and normal skin were acquired. Spectral differences in Raman spectra were revealed. Linear discriminant analysis (LDA) based on principal component analysis (PCA) were employed to generate diagnostic algorithms for the classification of skin SCC and normal. The results indicated that Raman spectroscopy combined with PCA-LDA demonstrated good potential for improving the diagnosis of skin cancers.

Phytochemical analysis of Hibiscus caesius using high performance liquid chromatography coupled with mass spectrometry.

PubMed

Ain, Quratul; Naveed, Muhammad Na; Mumtaz, Abdul Samad; Farman, Muhammad; Ahmed, Iftikhar; Khalid, Nauman

2015-09-01

Various species in genus Hibiscus are traditionally known for their therapeutic attributes. The present study focused on the phytochemical analysis of a rather unexplored species Hibiscus caesius (H. caesius), using high-pressure liquid chromatography coupled with mass spectrometry (HPLC-MS). The analysis revealed five major compounds in the aqueous extract, viz. vanillic acid, protocatechoic acid, quercetin, quercetin glucoside and apigenin, being reported for the first time in H. caesius. Literature suggests that these compounds have important pharmacological traits such as anti-cancer, anti-inflammatory, anti-bacterial and hepatoprotective etc. however, this requires further pharmacological investigations at in vitro and in vivo scale. The above study concluded the medicinal potential of H. caesius.

An in vitro study reveals nutraceutical properties of Ananas comosus (L.) Merr. var. Mauritius fruit residue beneficial to diabetes.

PubMed

Riya, Mariam Philip; Antu, Kalathookunnel Antony; Vinu, Thankamony; Chandrakanth, Karuvakandy Chandrasekharan; Anilkumar, Karunakaran Sasikala; Raghu, Kozhiparambil Gopalan

2014-03-30

Rapid urbanisation and nutritional transition is fuelling the increased global incidence of type 2 diabetes. Pineapple fruit residue was explored for its nutraceutical properties as an alternative or adjunct to currently available treatment regime. Ethyl acetate and methanolic extracts of pineapple fruit residue were evaluated for anti-diabetic activity in cell free and cell based systems. Specifically, we assessed: (1) antioxidant potential, (2) anti-glycation potential, (3) carbohydrate digestive enzyme inhibition, and (4) lipid accumulation and glycerol-3-phosphate dehydrogenase activity in differentiating 3T3-L1 cells. The active components in the ethyl acetate and methanolic extracts were identified as sinapic acid, daucosterol, 2-methylpropanoate, 2,5-dimethyl-4-hydroxy-3(2H)-furanone, methyl 2-methylbutanoate and triterpenoid ergosterol using DART/HRMS and ESI/HRMS. Micronutrient analysis revealed the presence of magnesium, potassium and calcium. Adipogenic potential, anti-glycation property of the ethyl acetate extract, and DNA damage protection capacity of the methanolic extract are promising. Results from this study clearly indicate that pineapple fruit residue could be utilised as a nutraceutical against diabetes and related complications. © 2013 Society of Chemical Industry.

Beneficial Phytochemicals with Anti-Tumor Potential Revealed through Metabolic Profiling of New Red Pigmented Lettuces (Lactuca sativa L.).

PubMed

Qin, Xiao-Xiao; Zhang, Ming-Yue; Han, Ying-Yan; Hao, Jing-Hong; Liu, Chao-Jie; Fan, Shuang-Xi

2018-04-11

The present study aimed to compare polyphenols among red lettuce cultivars and identify suitable cultivars for the development and utilization of healthy vegetables. Polyphenols, mineral elements, and antioxidant activity were analyzed in the leaves of six red pigmented lettuce ( Lactuca sativa L.) cultivars; thereafter, we assessed the anti-tumor effects of cultivar B-2, which displayed the highest antioxidant activity. Quadrupole-Orbitrap mass spectrometry analysis revealed four classes of polyphenols in these cultivars. The composition and contents of these metabolites varied significantly among cultivars and primarily depended on leaf color. The B-2 cultivar had the highest antioxidant potential than others because it contained the highest levels of polyphenols, especially anthocyanin, flavone, and phenolic acid; furthermore, this cultivar displayed anti-tumor effects against the human lung adenocarcinoma cell line A549, human hepatoma cell line Bel7402, human cancer colorectal adenoma cell line HCT-8, and HT-29 human colon cancer cell line. Hence, the new red-leaf lettuce cultivar B-2 has a distinct metabolite profile, with high potential for development and utilization of natural phytochemical and mineral resources in lettuces and can be used as a nutrient-dense food product.

Artificial spatiotemporal touch inputs reveal complementary decoding in neocortical neurons.

PubMed

Oddo, Calogero M; Mazzoni, Alberto; Spanne, Anton; Enander, Jonas M D; Mogensen, Hannes; Bengtsson, Fredrik; Camboni, Domenico; Micera, Silvestro; Jörntell, Henrik

2017-04-04

Investigations of the mechanisms of touch perception and decoding has been hampered by difficulties in achieving invariant patterns of skin sensor activation. To obtain reproducible spatiotemporal patterns of activation of sensory afferents, we used an artificial fingertip equipped with an array of neuromorphic sensors. The artificial fingertip was used to transduce real-world haptic stimuli into spatiotemporal patterns of spikes. These spike patterns were delivered to the skin afferents of the second digit of rats via an array of stimulation electrodes. Combined with low-noise intra- and extracellular recordings from neocortical neurons in vivo, this approach provided a previously inaccessible high resolution analysis of the representation of tactile information in the neocortical neuronal circuitry. The results indicate high information content in individual neurons and reveal multiple novel neuronal tactile coding features such as heterogeneous and complementary spatiotemporal input selectivity also between neighboring neurons. Such neuronal heterogeneity and complementariness can potentially support a very high decoding capacity in a limited population of neurons. Our results also indicate a potential neuroprosthetic approach to communicate with the brain at a very high resolution and provide a potential novel solution for evaluating the degree or state of neurological disease in animal models.

Artificial spatiotemporal touch inputs reveal complementary decoding in neocortical neurons

PubMed Central

Oddo, Calogero M.; Mazzoni, Alberto; Spanne, Anton; Enander, Jonas M. D.; Mogensen, Hannes; Bengtsson, Fredrik; Camboni, Domenico; Micera, Silvestro; Jörntell, Henrik

2017-01-01

Investigations of the mechanisms of touch perception and decoding has been hampered by difficulties in achieving invariant patterns of skin sensor activation. To obtain reproducible spatiotemporal patterns of activation of sensory afferents, we used an artificial fingertip equipped with an array of neuromorphic sensors. The artificial fingertip was used to transduce real-world haptic stimuli into spatiotemporal patterns of spikes. These spike patterns were delivered to the skin afferents of the second digit of rats via an array of stimulation electrodes. Combined with low-noise intra- and extracellular recordings from neocortical neurons in vivo, this approach provided a previously inaccessible high resolution analysis of the representation of tactile information in the neocortical neuronal circuitry. The results indicate high information content in individual neurons and reveal multiple novel neuronal tactile coding features such as heterogeneous and complementary spatiotemporal input selectivity also between neighboring neurons. Such neuronal heterogeneity and complementariness can potentially support a very high decoding capacity in a limited population of neurons. Our results also indicate a potential neuroprosthetic approach to communicate with the brain at a very high resolution and provide a potential novel solution for evaluating the degree or state of neurological disease in animal models. PMID:28374841

Genome-Wide Identification, Evolution and Expression Analysis of mTERF Gene Family in Maize

PubMed Central

Zhao, Yanxin; Cai, Manjun; Zhang, Xiaobo; Li, Yurong; Zhang, Jianhua; Zhao, Hailiang; Kong, Fei; Zheng, Yonglian; Qiu, Fazhan

2014-01-01

Plant mitochondrial transcription termination factor (mTERF) genes comprise a large family with important roles in regulating organelle gene expression. In this study, a comprehensive database search yielded 31 potential mTERF genes in maize (Zea mays L.) and most of them were targeted to mitochondria or chloroplasts. Maize mTERF were divided into nine main groups based on phylogenetic analysis, and group IX represented the mitochondria and species-specific clade that diverged from other groups. Tandem and segmental duplication both contributed to the expansion of the mTERF gene family in the maize genome. Comprehensive expression analysis of these genes, using microarray data and RNA-seq data, revealed that these genes exhibit a variety of expression patterns. Environmental stimulus experiments revealed differential up or down-regulation expression of maize mTERF genes in seedlings exposed to light/dark, salts and plant hormones, respectively, suggesting various important roles of maize mTERF genes in light acclimation and stress-related responses. These results will be useful for elucidating the roles of mTERF genes in the growth, development and stress response of maize. PMID:24718683

Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets.

PubMed

Lam, Max; Trampush, Joey W; Yu, Jin; Knowles, Emma; Davies, Gail; Liewald, David C; Starr, John M; Djurovic, Srdjan; Melle, Ingrid; Sundet, Kjetil; Christoforou, Andrea; Reinvang, Ivar; DeRosse, Pamela; Lundervold, Astri J; Steen, Vidar M; Espeseth, Thomas; Räikkönen, Katri; Widen, Elisabeth; Palotie, Aarno; Eriksson, Johan G; Giegling, Ina; Konte, Bettina; Roussos, Panos; Giakoumaki, Stella; Burdick, Katherine E; Payton, Antony; Ollier, William; Chiba-Falek, Ornit; Attix, Deborah K; Need, Anna C; Cirulli, Elizabeth T; Voineskos, Aristotle N; Stefanis, Nikos C; Avramopoulos, Dimitrios; Hatzimanolis, Alex; Arking, Dan E; Smyrnis, Nikolaos; Bilder, Robert M; Freimer, Nelson A; Cannon, Tyrone D; London, Edythe; Poldrack, Russell A; Sabb, Fred W; Congdon, Eliza; Conley, Emily Drabant; Scult, Matthew A; Dickinson, Dwight; Straub, Richard E; Donohoe, Gary; Morris, Derek; Corvin, Aiden; Gill, Michael; Hariri, Ahmad R; Weinberger, Daniel R; Pendleton, Neil; Bitsios, Panos; Rujescu, Dan; Lahti, Jari; Le Hellard, Stephanie; Keller, Matthew C; Andreassen, Ole A; Deary, Ian J; Glahn, David C; Malhotra, Anil K; Lencz, Todd

2017-11-28

Here, we present a large (n = 107,207) genome-wide association study (GWAS) of general cognitive ability ("g"), further enhanced by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with general cognitive ability. Results showed significant enrichment for genes causing Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis implicated the biological processes of neurogenesis and synaptic regulation, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker, and LY97241, a potassium channel inhibitor. Transcriptome-wide and epigenome-wide analysis revealed that the implicated loci were enriched for genes expressed across all brain regions (most strongly in the cerebellum). Enrichment was exclusive to genes expressed in neurons but not oligodendrocytes or astrocytes. Finally, we report genetic correlations between cognitive ability and disparate phenotypes including psychiatric disorders, several autoimmune disorders, longevity, and maternal age at first birth. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Validation of the Modified Fatigue Impact Scale in mild to moderate traumatic brain injury.

PubMed

Schiehser, Dawn M; Delano-Wood, Lisa; Jak, Amy J; Matthews, Scott C; Simmons, Alan N; Jacobson, Mark W; Filoteo, J Vincent; Bondi, Mark W; Orff, Henry J; Liu, Lin

2015-01-01

To evaluate the validity of the Modified Fatigue Impact Scale (MFIS) in veterans with a history of mild to moderate traumatic brain injury (TBI). Veterans (N = 106) with mild (92%) or moderate (8%) TBI. Veterans Administration Health System. Factor structure, internal consistency, convergent validity, sensitivity, and specificity of the MFIS were examined. Principal component analysis identified 2 viable MFIS factors: a Cognitive subscale and a Physical/Activities subscale. Item analysis revealed high internal consistency of the MFIS Total scale and subscale items. Strong convergent validity of the MFIS scales was established with 2 Beck Depression Inventory II fatigue items. Receiver operating characteristic curve analysis revealed good to excellent accuracy of the MFIS in classifying fatigued versus nonfatigued individuals. The MFIS is a valid multidimensional measure that can be used to evaluate the impact of fatigue on cognitive and physical functioning in individuals with mild to moderate TBI. The psychometric properties of the MFIS make it useful for evaluating fatigue and provide the potential for improving research on fatigue in this population.

Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism

PubMed Central

Yin, Ling; An, Yunhe; Qu, Junjie; Li, Xinlong; Zhang, Yali; Dry, Ian; Wu, Huijuan; Lu, Jiang

2017-01-01

Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate ‘JL-7-2’ obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host. PMID:28417959

Graft polymerization of guar gum with acryl amide irradiated by microwaves for colonic drug delivery.

PubMed

Shahid, Muhammad; Bukhari, Shazia Anwer; Gul, Yousra; Munir, Hira; Anjum, Fozia; Zuber, Mohammad; Jamil, Tahir; Zia, Khalid Mahmood

2013-11-01

This article is aimed to discuss the modification of guar gum through microwave irradiation by varying the time of irradiation. The characterization of the modified products was carried out using FTIR spectroscopic analysis. The FT-IR spectrum of the pure guar gum (GG) sample showed a broad peak at 3298 cm(-1) while the modified GG sample displayed a peak at 1541 cm(-1) which was absent in the crude sample. The X-ray diffraction (XRD) analysis confirmed the increase in crystallinity due to grafting of the sample with polyacrylamide (GG-g-PAM). Scanning electron microscope (SEM) images revealed that granular form of guar gum was changed into fibrillar structure after grafting. Thermo-gravimetric analysis of the modified samples was also carried out and discussed. The role of guar gum as a matrix for controlled release of drug triamcinolone was evaluated. The GG-acrylamide grafted samples presented a correlation between drug release and time of microwave exposure. The results revealed that such modified product has potential applications in colonic drug delivery system. Copyright © 2013 Elsevier B.V. All rights reserved.

Circuit board accident--organizational dimension hidden by prescribed safety.

PubMed

de Almeida, Ildeberto Muniz; Buoso, Eduardo; do Amaral Dias, Maria Dionísia; Vilela, Rodolfo Andrade Gouveia

2012-01-01

This study analyzes an accident in which two maintenance workers suffered severe burns while replacing a circuit breaker panel in a steel mill, following model of analysis and prevention of accidents (MAPA) developed with the objective of enlarging the perimeter of interventions and contributing to deconstruction of blame attribution practices. The study was based on materials produced by a health service team in an in-depth analysis of the accident. The analysis shows that decisions related to system modernization were taken without considering their implications in maintenance scheduling and creating conflicts of priorities and of interests between production and safety; and also reveals that the lack of a systemic perspective in safety management was its principal failure. To explain the accident as merely non-fulfillment of idealized formal safety rules feeds practices of blame attribution supported by alibi norms and inhibits possible prevention. In contrast, accident analyses undertaken in worker health surveillance services show potential to reveal origins of these events incubated in the history of the system ignored in practices guided by the traditional paradigm.

Aquatic insect ecophysiological traits reveal phylogenetically based differences in dissolved cadmium susceptibility.

PubMed

Buchwalter, David B; Cain, Daniel J; Martin, Caitrin A; Xie, Lingtian; Luoma, Samuel N; Garland, Theodore

2008-06-17

We used a phylogenetically based comparative approach to evaluate the potential for physiological studies to reveal patterns of diversity in traits related to susceptibility to an environmental stressor, the trace metal cadmium (Cd). Physiological traits related to Cd bioaccumulation, compartmentalization, and ultimately susceptibility were measured in 21 aquatic insect species representing the orders Ephemeroptera, Plecoptera, and Trichoptera. We mapped these experimentally derived physiological traits onto a phylogeny and quantified the tendency for related species to be similar (phylogenetic signal). All traits related to Cd bioaccumulation and susceptibility exhibited statistically significant phylogenetic signal, although the signal strength varied among traits. Conventional and phylogenetically based regression models were compared, revealing great variability within orders but consistent, strong differences among insect families. Uptake and elimination rate constants were positively correlated among species, but only when effects of body size and phylogeny were incorporated in the analysis. Together, uptake and elimination rates predicted dramatic Cd bioaccumulation differences among species that agreed with field-based measurements. We discovered a potential tradeoff between the ability to eliminate Cd and the ability to detoxify it across species, particularly mayflies. The best-fit regression models were driven by phylogenetic parameters (especially differences among families) rather than functional traits, suggesting that it may eventually be possible to predict a taxon's physiological performance based on its phylogenetic position, provided adequate physiological information is available for close relatives. There appears to be great potential for evolutionary physiological approaches to augment our understanding of insect responses to environmental stressors in nature.

Aquatic insect ecophysiological traits reveal phylogenetically based differences in dissolved cadmium susceptibility

PubMed Central

Buchwalter, David B.; Cain, Daniel J.; Martin, Caitrin A.; Xie, Lingtian; Luoma, Samuel N.; Garland, Theodore

2008-01-01

We used a phylogenetically based comparative approach to evaluate the potential for physiological studies to reveal patterns of diversity in traits related to susceptibility to an environmental stressor, the trace metal cadmium (Cd). Physiological traits related to Cd bioaccumulation, compartmentalization, and ultimately susceptibility were measured in 21 aquatic insect species representing the orders Ephemeroptera, Plecoptera, and Trichoptera. We mapped these experimentally derived physiological traits onto a phylogeny and quantified the tendency for related species to be similar (phylogenetic signal). All traits related to Cd bioaccumulation and susceptibility exhibited statistically significant phylogenetic signal, although the signal strength varied among traits. Conventional and phylogenetically based regression models were compared, revealing great variability within orders but consistent, strong differences among insect families. Uptake and elimination rate constants were positively correlated among species, but only when effects of body size and phylogeny were incorporated in the analysis. Together, uptake and elimination rates predicted dramatic Cd bioaccumulation differences among species that agreed with field-based measurements. We discovered a potential tradeoff between the ability to eliminate Cd and the ability to detoxify it across species, particularly mayflies. The best-fit regression models were driven by phylogenetic parameters (especially differences among families) rather than functional traits, suggesting that it may eventually be possible to predict a taxon's physiological performance based on its phylogenetic position, provided adequate physiological information is available for close relatives. There appears to be great potential for evolutionary physiological approaches to augment our understanding of insect responses to environmental stressors in nature. PMID:18559853

Identification of cyclin B1 and Sec62 as biomarkers for recurrence in patients with HBV-related hepatocellular carcinoma after surgical resection.

PubMed

Weng, Li; Du, Juan; Zhou, Qinghui; Cheng, Binbin; Li, Jun; Zhang, Denghai; Ling, Changquan

2012-06-08

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. Frequent tumor recurrence after surgery is related to its poor prognosis. Although gene expression signatures have been associated with outcome, the molecular basis of HCC recurrence is not fully understood, and there is no method to predict recurrence using peripheral blood mononuclear cells (PBMCs), which can be easily obtained for recurrence prediction in the clinical setting. According to the microarray analysis results, we constructed a co-expression network using the k-core algorithm to determine which genes play pivotal roles in the recurrence of HCC associated with the hepatitis B virus (HBV) infection. Furthermore, we evaluated the mRNA and protein expressions in the PBMCs from 80 patients with or without recurrence and 30 healthy subjects. The stability of the signatures was determined in HCC tissues from the same 80 patients. Data analysis included ROC analysis, correlation analysis, log-lank tests, and Cox modeling to identify independent predictors of tumor recurrence. The tumor-associated proteins cyclin B1, Sec62, and Birc3 were highly expressed in a subset of samples of recurrent HCC; cyclin B1, Sec62, and Birc3 positivity was observed in 80%, 65.7%, and 54.2% of the samples, respectively. The Kaplan-Meier analysis revealed that high expression levels of these proteins was associated with significantly reduced recurrence-free survival. Cox proportional hazards model analysis revealed that cyclin B1 (hazard ratio [HR], 4.762; p = 0.002) and Sec62 (HR, 2.674; p = 0.018) were independent predictors of HCC recurrence. These results revealed that cyclin B1 and Sec62 may be candidate biomarkers and potential therapeutic targets for HBV-related HCC recurrence after surgery.

Are Navy Weight Management Programs Ensuring Sailor Physical Readiness? An Analysis at Naval Medical Center San Diego.

PubMed

Wisbach, Gordon G; Peters, Joshua; Guerrero, Jenise Leon; Mozzini, Nelson; Metzger, Helen

2018-03-14

The obesity epidemic in the USA includes active duty service members in the military and effects physical readiness. At the Naval Medical Center San Diego command, the Health & Wellness Department is charged with administering the Weight Management Programs (WMP) for sailors in the San Diego area to ensure military physical readiness requirements. The optimal allocation of personnel and resources to manage these programs is paramount for mission success. We analyzed the cost and effectiveness of the WMPs for the active duty population stationed at Naval Medical Center San Diego (NMCSD) with the intent of offering potential recommendations for program optimization. As an approved quality improvement program, the cost and effectiveness of the WMP, namely Fitness Enhancement Program (FEP) and ShipShape (SS), for the active duty population stationed at NMCSD were analyzed from 2013 to 2014 by utilizing various official sources. Data analysis included reviewing historical data for trends and developing a budgetary analysis to include Direct Labor Hour rates and opportunity costs. Interviews were conducted with key staff and participants in the WMPs to determine essential aspects and potential beneficial changes to the programs. Overall results were evaluated to identify potential opportunities for program expansion and improvement. Data analysis revealed that the FEP is producing a 78% success rate, with approximately 30% of the enrolled personnel actively participating. Concurrently, the SS program at NMCSD is producing a 71% success rate with 90% course completion rate. This success rate is significantly higher than the national SS average of 34%. Furthermore, our cost analysis revealed that the SS program a significantly higher return on investment. Interviews conducted of key staff and participants yielded several commonalities regarding key factors involved with WMPs success or needed improvements. To improve the WMPs at NMCSD, the findings in this report support the following recommendations: (1) maximize the SS program, (2) increase utilization of FEP, and (3) increase the participation and training of Assistant Command Fitness Leaders. WMPs navy-wide may benefit from incorporating similar program improvements to increase physical readiness of service members and, therefore, support command mission success.

An integrated omic analysis of hepatic alteration in medaka fish chronically exposed to cyanotoxins with possible mechanisms of reproductive toxicity.

PubMed

Qiao, Qin; Le Manach, Séverine; Huet, Hélène; Duvernois-Berthet, Evelyne; Chaouch, Soraya; Duval, Charlotte; Sotton, Benoit; Ponger, Loïc; Marie, Arul; Mathéron, Lucrèce; Lennon, Sarah; Bolbach, Gérard; Djediat, Chakib; Bernard, Cécile; Edery, Marc; Marie, Benjamin

2016-12-01

Cyanobacterial blooms threaten human health as well as the population of other living organisms in the aquatic environment, particularly due to the production of natural toxic components, the cyanotoxin. So far, the most studied cyanotoxins are microcystins (MCs). In this study, the hepatic alterations at histological, proteome and transcriptome levels were evaluated in female and male medaka fish chronically exposed to 1 and 5 μg L -1 microcystin-LR (MC-LR) and to the extract of MC-producing Microcystis aeruginosa PCC 7820 (5 μg L -1 of equivalent MC-LR) by balneation for 28 days, aiming at enhancing our understanding of the potential reproductive toxicity of cyanotoxins in aquatic vertebrate models. Indeed, both MC and Microcystis extract adversely affect reproductive parameters including fecundity and egg hatchability. The liver of toxin treated female fish present glycogen storage loss and cellular damages. The quantitative proteomics analysis revealed that the quantities of 225 hepatic proteins are dysregulated. In particular, a notable decrease in protein quantities of vitellogenin and choriogenin was observed, which could explain the decrease in reproductive output. Liver transcriptome analysis through Illumina RNA-seq reveals that over 100-400 genes are differentially expressed under 5 μg L -1  MC-LR and Microcystis extract treatments, respectively. Ingenuity pathway analysis of the omic data attests that various metabolic pathways, such as energy production, protein biosynthesis and lipid metabolism, are disturbed by both MC-LR and the Microcystis extract, which could provoke the observed reproductive impairment. The transcriptomics analysis also constitutes the first report of the impairment of circadian rhythm-related gene induced by MCs. This study contributes to a better understanding of the potential consequences of chronic exposure of fish to environmental concentrations of cyanotoxins, suggesting that Microcystis extract could impact a wider range of biological pathways, compared with pure MC-LR, and even 1 μg L -1  MC-LR potentially induces a health risk for aquatic organisms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Global dynamics and diffusion in triaxial galactic models

NASA Astrophysics Data System (ADS)

Papaphilippou, Y.

We apply the Frequency Map Analysis method to the 3--dimensional logarithmic galactic potential in order to clarify the dynamical behaviour of triaxial power--law galactic models. All the fine dynamical details are displayed in the complete frequency map, a direct representation of the system's Arnol'd web. The influence of resonant lines and the extent of the chaotic zones are directly associated with the physical space of the system. Some new results related with the diffusion of galactic orbits are also discussed. This approach reveals many unknown dynamical features of triaxial galactic potentials and provides strong indications that chaos should be an innate characteristic of triaxial configurations.

Comparative analysis of 2D and 3D model of a PEMFC in COMSOL

NASA Astrophysics Data System (ADS)

Lakshmi, R. Bakiya; Harikrishnan, N. P.; Juliet, A. Vimala

2017-10-01

In this article, 2D and 3D model of a PEMFC has been simulated in order to study their performance when subjected to similar operating conditions. The comparison reveals interesting phenomena of performance enhancement of the fuel cell. Design of fuel cell channel and stationary studies were done in COMSOL. Variations in current density and electrolyte potential from simulation results were observed when operated at a temperature of 120 °C. The electrolyte potential was found to have increased from 1 to 2.5 V and the surface pressure due to fluid flow was found to have increased from 3 to 9.58 Pa.

Groundwater assessment in Salboni Block, West Bengal (India) using remote sensing, geographical information system and multi-criteria decision analysis techniques

NASA Astrophysics Data System (ADS)

Jha, Madan K.; Chowdary, V. M.; Chowdhury, Alivia

2010-11-01

An approach is presented for the evaluation of groundwater potential using remote sensing, geographic information system, geoelectrical, and multi-criteria decision analysis techniques. The approach divides the available hydrologic and hydrogeologic data into two groups, exogenous (hydrologic) and endogenous (subsurface). A case study in Salboni Block, West Bengal (India), uses six thematic layers of exogenous parameters and four thematic layers of endogenous parameters. These thematic layers and their features were assigned suitable weights which were normalized by analytic hierarchy process and eigenvector techniques. The layers were then integrated using ArcGIS software to generate two groundwater potential maps. The hydrologic parameters-based groundwater potential zone map indicated that the `good' groundwater potential zone covers 27.14% of the area, the `moderate' zone 45.33%, and the `poor' zone 27.53%. A comparison of this map with the groundwater potential map based on subsurface parameters revealed that the hydrologic parameters-based map accurately delineates groundwater potential zones in about 59% of the area, and hence it is dependable to a certain extent. More than 80% of the study area has moderate-to-poor groundwater potential, which necessitates efficient groundwater management for long-term water security. Overall, the integrated technique is useful for the assessment of groundwater resources at a basin or sub-basin scale.

Spontaneous cortical DC-potential shifts: modulation stereotypy; relationships to higher EEG-frequencies.

PubMed

Etlinger, S C; Guttmann, G; Bauer, H

1986-07-01

A description of scalp-recorded, spontaneous, cerebral DC-potential shifts is given independent of other variables (shift stereotypy), in relationship to higher frequencies (theta, alpha 1, alpha 2: 4-13 Hz) and as analyzed pairwise across the median sagittal line (Fz, Cz, Pz) separately according to frequency and condition (relaxation and moderate mental load). Spontaneous DC-shifts are shown to behave unpredictably. Whether measured jointly (up to triads) or as dyad and triad context entropy, the frontal DC-shifts are calculated as being random, whereby their definition as such within the context of the Principle Component Analysis is supported by the analysis of longitudinal registrations. Cross-correlation analysis of the cerebral slow potential's relationship to each of the higher frequencies (theta, alpha 1, alpha 2) reveals it to be highly independent, the highest correlation accounting for merely 11% of the common variance, the average being 9% (R congruent to 0.3). By matching the conjoint activity of the DC-potential between Fz-Cz, Cz-Pz, and Fz-Pz to that of theta, alpha 1, alpha 2 at the same paired sites, the DC-activity is shown to be operating at higher levels of synchronous activity than the higher frequencies, regardless of pairing and/or condition, although the general level of synchronous activity (DC, theta, alpha 1, alpha 2) is remarkably high along the median sagittal line, 75% of the correlation averages of all analysis-pairings being above 0.60.

The Critical Role of Arabidopsis Electron-Transfer Flavoprotein:Ubiquinone Oxidoreductase during Dark-Induced StarvationW⃞

PubMed Central

Ishizaki, Kimitsune; Larson, Tony R.; Schauer, Nicolas; Fernie, Alisdair R.; Graham, Ian A.; Leaver, Christopher J.

2005-01-01

In mammals, electron-transfer flavoprotein:ubiquinone oxidoreductase (ETFQO) and electron-transfer flavoprotein (ETF) are functionally associated, and ETF accepts electrons from at least nine mitochondrial matrix flavoprotein dehydrogenases and transfers them to ubiquinone in the inner mitochondrial membrane. In addition, the mammalian ETF/ETFQO system plays a key role in β-oxidation of fatty acids and catabolism of amino acids and choline. By contrast, nothing is known of the function of ETF and ETFQO in plants. Sequence analysis of the unique Arabidopsis thaliana homologue of ETFQO revealed high similarity to the mammalian ETFQO protein. Moreover, green fluorescent protein cellular localization experiments suggested a mitochondrial location for this protein. RNA gel blot analysis revealed that Arabidopsis ETFQO transcripts accumulated in long-term dark-treated leaves. Analysis of three independent insertional mutants of Arabidopsis ETFQO revealed a dramatic reduction in their ability to withstand extended darkness, resulting in senescence and death within 10 d after transfer, whereas wild-type plants remained viable for at least 15 d. Metabolite profiling of dark-treated leaves of the wild type and mutants revealed a dramatic decline in sugar levels. In contrast with the wild type, the mutants demonstrated a significant accumulation of several amino acids, an intermediate of Leu catabolism, and, strikingly, high-level accumulation of phytanoyl-CoA. These data demonstrate the involvement of a mitochondrial protein, ETFQO, in the catabolism of Leu and potentially of other amino acids in higher plants and also imply a novel role for this protein in the chlorophyll degradation pathway activated during dark-induced senescence and sugar starvation. PMID:16055629

Identification of key regulators of pancreatic cancer progression through multidimensional systems-level analysis.

PubMed

Rajamani, Deepa; Bhasin, Manoj K

2016-05-03

Pancreatic cancer is an aggressive cancer with dismal prognosis, urgently necessitating better biomarkers to improve therapeutic options and early diagnosis. Traditional approaches of biomarker detection that consider only one aspect of the biological continuum like gene expression alone are limited in their scope and lack robustness in identifying the key regulators of the disease. We have adopted a multidimensional approach involving the cross-talk between the omics spaces to identify key regulators of disease progression. Multidimensional domain-specific disease signatures were obtained using rank-based meta-analysis of individual omics profiles (mRNA, miRNA, DNA methylation) related to pancreatic ductal adenocarcinoma (PDAC). These domain-specific PDAC signatures were integrated to identify genes that were affected across multiple dimensions of omics space in PDAC (genes under multiple regulatory controls, GMCs). To further pin down the regulators of PDAC pathophysiology, a systems-level network was generated from knowledge-based interaction information applied to the above identified GMCs. Key regulators were identified from the GMC network based on network statistics and their functional importance was validated using gene set enrichment analysis and survival analysis. Rank-based meta-analysis identified 5391 genes, 109 miRNAs and 2081 methylation-sites significantly differentially expressed in PDAC (false discovery rate ≤ 0.05). Bimodal integration of meta-analysis signatures revealed 1150 and 715 genes regulated by miRNAs and methylation, respectively. Further analysis identified 189 altered genes that are commonly regulated by miRNA and methylation, hence considered GMCs. Systems-level analysis of the scale-free GMCs network identified eight potential key regulator hubs, namely E2F3, HMGA2, RASA1, IRS1, NUAK1, ACTN1, SKI and DLL1, associated with important pathways driving cancer progression. Survival analysis on individual key regulators revealed that higher expression of IRS1 and DLL1 and lower expression of HMGA2, ACTN1 and SKI were associated with better survival probabilities. It is evident from the results that our hierarchical systems-level multidimensional analysis approach has been successful in isolating the converging regulatory modules and associated key regulatory molecules that are potential biomarkers for pancreatic cancer progression.

Comparative Genome Analysis and Global Phylogeny of the Toxin Variant Clostridium difficile PCR Ribotype 017 Reveals the Evolution of Two Independent Sublineages

PubMed Central

Cairns, M. D.; Preston, M. D.; Hall, C. L.; Gerding, D. N.; Hawkey, P. M.; Kato, H.; Kim, H.; Kuijper, E. J.; Lawley, T. D.; Pituch, H.; Reid, S.; Kullin, B.; Riley, T. V.; Solomon, K.; Tsai, P. J.; Weese, J. S.

2016-01-01

ABSTRACT The diarrheal pathogen Clostridium difficile consists of at least six distinct evolutionary lineages. The RT017 lineage is anomalous, as strains only express toxin B, compared to strains from other lineages that produce toxins A and B and, occasionally, binary toxin. Historically, RT017 initially was reported in Asia but now has been reported worldwide. We used whole-genome sequencing and phylogenetic analysis to investigate the patterns of global spread and population structure of 277 RT017 isolates from animal and human origins from six continents, isolated between 1990 and 2013. We reveal two distinct evenly split sublineages (SL1 and SL2) of C. difficile RT017 that contain multiple independent clonal expansions. All 24 animal isolates were contained within SL1 along with human isolates, suggesting potential transmission between animals and humans. Genetic analyses revealed an overrepresentation of antibiotic resistance genes. Phylogeographic analyses show a North American origin for RT017, as has been found for the recently emerged epidemic RT027 lineage. Despite having only one toxin, RT017 strains have evolved in parallel from at least two independent sources and can readily transmit between continents. PMID:28031436

Implications of fullerene-60 upon in-vitro LDPE biodegradation.

PubMed

Sah, Aditi; Kapri, Anil; Zaidi, M G H; Negi, Harshita; Goel, Reeta

2010-05-01

Fullerene-60 nanoparticles were used for studying their influence upon the LDPE biodegradation efficiency of two potential polymer-degrading consortia comprising of three bacterial strains each. At a concentration of 0.01% (w/v) in minimal broth lacking dextrose, fullerene did not have any negative influence upon the consortial growth. However, fullerene was found to be detrimental for bacterial growth at higher concentrations (viz. 0.25%, 0.5% and 1%). Although, addition of 0.01% fullerene into the biodegradation assays containing 5 mg/ml LDPE subsided growth-curves significantly, but subsequent analysis of degraded products revealed enhanced biodegradation. Fourier transform infrared spectroscopy (FT-IR) revealed breakage and formation of chemical bonds along with introduction of nu C-O frequencies into hydrocarbon backbone of LDPE. Further, simultaneous thermogravimetric-differential thermogravimetry-differential thermal analysis (TG-DTG-DTA) revealed higher number of decomposition steps along with a 1,000-fold decrease in the heat of reactions (DeltaH) in fullerene-assisted biodegraded LDPE suggesting probable formation of multiple, macromolecular by-products. This is the first report whereby fullerene-60, which is otherwise considered toxic, has helped to alleviate polymer biodegradation process of bacterial consortia.

Structure of glycosylated NPC1 luminal domain C reveals insights into NPC2 and Ebola virus interactions.

PubMed

Zhao, Yuguang; Ren, Jingshan; Harlos, Karl; Stuart, David I

2016-03-01

Niemann-pick type C1 (NPC1) is an endo/lysosomal membrane protein involved in intracellular cholesterol trafficking, and its luminal domain C is an essential endosomal receptor for Ebola and Marburg viruses. We have determined the crystal structure of glycosylated NPC1 luminal domain C and find all seven possible sites are glycosylated. Mapping the disease mutations onto the glycosylated structure reveals a potential binding face for NPC2. Knowledge-based docking of NPC1 onto Ebola viral glycoprotein and sequence analysis of filovirus susceptible and refractory species reveals four critical residues, H418, Q421, F502 and F504, some or all of which are likely responsible for the species-specific susceptibility to the virus infection. © 2016 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

Starch as a major integrator in the regulation of plant growth

PubMed Central

Sulpice, Ronan; Pyl, Eva-Theresa; Ishihara, Hirofumi; Trenkamp, Sandra; Steinfath, Matthias; Witucka-Wall, Hanna; Gibon, Yves; Usadel, Björn; Poree, Fabien; Piques, Maria Conceição; Von Korff, Maria; Steinhauser, Marie Caroline; Keurentjes, Joost J. B.; Guenther, Manuela; Hoehne, Melanie; Selbig, Joachim; Fernie, Alisdair R.; Altmann, Thomas; Stitt, Mark

2009-01-01

Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light and is degraded at night to provide a sustained supply of carbon for growth. Multivariate analysis revealed that starch is an integrator of the overall metabolic response. We hypothesized that this reflects variation in a regulatory network that balances growth with the carbon supply. Transcript profiling in 21 accessions revealed coordinated changes of transcripts of more than 70 carbon-regulated genes and identified 2 genes (myo-inositol-1-phosphate synthase, a Kelch-domain protein) whose transcripts correlate with biomass. The impact of allelic variation at these 2 loci was shown by association mapping, identifying them as candidate lead genes with the potential to increase biomass production. PMID:19506259

Modulation of Tropical Cyclone Genesis by Boreal Summer Intraseasonal Oscillation: An Anomalous Dynamic Genesis Potential Index

NASA Astrophysics Data System (ADS)

Moon, J.; Wang, B.

2016-12-01

The large scale circulation anomalies associated with boreal summer intraseasonal oscillation (BSISO) strongly controls the genesis of tropical cyclone in a global perspective. The present study attempts to reveal factors by which BSISO modulation of tropical cyclone genesis (TCG) using two genesis potential indices (GPI): Dynamic GPI (DGPI) and Emanuel and Nolan's GPI (ENGPI). The ENGPI contains two dynamic (the vertical wind shear and absolute vorticity at 850 hPa) and two thermodynamic factors (relative humidity at 600 hPa and maximum potential intensity), while DPGI replaced the two thermodynamic factors by two additional dynamic factors (500 hPa vertical velocity and meridional shear of zonal winds). The major basins of tropical cyclone genesis during May to October from 1979 to 2014 are divided into North Indian Ocean (NIO), Western North Pacific (WNP), Eastern North Pacific (ENP), and North Atlantic (NAT). The genesis numbers of tropical cyclone at each basin increased distinctively at its maximum active phase of BSISO, showing the significant modulation of ISO on tropical cyclone genesis in the Northern Hemisphere. Analysis of the individual contribution of each factors in GPI reveals that the vertical velocity at 500hPa of DGPI and the relative humidity at 600hPa of ENGPI play the most important role in modulating TCG by BSISO. The SST and maximum potential intensity of ENGPI did not represent important physical processes by which the BSISO circulation anomalies affect TCG. The evolution of eight-phase BSISO with intraseasonal prediction of TCG revealed great improvement by DGPI. The evolution of TCG associated with BSISO by basins, such as NIO, WNP, ENP, and NAT showed good performance in featuring the TCG variability, indicating the possibility of improving subseasonal prediction of TCG by our new DGPI.

Novel Nano-Therapeutic Approach Actively Targets Human Ovarian Cancer Stem Cells after Xenograft into Nude Mice.

PubMed

Abou-ElNaga, Amoura; Mutawa, Ghada; El-Sherbiny, Ibrahim M; Abd-ElGhaffar, Hassan; Allam, Ahmed A; Ajarem, Jamaan; Mousa, Shaker A

2017-04-12

The power of tumorigenesis, chemo-resistance and metastasis in malignant ovarian tumors resides in a tiny population of cancer cells known as ovarian cancer stem cells (OCSCs). Developing nano-therapeutic targeting of OCSCs is considered a great challenge. The potential use of poly(lactic-co-glycolic acid) nanoparticles (PLGA NPs) was investigated as a drug delivery system for paclitaxel (PTX) against OCSCs in vitro and in vivo. PTX-loaded PLGA NPs were prepared by an emulsion solvent evaporation method, supported by incorporation of folic acid (FA) as the ligand. NPs were characterized for size, surface morphology, drug loading, and encapsulation efficiency. In vitro cytotoxicity of PTX-loaded FA/PLGA NPs was tested against OCSCs with MTT assay. In vivo anti-tumoral efficiency and active targeting potential of prepared NPs against tumors in nude mice were investigated. In vitro results revealed that IC 50 of PTX was significantly reduced after loading on PLGA NPs. On the other hand, in vivo results showed that PLGA NPs enhanced the tumor suppression efficiency of PTX. Investigation with real time quantitative PCR analysis revealed the limiting expression of chemo-resistant genes ( ABCG2 and MDR1 ) after applying PLGA NPs as a drug delivery system for PTX. Histopathological examination of tumors showed the effective biological influence of PTX-loaded FA/PLGA NPs through the appearance of reactive lymphoid follicles. Targeting potential of PTX was activated by FA/PLGA NPs through significant preservation of body weight ( p < 0.0001) and minimizing the systemic toxicity in healthy tissues. Immunohistochemical investigation revealed a high expression of apoptotic markers in tumor tissue, supporting the targeting effect of FA/PLGA NPs. A drug delivery system based on FA/PLGA NPs can enhance PTX's in vitro cytotoxicity and in vivo targeting potential against OCSCs.

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

DOE PAGES

Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; ...

2015-04-30

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore » of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

PubMed Central

Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

2015-01-01

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below −10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface. PMID:25983731

Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

PubMed

Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

2015-03-03

Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data.

Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer.

PubMed

Jadhav, Rohit R; Ye, Zhenqing; Huang, Rui-Lan; Liu, Joseph; Hsu, Pei-Yin; Huang, Yi-Wen; Rangel, Leticia B; Lai, Hung-Cheng; Roa, Juan Carlos; Kirma, Nameer B; Huang, Tim Hui-Ming; Jin, Victor X

2015-01-01

Recent genome-wide analysis has shown that DNA methylation spans long stretches of chromosome regions consisting of clusters of contiguous CpG islands or gene families. Hypermethylation of various gene clusters has been reported in many types of cancer. In this study, we conducted methyl-binding domain capture (MBDCap) sequencing (MBD-seq) analysis on a breast cancer cohort consisting of 77 patients and 10 normal controls, as well as a panel of 38 breast cancer cell lines. Bioinformatics analysis determined seven gene clusters with a significant difference in overall survival (OS) and further revealed a distinct feature that the conservation of a large gene cluster (approximately 70 kb) metallothionein-1 (MT1) among 45 species is much lower than the average of all RefSeq genes. Furthermore, we found that DNA methylation is an important epigenetic regulator contributing to gene repression of MT1 gene cluster in both ERα positive (ERα+) and ERα negative (ERα-) breast tumors. In silico analysis revealed much lower gene expression of this cluster in The Cancer Genome Atlas (TCGA) cohort for ERα + tumors. To further investigate the role of estrogen, we conducted 17β-estradiol (E2) and demethylating agent 5-aza-2'-deoxycytidine (DAC) treatment in various breast cancer cell types. Cell proliferation and invasion assays suggested MT1F and MT1M may play an anti-oncogenic role in breast cancer. Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer. Further investigation of these clusters revealed that estrogen mediates epigenetic repression of MT1 cluster in ERα + breast cancer cell lines. In all, our studies identify thousands of breast tumor hypermethylated regions for the first time, in particular, discovering seven large contiguous hypermethylated gene clusters.

Bioinformatics functional analysis of let-7a, miR-34a, and miR-199a/b reveals novel insights into immune system pathways and cancer hallmarks for hepatocellular carcinoma.

PubMed

Soliman, Bangly; Salem, Ahmed; Ghazy, Mohamed; Abu-Shahba, Nourhan; El Hefnawi, Mahmoud

2018-05-01

Let-7a, miR-34a, and miR-199 a/b have gained a great attention as master regulators for cellular processes. In particular, these three micro-RNAs act as potential onco-suppressors for hepatocellular carcinoma. Bioinformatics can reveal the functionality of these micro-RNAs through target prediction and functional annotation analysis. In the current study, in silico analysis using innovative servers (miRror Suite, DAVID, miRGator V3.0, GeneTrail) has demonstrated the combinatorial and the individual target genes of these micro-RNAs and further explored their roles in hepatocellular carcinoma progression. There were 87 common target messenger RNAs (p ≤ 0.05) that were predicted to be regulated by the three micro-RNAs using miRror 2.0 target prediction tool. In addition, the functional enrichment analysis of these targets that was performed by DAVID functional annotation and REACTOME tools revealed two major immune-related pathways, eight hepatocellular carcinoma hallmarks-linked pathways, and two pathways that mediate interconnected processes between immune system and hepatocellular carcinoma hallmarks. Moreover, protein-protein interaction network for the predicted common targets was obtained by using STRING database. The individual analysis of target genes and pathways for the three micro-RNAs of interest using miRGator V3.0 and GeneTrail servers revealed some novel predicted target oncogenes such as SOX4, which we validated experimentally, in addition to some regulated pathways of immune system and hepatocarcinogenesis such as insulin signaling pathway and adipocytokine signaling pathway. In general, our results demonstrate that let-7a, miR-34a, and miR-199 a/b have novel interactions in different immune system pathways and major hepatocellular carcinoma hallmarks. Thus, our findings shed more light on the roles of these miRNAs as cancer silencers.

Genetic analysis and CRISPR typing of Salmonella enterica serovar Enteritidis from different sources revealed potential transmission from poultry and pig to human.

PubMed

Li, Qiuchun; Wang, Xin; Yin, Kequan; Hu, Yachen; Xu, Haiyan; Xie, Xiaolei; Xu, Lijuan; Fei, Xiao; Chen, Xiang; Jiao, Xinan

2018-02-02

Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most prevalent serotypes in Salmonella isolated from poultry and the most commonly reported cause of human salmonellosis. In this study, we aimed to assess the genetic diversity of 329 S. Enteritidis strains isolated from different sources from 2009 to 2016 in China. Clustered regularly interspaced short palindromic repeat (CRISPR) typing was used to characterize these 262 chicken clinical isolates, 38 human isolates, 18 pig isolates, six duck isolates, three goose isolates and two isolates of unknown source. A total of 18 Enteritidis CRISPR types (ECTs) were identified, with ECT2, ECT8 and ECT4 as the top three ECTs. CRISPR typing identified ECT2 as the most prevalent ECT, which accounted for 41% of S. Enteritidis strains from all the sources except duck. ECT9 and ECT13 were identified in both pig and human isolates and revealed potential transmission from pig to human. A cluster analysis distributed 18 ECTs, including the top three ECTs, into four lineages with LI as the predominant lineage. Forty-eight out of 329 isolates were subjected to whole genome sequence typing, which divided them into four clusters, with Cluster I as the predominant cluster. Cluster I included 92% (34/37) of strains located in LI identified from the CRISPR typing, confirming the good correspondence between both typing methods. In addition, the CRISPR typing also revealed the close relationship between ECTs and isolated areas, confirming that CRISPR spacers might be obtained by bacteria from the unique phage or plasmid pools in the environment. However, further analysis is needed to determine the function of CRISPR-Cas systems in Salmonella and the relationship between spacers and the environment. Copyright © 2017 Elsevier B.V. All rights reserved.

Metabolomic profiles delineate the potential role of glycine in gold nanorod-induced disruption of mitochondria and blood-testis barrier factors in TM-4 cells

NASA Astrophysics Data System (ADS)

Xu, Bo; Chen, Minjian; Ji, Xiaoli; Mao, Zhilei; Zhang, Xuemei; Wang, Xinru; Xia, Yankai

2014-06-01

Gold nanorods (GNRs) are commonly used nanomaterials with potential harmful effects on male reproduction. However, the mechanism by which GNRs affect male reproduction remains largely undetermined. In this study, the metabolic changes in spermatocyte-derived cells GC-2 and Sertoli cell line TM-4 were analyzed after GNR treatment for 24 h. Metabolomic analysis revealed that glycine was highly decreased in TM-4 cells after GNR-10 nM treatment while there was no significant change in GC-2 cells. RT-PCR showed that the mRNA levels of glycine synthases in the mitochondrial pathway decreased after GNR treatment, while there was no significant difference in mRNA levels of glycine synthases in the cytoplasmic pathway. High content screening (HCS) showed that GNRs decreased membrane permeability and mitochondrial membrane potential of TM-4 cells, which was also confirmed by JC-1 staining. In addition, RT-PCR and Western blot indicated that the mRNA and protein levels of blood-testis barrier (BTB) factors (ZO-1, occludin, claudin-5, and connexin-43) in TM-4 cells were also disrupted by GNRs. After glycine was added into the medium, the GNR-induced harmful effects on mitochondria and BTB factors were recovered in TM-4 cells. Our results showed that even low doses of GNRs could induce significant toxic effects on mitochondria and BTB factors in TM-4 cells. Furthermore, we revealed that glycine was a potentially important metabolic intermediary for the changes of membrane permeability, mitochondrial membrane potential and BTB factors after GNR treatment in TM-4 cells.Gold nanorods (GNRs) are commonly used nanomaterials with potential harmful effects on male reproduction. However, the mechanism by which GNRs affect male reproduction remains largely undetermined. In this study, the metabolic changes in spermatocyte-derived cells GC-2 and Sertoli cell line TM-4 were analyzed after GNR treatment for 24 h. Metabolomic analysis revealed that glycine was highly decreased in TM-4 cells after GNR-10 nM treatment while there was no significant change in GC-2 cells. RT-PCR showed that the mRNA levels of glycine synthases in the mitochondrial pathway decreased after GNR treatment, while there was no significant difference in mRNA levels of glycine synthases in the cytoplasmic pathway. High content screening (HCS) showed that GNRs decreased membrane permeability and mitochondrial membrane potential of TM-4 cells, which was also confirmed by JC-1 staining. In addition, RT-PCR and Western blot indicated that the mRNA and protein levels of blood-testis barrier (BTB) factors (ZO-1, occludin, claudin-5, and connexin-43) in TM-4 cells were also disrupted by GNRs. After glycine was added into the medium, the GNR-induced harmful effects on mitochondria and BTB factors were recovered in TM-4 cells. Our results showed that even low doses of GNRs could induce significant toxic effects on mitochondria and BTB factors in TM-4 cells. Furthermore, we revealed that glycine was a potentially important metabolic intermediary for the changes of membrane permeability, mitochondrial membrane potential and BTB factors after GNR treatment in TM-4 cells. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01035c

Identification and expression profiling of novel plant cell wall degrading enzymes from a destructive pest of palm trees, Rhynchophorus ferrugineus.

PubMed

Antony, B; Johny, J; Aldosari, S A; Abdelazim, M M

2017-08-01

Plant cell wall degrading enzymes (PCWDEs) from insects were recently identified as a multigene family of proteins that consist primarily of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) and play essential roles in the degradation of the cellulose/hemicellulose/pectin network in the invaded host plant. Here we applied transcriptomic and degenerate PCR approaches to identify the PCWDEs from a destructive pest of palm trees, Rhynchophorus ferrugineus, followed by a gut-specific and stage-specific differential expression analysis. We identified a total of 27 transcripts encoding GH family members and three transcripts of the CE family with cellulase, hemicellulase and pectinase activities. We also identified two GH9 candidates, which have not previously been reported from Curculionidae. The gut-specific quantitative expression analysis identified key cellulases, hemicellulases and pectinases from R. ferrugineus. The expression analysis revealed a pectin methylesterase, RferCE8u02, and a cellulase, GH45c34485, which showed the highest gut enriched expression. Comparison of PCWDE expression patterns revealed that cellulases and pectinases are significantly upregulated in the adult stages, and we observed specific high expression of the hemicellulase RferGH16c4170. Overall, our study revealed the potential of PCWDEs from R. ferrugineus, which may be useful in biotechnological applications and may represent new tools in R. ferrugineus pest management strategies. © 2017 The Royal Entomological Society.

Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

PubMed

Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

2015-01-01

Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

Characteristics of white, yellow, purple corn accessions: phenolic profile, textural, rheological properties and muffin making potential.

PubMed

Trehan, Shalini; Singh, Narpinder; Kaur, Amritpal

2018-06-01

Physicochemical, antioxidant, phenolic profile and muffin-making properties of white, yellow and purple corn accessions were evaluated. HPLC analysis revealed the presence of ferulic acid, quercetin, sinapic acid, gallic acid and protocatechuic acid in different corn accessions. Ferulic acid was the major phenolic acid present in all accessions. Total phenolic content (TPC), DPPH and ABTS inhibition ranged from 903 to 1843 µg GAE/g, 0.73-0.89 and 3.81-4.92 µM trolox/mg, respectively. Purple accessions had higher TPC than yellow and white accessions. Pasting profiles of different accessions revealed high thermal stability indicated by low breakdown viscosity. Muffin-making properties were determined as batter rheology and muffin specific volume, texture and sensory analysis. Storage modulus ( G ') and loss modulus ( G ″) of batters for white colored exhibited the highest while yellow colored had the lowest value. Firmness and TPC of muffins ranged from 3.1 to 5.9 N and 811-1406 µg GAE/g, respectively. Muffin cohesiveness and chewiness were correlated positively, whereas firmness was negatively related to paste viscosities. Antioxidant activity was correlated to phenolic content of the muffins. Sensory analysis revealed that muffins prepared from yellow corn accession (IC447648) were highly acceptable, while those made from purple corn (IC447644) were not liked much.

Perceptual suppression revealed by adaptive multi-scale entropy analysis of local field potential in monkey visual cortex.

PubMed

Hu, Meng; Liang, Hualou

2013-04-01

Generalized flash suppression (GFS), in which a salient visual stimulus can be rendered invisible despite continuous retinal input, provides a rare opportunity to directly study the neural mechanism of visual perception. Previous work based on linear methods, such as spectral analysis, on local field potential (LFP) during GFS has shown that the LFP power at distinctive frequency bands are differentially modulated by perceptual suppression. Yet, the linear method alone may be insufficient for the full assessment of neural dynamic due to the fundamentally nonlinear nature of neural signals. In this study, we set forth to analyze the LFP data collected from multiple visual areas in V1, V2 and V4 of macaque monkeys while performing the GFS task using a nonlinear method - adaptive multi-scale entropy (AME) - to reveal the neural dynamic of perceptual suppression. In addition, we propose a new cross-entropy measure at multiple scales, namely adaptive multi-scale cross-entropy (AMCE), to assess the nonlinear functional connectivity between two cortical areas. We show that: (1) multi-scale entropy exhibits percept-related changes in all three areas, with higher entropy observed during perceptual suppression; (2) the magnitude of the perception-related entropy changes increases systematically over successive hierarchical stages (i.e. from lower areas V1 to V2, up to higher area V4); and (3) cross-entropy between any two cortical areas reveals higher degree of asynchrony or dissimilarity during perceptual suppression, indicating a decreased functional connectivity between cortical areas. These results, taken together, suggest that perceptual suppression is related to a reduced functional connectivity and increased uncertainty of neural responses, and the modulation of perceptual suppression is more effective at higher visual cortical areas. AME is demonstrated to be a useful technique in revealing the underlying dynamic of nonlinear/nonstationary neural signal.

Identifying changes in the support networks of end-of-life carers using social network analysis

PubMed Central

Leonard, Rosemary; Horsfall, Debbie; Noonan, Kerrie

2015-01-01

End-of-life caring is often associated with reduced social networks for both the dying person and for the carer. However, those adopting a community participation and development approach, see the potential for the expansion and strengthening of networks. This paper uses Knox, Savage and Harvey's definitions of three generations social network analysis to analyse the caring networks of people with a terminal illness who are being cared for at home and identifies changes in these caring networks that occurred over the period of caring. Participatory network mapping of initial and current networks was used in nine focus groups. The analysis used key concepts from social network analysis (size, density, transitivity, betweenness and local clustering) together with qualitative analyses of the group's reflections on the maps. The results showed an increase in the size of the networks and that ties between the original members of the network strengthened. The qualitative data revealed the importance between core and peripheral network members and the diverse contributions of the network members. The research supports the value of third generation social network analysis and the potential for end-of-life caring to build social capital. PMID:24644162

Systemic bioinformatics analysis of skeletal muscle gene expression profiles of sepsis

PubMed Central

Yang, Fang; Wang, Yumei

2018-01-01

Sepsis is a type of systemic inflammatory response syndrome with high morbidity and mortality. Skeletal muscle dysfunction is one of the major complications of sepsis that may also influence the outcome of sepsis. The aim of the present study was to explore and identify potential mechanisms and therapeutic targets of sepsis. Systemic bioinformatics analysis of skeletal muscle gene expression profiles from the Gene Expression Omnibus was performed. Differentially expressed genes (DEGs) in samples from patients with sepsis and control samples were screened out using the limma package. Differential co-expression and coregulation (DCE and DCR, respectively) analysis was performed based on the Differential Co-expression Analysis package to identify differences in gene co-expression and coregulation patterns between the control and sepsis groups. Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways of DEGs were identified using the Database for Annotation, Visualization and Integrated Discovery, and inflammatory, cancer and skeletal muscle development-associated biological processes and pathways were identified. DCE and DCR analysis revealed several potential therapeutic targets for sepsis, including genes and transcription factors. The results of the present study may provide a basis for the development of novel therapeutic targets and treatment methods for sepsis. PMID:29805480

Physico-chemical studies of the experimental and theoretical properties of organic nonlinear optical material 4-chloro-4'methoxy benzylideneaniline

NASA Astrophysics Data System (ADS)

George, Merin; John, Nimmy L.; Saravana Kumar, M.; Subashini, A.; Sajan, D.

2017-01-01

The FT-IR, FT-Raman and UV-visible spectral analysis of 4-chloro 4'-methoxy benzylidene aniline were done experimentally and interpreted with the aid of normal coordinate analysis based on density functional theory (DFT) at the B3LYP/6-311++G (d, p) level of theory. Natural Bond orbital analysis was performed to understand the charge transfer interactions and reactive sites within the system. HOMO-LUMO analysis and first static and dynamic hyperpolarizability calculations were carried out in order to confirm the NLO activity of CMOBA. Photophysical characterization was done to understand the fluorescence emission and lifetime of CMOBA leading to application in blue OLEDs. The Molecular Electrostatic Potential Map was simulated to identify the active sites for electrophilic and nucleophilic attack or the active sites of the molecule which can bind to proteins. Molecular docking analysis revealed its potential as an inhibitor for different proteins which are responsible for cancer and many inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease, Crohn's disease and psoriasis. Experimental studies of invitro antiproliferative effect by MTT assay verified the anticancer properties of CMOBA.

Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes

DOE PAGES

Kotak, Malini; Isanapong, Jantiya; Goodwin, Lynne A.; ...

2015-03-05

The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated from the wood-feeding termite hindgut. Here, we report here its complete genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and 99,831 bp, respectively. In conclusion, genomic analysis reveals genes for methylotrophy, lignocellulose degradation, and ammonia and sulfate assimilation.

Changing the Graduate Medical Education Funding Path to Reduce the Price of Health Care Services.

PubMed

Martin, Ralph A

2015-01-01

An analysis of the current Graduate Medical Education (GME) funding stream reveals undesired aspects that limit the number of graduates and may tend to raise the price of health care services. The author shows that a different model of GME funding changes the economic dynamics and takes advantage of economic forces to increase the supply of graduates, while potentially reducing the price of health care services.

Gene array analysis reveals a common Runx transcriptional program controlling cell adhesion and survival

PubMed Central

Wotton, Sandy; Terry, Anne; Kilbey, Anna; Jenkins, Alma; Herzyk, Pawel; Cameron, Ewan; Neil, James C.

2008-01-01

The Runx genes play divergent roles in development and cancer, where they can act either as oncogenes or tumour suppressors. We compared the effects of ectopic Runx expression in established fibroblasts, where all three genes produce an indistinguishable phenotype entailing epithelioid morphology and increased cell survival under stress conditions. Gene array analysis revealed a strongly overlapping transcriptional signature, with no examples of opposing regulation of the same target gene. A common set of 50 highly regulated genes was identified after further filtering on regulation by inducible RUNX1-ER. This set revealed a strong bias towards genes with annotated roles in cancer and development, and a preponderance of targets encoding extracellular or surface proteins, reflecting the marked effects of Runx on cell adhesion. Furthermore, in silico prediction of resistance to glucocorticoid growth inhibition was confirmed in fibroblasts and lymphoid cells expressing ectopic Runx. The effects of fibroblast expression of common RUNX1 fusion oncoproteins (RUNX1-ETO, TEL-RUNX1, CBFB-MYH11) were also tested. While two direct Runx activation target genes were repressed (Ncam1, Rgc32), the fusion proteins appeared to disrupt regulation of down-regulated targets (Cebpd, Id2, Rgs2) rather than impose constitutive repression. These results elucidate the oncogenic potential of the Runx family and reveal novel targets for therapeutic inhibition. PMID:18560354

Identification of expressed sequences in the coffee genome potentially associated with somatic embryogenesis.

PubMed

Silva, A T; Paiva, L V; Andrade, A C; Barduche, D

2013-05-21

Brazil possesses the most modern and productive coffee growing farms in the world, but technological development is desired to cope with the increasing world demand. One way to increase Brazilian coffee growing productivity is wide scale production of clones with superior genotypes, which can be obtained with in vitro propagation technique, or from tissue culture. These procedures can generate thousands of clones. However, the methodologies for in vitro cultivation are genotype-dependent, which leads to an almost empirical development of specific protocols for each species. Therefore, molecular markers linked to the biochemical events of somatic embryogenesis would greatly facilitate the development of such protocols. In this context, sequences potentially involved in embryogenesis processes in the coffee plant were identified in silico from libraries generated by the Brazilian Coffee Genome Project. Through these in silico analyses, we identified 15 EST-contigs related to the embryogenesis process. Among these, 5 EST-contigs (3605, 9850, 13686, 17240, and 17265) could readily be associated with plant embryogenesis. Sequence analysis of EST-contig 3605, 9850, and 17265 revealed similarity to a polygalacturonase, to a cysteine-proteinase, and to an allergenine, respectively. Results also show that EST-contig 17265 sequences presented similarity to an expansin. Finally, analysis of EST-contig 17240 revealed similarity to a protein of unknown function, but it grouped in the similarity dendrogram with the WUSCHEL transcription factor. The data suggest that these EST-contigs are related to the embryogenic process and have potential as molecular markers to increase methodological efficiency in obtaining coffee plant embryogenic materials.

Multimodal Fluorescence and Bioluminescence Imaging Reveals Transfection Potential of Intratracheally Administered Polyplexes for Breast Cancer Lung Metastases.

PubMed

Geyer, Antonia; Taschauer, Alexander; Alioglu, Fatih; Anton, Martina; Maier, Julia; Drothler, Elisabeth; Simlinger, Manuela; Yavuz, Sümeyye; Sami, Haider; Ogris, Manfred

2017-12-01

Local delivery of anticancer agents or gene therapeutics to lung tumors can circumvent side effects or accumulation in non-target organs, but accessibility via the alveolar side of the blood-air barrier remains challenging. Polyplexes based on plasmid and linear polyethylenimine (LPEI) transfect healthy lung tissue when applied intravenously (i.v.) in the mouse, but direct delivery into the lungs results in low transfection of lung tissue. Nevertheless, LPEI could offer the potential to transfect lung tumors selectively, if accessible from the alveolar side. This study combined near infrared fluorescent protein 720 (iRFP720) and firefly luciferase as reporter genes for detection of tumor lesions and transfection efficiency of LPEI polyplexes, after intratracheal microspraying in mice bearing 4T1 triple negative breast cancer lung metastases. Simultaneous flow cytometric analysis of iRFP720 and enhanced green fluorescent protein expression in vitro demonstrated the potential to combine these reporter genes within transfection studies. Polyplex biophysics was characterized by single nanoparticle tracking analysis (NTA) to monitor physical integrity after microspraying in vitro. 4T1 cells were transduced with iRFP720-encoding lentivirus and evaluated by flow cytometry for stable iRFP720 expression. Growth of 4T1-iRFP720 cells was monitored in Balb/c mice by tomographic near infrared imaging, tissue and tumor morphology by computed tomography and magnetic resonance imaging. In 4T1-iRFP720 tumor-bearing mice, intratracheal administration of luciferase-encoding plasmid DNA by LPEI polyplexes resulted in successful tumor transfection, as revealed by bioluminescence imaging.

Potential sources of bacteria that are isolated from contact lenses during wear.

PubMed

Willcox, M D; Power, K N; Stapleton, F; Leitch, C; Harmis, N; Sweeney, D F

1997-12-01

The aim of this paper was to determine the possible contamination sources of contact lenses during wear. Potential sources of the microbiota that colonized hydrogel contact lenses during wear were examined. The microorganisms that colonize contact lenses were grown, identified, and compared to those microorganisms that colonized the lower lid margins, upper bulbar conjunctiva, hands, and contact lens cases of contact lens wearers. In addition, the incidence of contamination of the domestic water supply in the Sydney area was obtained, and this was compared to the incidence of colonization of contact lenses by microorganisms in general and gram-negative bacteria in particular. There was a wide diversity of bacteria that were isolated from each site sampled. Coagulase-negative staphylococci and Propionibacterium spp. were the most common isolates from all ocular sites examined, and constituted the normal ocular microbiota. Other bacteria, including members of the families Enterobacteriaceae and Pseudomonadaceae, were isolated infrequently from all sites, but most frequently from contact lens cases. Statistical analysis revealed that there was a correlation between the isolation of bacteria from the contact lens and the lower lid margin (p < 0.001). Analysis of this correlation revealed that this was true for the normal microbiota. A correlation was also noted between the colonization of contact lenses by gram-negative bacteria and contamination of the domestic water supply. This study has demonstrated that the likely route for the normal ocular microbiota colonizing contact lenses is via the lid margins, whereas colonization by gram-negative bacteria, including potential agents of microbial keratitis, is likely to be from the domestic water supply.

Generation of “LYmph Node Derived Antibody Libraries” (LYNDAL) for selecting fully human antibody fragments with therapeutic potential

PubMed Central

Diebolder, Philipp; Keller, Armin; Haase, Stephanie; Schlegelmilch, Anne; Kiefer, Jonathan D; Karimi, Tamana; Weber, Tobias; Moldenhauer, Gerhard; Kehm, Roland; Eis-Hübinger, Anna M; Jäger, Dirk; Federspil, Philippe A; Herold-Mende, Christel; Dyckhoff, Gerhard; Kontermann, Roland E; Arndt, Michaela AE; Krauss, Jürgen

2014-01-01

The development of efficient strategies for generating fully human monoclonal antibodies with unique functional properties that are exploitable for tailored therapeutic interventions remains a major challenge in the antibody technology field. Here, we present a methodology for recovering such antibodies from antigen-encountered human B cell repertoires. As the source for variable antibody genes, we cloned immunoglobulin G (IgG)-derived B cell repertoires from lymph nodes of 20 individuals undergoing surgery for head and neck cancer. Sequence analysis of unselected “LYmph Node Derived Antibody Libraries” (LYNDAL) revealed a naturally occurring distribution pattern of rearranged antibody sequences, representing all known variable gene families and most functional germline sequences. To demonstrate the feasibility for selecting antibodies with therapeutic potential from these repertoires, seven LYNDAL from donors with high serum titers against herpes simplex virus (HSV) were panned on recombinant glycoprotein B of HSV-1. Screening for specific binders delivered 34 single-chain variable fragments (scFvs) with unique sequences. Sequence analysis revealed extensive somatic hypermutation of enriched clones as a result of affinity maturation. Binding of scFvs to common glycoprotein B variants from HSV-1 and HSV-2 strains was highly specific, and the majority of analyzed antibody fragments bound to the target antigen with nanomolar affinity. From eight scFvs with HSV-neutralizing capacity in vitro, the most potent antibody neutralized 50% HSV-2 at 4.5 nM as a dimeric (scFv)2. We anticipate our approach to be useful for recovering fully human antibodies with therapeutic potential. PMID:24256717

Generation of “LYmph Node Derived Antibody Libraries” (LYNDAL) for selecting fully human antibody fragments with therapeutic potential.

PubMed

Diebolder, Philipp; Keller, Armin; Haase, Stephanie; Schlegelmilch, Anne; Kiefer, Jonathan D; Karimi, Tamana; Weber, Tobias; Moldenhauer, Gerhard; Kehm, Roland; Eis-Hübinger, Anna M; Jäger, Dirk; Federspil, Philippe A; Herold-Mende, Christel; Dyckhoff, Gerhard; Kontermann, Roland E; Arndt, Michaela A E; Krauss, Jürgen

2014-01-01

The development of efficient strategies for generating fully human monoclonal antibodies with unique functional properties that are exploitable for tailored therapeutic interventions remains a major challenge in the antibody technology field. Here, we present a methodology for recovering such antibodies from antigen-encountered human B cell repertoires. As the source for variable antibody genes, we cloned immunoglobulin G (IgG)-derived B cell repertoires from lymph nodes of 20 individuals undergoing surgery for head and neck cancer. Sequence analysis of unselected “LYmph Node Derived Antibody Libraries” (LYNDAL) revealed a naturally occurring distribution pattern of rearranged antibody sequences, representing all known variable gene families and most functional germline sequences. To demonstrate the feasibility for selecting antibodies with therapeutic potential from these repertoires, seven LYNDAL from donors with high serum titers against herpes simplex virus (HSV) were panned on recombinant glycoprotein B of HSV-1. Screening for specific binders delivered 34 single-chain variable fragments (scFvs) with unique sequences. Sequence analysis revealed extensive somatic hypermutation of enriched clones as a result of affinity maturation. Binding of scFvs to common glycoprotein B variants from HSV-1 and HSV-2 strains was highly specific, and the majority of analyzed antibody fragments bound to the target antigen with nanomolar affinity. From eight scFvs with HSV-neutralizing capacity in vitro,the most potent antibody neutralized 50% HSV-2 at 4.5 nM as a dimeric (scFv)2. We anticipate our approach to be useful for recovering fully human antibodies with therapeutic potential.

Analysis of the effects of polyphenols on human spermatozoa reveals unexpected impacts on mitochondrial membrane potential, oxidative stress and DNA integrity; implications for assisted reproductive technology.

PubMed

Aitken, R J; Muscio, L; Whiting, S; Connaughton, H S; Fraser, B A; Nixon, B; Smith, N D; De Iuliis, G N

2016-12-01

The need to protect human spermatozoa from oxidative stress during assisted reproductive technology, has prompted a detailed analysis of the impacts of phenolic compounds on the functional integrity of these cells. Investigation of 16 individual compounds revealed a surprising variety of negative effects including: (i) a loss of mitochondrial membrane potential (Δψm) via mechanisms that were not related to opening of the permeability transition pore but associated with a reduction in thiol expression, (ii) a decline in intracellular reduced glutathione, (iii) the stimulation of pro-oxidant activity including the induction of ROS generation from mitochondrial and non-mitochondrial sources, (iv) stimulation of lipid peroxidation, (v) the generation of oxidative DNA damage, and (vi) impaired sperm motility. For most of the polyphenolic compounds examined, the loss of motility was gradual and highly correlated with the induction of lipid peroxidation (r=0.889). The exception was gossypol, which induced a rapid loss of motility due to its inherent alkylating activity; one consequence of which was a marked reduction in carboxymethyl lysine expression on the sperm tail; a post-translational modification that is known to play a key role in the regulation of sperm movement. The only polyphenols that did not appear to have adverse effects on spermatozoa were resveratrol, genistein and THP at doses below 100μM. These compounds could, therefore, have some therapeutic potential in a clinical setting. Copyright © 2016 Elsevier Inc. All rights reserved.

Prognostic value of long noncoding RNA ZFAS1 in various carcinomas: a meta-analysis.

PubMed

Dong, Dan; Mu, Zhongyi; Wang, Wei; Xin, Na; Song, Xiaowen; Shao, Yue; Zhao, Chenghai

2017-10-13

A number of studies have revealed that zinc finger antisense 1 (ZFAS1), a long noncoding RNA (lncRNA), is aberrantly regulated in various cancers, and high ZFAS1 expression is associated with poor prognosis and increased risk of lymph node metastasis (LNM). This meta-analysis was conducted to identify the potential value of ZFAS1 as a biomarker for cancer prognosis. We searched electronic database PubMed, Web of Science, and China Wanfang Data (up to June 1, 2017) to collect all relevant studies and explore the association of ZFAS1 expression with overall survival (OS) and LNM. The results showed that cancer patients with high ZFAS1 expression had a worse OS than those with low ZFAS1 expression (HR: 1.94, 95% confidence interval [CI]: 1.41-2.47, P < 0.001), and high ZFAS1 expression was significantly associated with LNM (OR: 2.60, 95% CI: 1.54-4.42, P < 0.001). Subgroup analysis revealed that high ZFAS1 expression was significantly related to high incidence of LNM in subgroups of sample size more than 88 (OR: 3.16, 95% CI: 2.06-4.86, P < 0.001), non-digestive system malignancies (OR: 4.05, 95% CI: 2.49-6.60, P < 0.001), and studies reported in 2017 (OR: 4.86, 95% CI: 2.67-8.84, P < 0.001) without significant heterogeneity. Further meta-regression by the covariates showed that tumor type, sample size, quality score, cut off value and publication year did not result in the inter-study heterogeneity. In conclusion, the present meta-analysis demonstrates that high ZFAS1 expression may potentially serve as a reliable biomarker for poor clinical outcome in various cancers.

Illumina MiSeq sequencing analysis of fungal diversity in stored dates.

PubMed

Al-Bulushi, Ismail M; Bani-Uraba, Muna S; Guizani, Nejib S; Al-Khusaibi, Mohammed K; Al-Sadi, Abdullah M

2017-03-27

Date palm has been a major fruit tree in the Middle East over thousands of years, especially in the Arabian Peninsula. Dates are consumed fresh (Rutab) or after partial drying and storage (Tamar) during off-season. The aim of the study was to provide in-depth analysis of fungal communities associated with the skin (outer part) and mesocarp (inner fleshy part) of stored dates (Tamar) of two cultivars (Khenizi and Burny) through the use of Illumina MiSeq sequencing. The study revealed the dominance of Ascomycota (94%) in both cultivars, followed by Chytridiomycota (4%) and Zygomycota (2%). Among the classes recovered, Eurotiomycetes, Dothideomycetes, Saccharomycetes and Sordariomycetes were the most dominant. A total of 54 fungal species were detected, with species belonging to Penicillium, Alternaria, Cladosporium and Aspergillus comprising more than 60% of the fungal reads. Some potentially mycotoxin-producing fungi were detected in stored dates, including Aspergillus flavus, A. versicolor and Penicillium citrinum, but their relative abundance was very limited (<0.5%). PerMANOVA analysis revealed the presence of insignificant differences in fungal communities between date parts or date cultivars, indicating that fungal species associated with the skin may also be detected in the mesocarp. It also indicates the possible contamination of dates from different cultivars with similar fungal species, even though if they are obtained from different areas. The analysis shows the presence of different fungal species in dates. This appears to be the first study to report 25 new fungal species in Oman and 28 new fungal species from date fruits. The study discusses the sources of fungi on dates and the presence of potentially mycotoxin producing fungi on date skin and mesocarp.

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.

PubMed

Fang, Xin; Monk, Jonathan M; Mih, Nathan; Du, Bin; Sastry, Anand V; Kavvas, Erol; Seif, Yara; Smarr, Larry; Palsson, Bernhard O

2018-06-11

Escherichia coli is considered a leading bacterial trigger of inflammatory bowel disease (IBD). E. coli isolates from IBD patients primarily belong to phylogroup B2. Previous studies have focused on broad comparative genomic analysis of E. coli B2 isolates, and identified virulence factors that allow B2 strains to reside within human intestinal mucosa. Metabolic capabilities of E. coli strains have been shown to be related to their colonization site, but remain unexplored in IBD-associated strains. In this study, we utilized pan-genome analysis and genome-scale models (GEMs) of metabolism to study metabolic capabilities of IBD-associated E. coli B2 strains. The study yielded three results: i) Pan-genome analysis of 110 E. coli strains (including 53 isolates from IBD studies) revealed discriminating metabolic genes between B2 strains and other strains; ii) Both comparative genomic analysis and GEMs suggested that B2 strains have an advantage in degrading and utilizing sugars derived from mucus glycan, and iii) GEMs revealed distinct metabolic features in B2 strains that potentially allow them to utilize energy more efficiently. For example, B2 strains lack the enzymes to degrade amadori products, but instead rely on neighboring bacteria to convert these substrates into a more readily usable and potentially less sought after product. Taken together, these results suggest that the metabolic capabilities of B2 strains vary significantly from those of other strains, enabling B2 strains to colonize intestinal mucosa.The results from this study motivate a broad experimental assessment of the nutritional effects on E. coli B2 pathophysiology in IBD patients.

Surface potential driven dissolution phenomena of [0 0 0 1]-oriented ZnO nanorods grown from ZnO and Pt seed layers

NASA Astrophysics Data System (ADS)

Seo, Youngmi; Kim, Jung Hyeun

2011-06-01

Highly oriented ZnO nanorods are synthesized hydrothermally on ZnO and Pt seed layers, and they are dissolved in KOH solution. The rods grown on ZnO seed layer show uniform dissolution, but those grown on Pt seed layer are rod-selectively dissolved. The ZnO nanorods from both seed layers show the same crystalline structure through XRD and Raman spectrometer data. However, the surface potential analysis reveals big difference for ZnO and Pt seed cases. The surface potential distribution is very uniform for the ZnO seed case, but it is much fluctuated on the Pt seed case. It suggests that the rod-selective dissolution phenomena on Pt seed case are likely due to the surface energy difference.

Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions.

PubMed

Wachsmuth, Leah M; Johnson, Meredith G; Gavenonis, Jason

2017-06-01

Parasitic diseases caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania are an urgent public health crisis in the developing world. These closely related species possess a number of multimeric enzymes in highly conserved pathways involved in vital functions, such as redox homeostasis and nucleotide synthesis. Computational alanine scanning of these protein-protein interfaces has revealed a host of potentially ligandable sites on several established and emerging anti-parasitic drug targets. Analysis of interfaces with multiple clustered hotspots has suggested several potentially inhibitable protein-protein interactions that may have been overlooked by previous large-scale analyses focusing solely on secondary structure. These protein-protein interactions provide a promising lead for the development of new peptide and macrocycle inhibitors of these enzymes.

Proteasome inhibitory, antioxidant, and synergistic antibacterial and anticandidal activity of green biosynthesized magnetic Fe3O4 nanoparticles using the aqueous extract of corn (Zea mays L.) ear leaves.

PubMed

Patra, Jayanta Kumar; Ali, Md Sarafat; Oh, In-Gyung; Baek, Kwang-Hyun

2017-03-01

Herein, Fe 3 O 4 nanoparticles synthesized using aqueous extract of corn ear leaves were investigated for proteasome inhibitory activity, antioxidant activity, synergistic antibacterial, and anticandidal potential. The UV-Vis spectrum displayed an absorption band at 355 nm that indicated the formation of nano-sized Fe 3 O 4 particles. Vibrating sample magnetometer analysis revealed its superparamagnetic nature. Fe 3 O 4 nanoparticles exhibited strong proteasome inhibitory potential and antioxidant activity and exerted strong synergistic antibacterial and anticandidal activity. Its significant proteasome inhibitory potential could be useful in cancer treatment and drug delivery. Furthermore, strong antioxidant, antibacterial, and anticandidal activity make them a promising candidate for biomedical and pharmaceutical applications.

Diatomite silica nanoparticles for drug delivery

NASA Astrophysics Data System (ADS)

Ruggiero, Immacolata; Terracciano, Monica; Martucci, Nicola M.; De Stefano, Luca; Migliaccio, Nunzia; Tatè, Rosarita; Rendina, Ivo; Arcari, Paolo; Lamberti, Annalisa; Rea, Ilaria

2014-07-01

Diatomite is a natural fossil material of sedimentary origin, constituted by fragments of diatom siliceous skeletons. In this preliminary work, the properties of diatomite nanoparticles as potential system for the delivery of drugs in cancer cells were exploited. A purification procedure, based on thermal treatments in strong acid solutions, was used to remove inorganic and organic impurities from diatomite and to make them a safe material for medical applications. The micrometric diatomite powder was reduced in nanoparticles by mechanical crushing, sonication, and filtering. Morphological analysis performed by dynamic light scattering and transmission electron microscopy reveals a particles size included between 100 and 300 nm. Diatomite nanoparticles were functionalized by 3-aminopropyltriethoxysilane and labeled by tetramethylrhodamine isothiocyanate. Different concentrations of chemically modified nanoparticles were incubated with cancer cells and confocal microscopy was performed. Imaging analysis showed an efficient cellular uptake and homogeneous distribution of nanoparticles in cytoplasm and nucleus, thus suggesting their potentiality as nanocarriers for drug delivery.

Thermokinetic analysis and product characterization of Medium Density Fiberboard pyrolysis.

PubMed

Aslan, Dilan Irmak; Özoğul, Buğçe; Ceylan, Selim; Geyikçi, Feza

2018-06-01

This study investigates the pyrolysis of Medium Density Fiberboard (MDF) as a potential waste management solution. Thermal behaviour of MDF was analysed via TG/DSC. The primary decomposition step occurred between 190 °C and 425 °C. Evolved gaseous products over this step were evaluated by a FTIR spectrometer coupled with TGA. Peaks for phenolic, alcohols and aldehydes were detected at the maximum decomposition temperature. Py-GC/MS analysis revealed phenols, ketones and cyclic compounds as the primary non-condensable pyrolysis products. The kinetics of pyrolysis were investigated by the widely applied Distributed Activation Energy Model, resulting in an average activation energy and pre-exponential factor of 127.40 kJ mol -1 and 8.4E+11. The results of this study suggest that pyrolyzing MDF could potentially provide renewable fuels and prevent environmental problems related with MDF disposal. Copyright © 2018 Elsevier Ltd. All rights reserved.

Synthesis of Some Benzofuran Derivatives Containing Pyrimidine Moiety as Potent Antimicrobial Agents.

PubMed

Venkatesh, Talavara; Bodke, Yadav Dasharathrao; Joy, Muthipeedika Nibin; Dhananjaya, Bhadrapura Lakkappa; Venkataraman, Sivaramakrishnan

2018-01-01

In this investigation, the synthesis of 2-substituted pyrimidines by the reaction of benzofuran chalcones (3a-d) with urea, thiourea and guanidine hydrochloride was reported. The structures of title compounds (4a-d), (5a-d) and (6a-d) were established on the basis of analytical and spectral data. The synthesized compounds were screened for antimicrobial activity and molecular docking studies. Some of the compounds displayed excellent antimicrobial activity. The molecular docking analysis revealed that compounds 5a and 5c with the lowest binding energy in comparison to others suggesting its potential as best inhibitor of GluN-6-P. Consequently, it is confirmed from the above analysis that the compounds 5a and 5c might serve as a useful backbone scaffold for rational design, adaptation and investigation of more active analogs as potential broad spectrum antimicrobial agents.

Analysis of Improved Nutritional Composition of Potential Functional Food (Okara) after Probiotic Solid-State Fermentation.

PubMed

Gupta, Sulagna; Lee, Jaslyn J L; Chen, Wei Ning

2018-05-30

Okara is a major agro-waste, generated as a byproduct from the soymilk and tofu industry. Since okara has a high nutritive value, reusing it as a substrate for solid state biofermentation is an economical and environmental friendly option. Rhizopus oligosporus and Lactobacillus plantarum were the probiotic FDA-approved food-grade cultures used in this study. The study revealed that biofermenting okara improves its nutritional composition. It was found that the metabolomic composition (by GC-MS analysis) and antioxidant activity (by DPPH test) improved after the microbial fermentations. Of the two, okara fermented with R. oligosporus showed better results. Further, the metabolites were traced back to their respective biosynthesis pathways, in order to understand the biochemical reactions being triggered during the fermentation processes. The findings of this entire work open up the possibility of employing fermented okara as a potential functional food for animal feed.

A spatial analysis of population dynamics and climate change in Africa: potential vulnerability hot spots emerge where precipitation declines and demographic pressures coincide

USGS Publications Warehouse

López-Carr, David; Pricope, Narcisa G.; Aukema, Juliann E.; Jankowska, Marta M.; Funk, Christopher C.; Husak, Gregory J.; Michaelsen, Joel C.

2014-01-01

We present an integrative measure of exposure and sensitivity components of vulnerability to climatic and demographic change for the African continent in order to identify “hot spots” of high potential population vulnerability. Getis-Ord Gi* spatial clustering analyses reveal statistically significant locations of spatio-temporal precipitation decline coinciding with high population density and increase. Statistically significant areas are evident, particularly across central, southern, and eastern Africa. The highly populated Lake Victoria basin emerges as a particularly salient hot spot. People located in the regions highlighted in this analysis suffer exceptionally high exposure to negative climate change impacts (as populations increase on lands with decreasing rainfall). Results may help inform further hot spot mapping and related research on demographic vulnerabilities to climate change. Results may also inform more suitable geographical targeting of policy interventions across the continent.

Assessment of Culturable Tea Rhizobacteria Isolated from Tea Estates of Assam, India for Growth Promotion in Commercial Tea Cultivars

PubMed Central

Dutta, Jintu; Handique, Pratap J.; Thakur, Debajit

2015-01-01

In the present study, 217 rhizobacterial isolates were obtained from six different tea estates of Assam, India and subjected to preliminary in vitro plant growth promotion (PGP) screening for indole acetic acid (IAA) production, phosphate solubilization, siderophore production and ammonia production. Fifty isolates showed all the PGP traits and five isolates did not exhibit any PGP traits. These 50 potential isolates were further analyzed for quantitative estimation of the PGP traits along with the aminocyclopropane-1-carboxylate (ACC) deaminase, protease and cellulose production. After several rounds of screening, four rhizobacteria were selected based on their maximum ability to produce in vitro PGP traits and their partial 16S rRNA gene sequence analysis revealed that they belong to Enterobacter lignolyticus strain TG1, Burkholderia sp. stain TT6, Bacillus pseudomycoides strain SN29 and Pseudomonas aeruginosa strain KH45. To evaluate the efficacy of these four rhizobacteria as plant growth promoters, three different commercially important tea clones TV1, TV19, and TV20 plants were inoculated with these rhizobacteria in greenhouse condition and compared to the uninoculated control plants. Though, all the rhizobacterial treatments showed an increase in plant growth compared to control but the multivariate PCA analysis confirmed more growth promotion by TG1 and SN29 strains than the other treatments in all three clones. To validate this result, the fold change analysis was performed and it revealed that the tea clone TV19 plants inoculated with the E. lignolyticus strain TG1 showed maximum root biomass production with an increase in 4.3-fold, shoot biomass with increase in 3.1-fold, root length by 2.2-fold and shoot length by 1.6-fold. Moreover, two way ANOVA analysis also revealed that rhizobacterial treatment in different tea clones showed the significant increase (P < 0.05) in growth promotion compared to the control. Thus, this study indicates that the potential of these indigenous plant growth promoting rhizobacteria isolates to use as microbial inoculation or biofertilizer for growth promotion of tea crops. PMID:26617590

Genome-wide copy number analysis reveals candidate gene loci that confer susceptibility to high-grade prostate cancer.

PubMed

Poniah, Prevathe; Mohd Zain, Shamsul; Abdul Razack, Azad Hassan; Kuppusamy, Shanggar; Karuppayah, Shankar; Sian Eng, Hooi; Mohamed, Zahurin

2017-09-01

Two key issues in prostate cancer (PCa) that demand attention currently are the need for a more precise and minimally invasive screening test owing to the inaccuracy of prostate-specific antigen and differential diagnosis to distinguish advanced vs. indolent cancers. This continues to pose a tremendous challenge in diagnosis and prognosis of PCa and could potentially lead to overdiagnosis and overtreatment complications. Copy number variations (CNVs) in the human genome have been linked to various carcinomas including PCa. Detection of these variants may improve clinical treatment as well as an understanding of the pathobiology underlying this complex disease. To this end, we undertook a pilot genome-wide CNV analysis approach in 36 subjects (18 patients with high-grade PCa and 18 controls that were matched by age and ethnicity) in search of more accurate biomarkers that could potentially explain susceptibility toward high-grade PCa. We conducted this study using the array comparative genomic hybridization technique. Array results were validated in 92 independent samples (46 high-grade PCa, 23 benign prostatic hyperplasia, and 23 healthy controls) using polymerase chain reaction-based copy number counting method. A total of 314 CNV regions were found to be unique to PCa subjects in this cohort (P<0.05). A log 2 ratio-based copy number analysis revealed 5 putative rare or novel CNV loci or both associated with susceptibility to PCa. The CNV gain regions were 1q21.3, 15q15, 7p12.1, and a novel CNV in PCa 12q23.1, harboring ARNT, THBS1, SLC5A8, and DDC genes that are crucial in the p53 and cancer pathways. A CNV loss and deletion event was observed at 8p11.21, which contains the SFRP1 gene from the Wnt signaling pathway. Cross-comparison analysis with genes associated to PCa revealed significant CNVs involved in biological processes that elicit cancer pathogenesis via cytokine production and endothelial cell proliferation. In conclusion, we postulated that the CNVs identified in this study could provide an insight into the development of advanced PCa. Copyright © 2017 Elsevier Inc. All rights reserved.

Global threat to agriculture from invasive species.

PubMed

Paini, Dean R; Sheppard, Andy W; Cook, David C; De Barro, Paul J; Worner, Susan P; Thomas, Matthew B

2016-07-05

Invasive species present significant threats to global agriculture, although how the magnitude and distribution of the threats vary between countries and regions remains unclear. Here, we present an analysis of almost 1,300 known invasive insect pests and pathogens, calculating the total potential cost of these species invading each of 124 countries of the world, as well as determining which countries present the greatest threat to the rest of the world given their trading partners and incumbent pool of invasive species. We find that countries vary in terms of potential threat from invasive species and also their role as potential sources, with apparently similar countries sometimes varying markedly depending on specifics of agricultural commodities and trade patterns. Overall, the biggest agricultural producers (China and the United States) could experience the greatest absolute cost from further species invasions. However, developing countries, in particular, Sub-Saharan African countries, appear most vulnerable in relative terms. Furthermore, China and the United States represent the greatest potential sources of invasive species for the rest of the world. The analysis reveals considerable scope for ongoing redistribution of known invasive pests and highlights the need for international cooperation to slow their spread.

Global threat to agriculture from invasive species

PubMed Central

Paini, Dean R.; Sheppard, Andy W.; Cook, David C.; De Barro, Paul J.; Worner, Susan P.; Thomas, Matthew B.

2016-01-01

Invasive species present significant threats to global agriculture, although how the magnitude and distribution of the threats vary between countries and regions remains unclear. Here, we present an analysis of almost 1,300 known invasive insect pests and pathogens, calculating the total potential cost of these species invading each of 124 countries of the world, as well as determining which countries present the greatest threat to the rest of the world given their trading partners and incumbent pool of invasive species. We find that countries vary in terms of potential threat from invasive species and also their role as potential sources, with apparently similar countries sometimes varying markedly depending on specifics of agricultural commodities and trade patterns. Overall, the biggest agricultural producers (China and the United States) could experience the greatest absolute cost from further species invasions. However, developing countries, in particular, Sub-Saharan African countries, appear most vulnerable in relative terms. Furthermore, China and the United States represent the greatest potential sources of invasive species for the rest of the world. The analysis reveals considerable scope for ongoing redistribution of known invasive pests and highlights the need for international cooperation to slow their spread. PMID:27325781

Evaluation of biological and male reproductive-function responses to potential lead exposures in 155-mm-howitzer crewmen. Technical report, Jul 90-Dec 91

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

Weyandt, T.B.

1992-01-01

A collaborative pilot study between the U.S. Army Biomedical Research and Development Laboratory and the National Institute for Occupational Safety and Health was designed to assess the fecundity of male artillery soldiers with potential exposures to airborne lead aerosols. Many soldiers in the initial control population reported possible job-related microwave exposure as radar equipment operators. As a result, a third group of soldiers without potential for lead or microwave exposure, but with similar duty-associated environmental exposure conditions, was selected as a comparison population. Blood hormone levels and semen analyses were conducted on artillerymen (n=30), radar equipment operators (n=20), and themore » comparison group (n=31). Analysis of the questionnaire information revealed that concern about fertility problems motivated participation of some soldiers with potential artillery or microwave exposures. Data analysis was complicated by the small study population size and the confounding variable of perceived infertility. Although the small number of subjects and infertility concerns somewhat compromise the statistical power and general applicability of the study, several statistically significant findings were identified.« less

Intrinsic potential for immediate biodegradation of toluene in a pristine, energy-limited aquifer.

PubMed

Herzyk, Agnieszka; Maloszewski, Piotr; Qiu, Shiran; Elsner, Martin; Griebler, Christian

2014-06-01

Pristine and energy-limited aquifers are considered to have a low resistance and resilience towards organic pollution. An experiment in an indoor aquifer system revealed an unexpected high intrinsic potential for the attenuation of a short-term toluene contamination. A 30 h pulse of 486 mg of toluene, used as a model contaminant, and deuterated water (D2O) through an initially pristine, oxic, and organic carbon poor sandy aquifer revealed an immediate aerobic toluene degradation potential. Based on contaminant and tracer break-through curves, as well as mass balance analyses and reactive transport modelling, a contaminant removal of 40 % over a transport distance of only 4.2 m in less than one week of travel time was obtained. The mean first-order degradation rate constant was λ = 0.178 day(-1), corresponding to a half-life time constant T1/2 of 3.87 days. Toluene-specific stable carbon isotope analysis independently proved that the contaminant mass removal can be attributed to microbial biodegradation. Since average doubling times of indigenous bacterial communities were in the range of months to years, the aerobic biodegradation potential observed is assumed to be present and active in the pristine, energy-limited groundwater ecosystems at any time. Follow-up experiments and field studies will help to quantify the immediate natural attenuation potential of aquifers for selected priority contaminants and will try to identify the key-degraders within the autochthonous microbial communities.

Electroosmotic flow of Phan-Thien-Tanner fluids at high zeta potentials: An exact analytical solution

NASA Astrophysics Data System (ADS)

Sarma, Rajkumar; Deka, Nabajit; Sarma, Kuldeep; Mondal, Pranab Kumar

2018-06-01

We present a mathematical model to study the electroosmotic flow of a viscoelastic fluid in a parallel plate microchannel with a high zeta potential, taking hydrodynamic slippage at the walls into account in the underlying analysis. We use the simplified Phan-Thien-Tanner (s-PTT) constitutive relationships to describe the rheological behavior of the viscoelastic fluid, while Navier's slip law is employed to model the interfacial hydrodynamic slip. Here, we derive analytical solutions for the potential distribution, flow velocity, and volumetric flow rate based on the complete Poisson-Boltzmann equation (without considering the frequently used Debye-Hückel linear approximation). For the underlying electrokinetic transport, this investigation primarily reveals the influence of fluid rheology, wall zeta potential as modulated by the interfacial electrochemistry and interfacial slip on the velocity distribution, volumetric flow rate, and fluid stress, as well as the apparent viscosity. We show that combined with the viscoelasticity of the fluid, a higher wall zeta potential and slip coefficient lead to a phenomenal enhancement in the volumetric flow rate. We believe that this analysis, besides providing a deep theoretical insight to interpret the transport process, will also serve as a fundamental design tool for microfluidic devices/systems under electrokinetic influence.

Tentacle Transcriptome and Venom Proteome of the Pacific Sea Nettle, Chrysaora fuscescens (Cnidaria: Scyphozoa)

PubMed Central

Ponce, Dalia; Brinkman, Diane L.; Potriquet, Jeremy; Mulvenna, Jason

2016-01-01

Jellyfish venoms are rich sources of toxins designed to capture prey or deter predators, but they can also elicit harmful effects in humans. In this study, an integrated transcriptomic and proteomic approach was used to identify putative toxins and their potential role in the venom of the scyphozoan jellyfish Chrysaora fuscescens. A de novo tentacle transcriptome, containing more than 23,000 contigs, was constructed and used in proteomic analysis of C. fuscescens venom to identify potential toxins. From a total of 163 proteins identified in the venom proteome, 27 were classified as putative toxins and grouped into six protein families: proteinases, venom allergens, C-type lectins, pore-forming toxins, glycoside hydrolases and enzyme inhibitors. Other putative toxins identified in the transcriptome, but not the proteome, included additional proteinases as well as lipases and deoxyribonucleases. Sequence analysis also revealed the presence of ShKT domains in two putative venom proteins from the proteome and an additional 15 from the transcriptome, suggesting potential ion channel blockade or modulatory activities. Comparison of these potential toxins to those from other cnidarians provided insight into their possible roles in C. fuscescens venom and an overview of the diversity of potential toxin families in cnidarian venoms. PMID:27058558

Extract of Vernonia condensata, Inhibits Tumor Progression and Improves Survival of Tumor-allograft Bearing Mouse

PubMed Central

Thomas, Elizabeth; Gopalakrishnan, Vidya; Somasagara, Ranganatha R.; Choudhary, Bibha; Raghavan, Sathees C.

2016-01-01

Medicinal plants are considered as one of the ideal sources for cancer therapy due to their bioactive contents and low toxicity to humans. Vernonia genus is one of the common medicinal plants, which has wide spread usage in food and medicine. However, there are limited studies to explore its anticancer properties. In the current study, we have used Vernonia condensata, to explore its anticancer activity using various approaches. Here, we show that extract prepared from Vernonia condensata (VCE) exhibits cytotoxic properties against various cancer cells in a dose- and time-dependent manner. Interestingly, when treated with VCE, there was no significant cytotoxicity in peripheral blood mononuclear cells (PBMCs). Flow cytometry analysis revealed that although VCE induced cell death, arrest was not observed. VCE treatment led to disruption of mitochondrial membrane potential in a concentration dependent manner resulting in activation of apoptosis culminating in cell death. Immunoblotting studies revealed that VCE activated intrinsic pathway of apoptosis. More importantly, VCE treatment resulted in tumor regression leading to significant enhancement in life span in treated mice, without showing any detectable side effects. Therefore, for the first time our study reveals the potential of extract from Vernonia condensata to be used as an anticancer agent. PMID:27009490

Identification and structural characterization of a new pro-apoptotic cyclic octapeptide cyclosaplin from somatic seedlings of Santalum album L.

PubMed

Mishra, Abheepsa; Gauri, Samiran S; Mukhopadhyay, Sourav K; Chatterjee, Soumya; Das, Shibendu S; Mandal, Santi M; Dey, Satyahari

2014-04-01

Small cyclic peptides exhibiting potent biological activity have great potential for anticancer therapy. An antiproliferative cyclic octapeptide, cyclosaplin was purified from somatic seedlings of Santalum album L. (sandalwood) using gel filtration and RP-HPLC separation process. The molecular mass of purified peptide was found to be 858 Da and the sequence was determined by MALDI-ToF-PSD-MS as 'RLGDGCTR' (cyclic). The cytotoxic activity of the peptide was tested against human breast cancer (MDA-MB-231) cell line in a dose and time-dependent manner. The purified peptide exhibited significant antiproliferative activity with an IC50 2.06 μg/mL. In a mechanistic approach, apoptosis was observed in differential microscopic studies for peptide treated MDA-MB-231 cells, which was further confirmed by mitochondrial membrane potential, DNA fragmentation assay, cell cycle analysis and caspase 3 activities. The modeling and docking experiments revealed strong affinity (kcal/mol) of peptide toward EGFR and procaspase 3. The co-localization studies revealed that the peptide sensitizes MDA-MB-231 cells by possibly binding to EGFR and induces apoptosis. This unique cyclic octapeptide revealed to be a favorable candidate for development of anticancer agents. Copyright © 2014 Elsevier Inc. All rights reserved.

Exploring Powered Wheelchair Users and Their Caregivers’ Perspectives on Potential Intelligent Power Wheelchair Use: A Qualitative Study

PubMed Central

Kairy, Dahlia; Rushton, Paula W.; Archambault, Philippe; Pituch, Evelina; Torkia, Caryne; El Fathi, Anas; Stone, Paula; Routhier, François; Forget, Robert; Demers, Louise; Pineau, Joelle; Gourdeau, Richard

2014-01-01

Power wheelchairs (PWCs) can have a positive impact on user well-being, self-esteem, pain, activity and participation. Newly developed intelligent power wheelchairs (IPWs), allowing autonomous or collaboratively-controlled navigation, could enhance mobility of individuals not able to use, or having difficulty using, standard PWCs. The objective of this study was to explore the perspectives of PWC users (PWUs) and their caregivers regarding if and how IPWs could impact on current challenges faced by PWUs, as well as inform current development of IPWs. A qualitative exploratory study using individual interviews was conducted with PWUs (n = 12) and caregivers (n = 4). A semi-structured interview guide and video were used to facilitate informed discussion regarding IPWs. Thematic analysis revealed three main themes: (1) “challenging situations that may be overcome by an IPW” described how the IPW features of obstacle avoidance, path following, and target following could alleviate PWUs’ identified mobility difficulties; (2) “cautious optimism concerning IPW use revealed participants” addresses concerns regarding using an IPW as well as technological suggestions; (3) “defining the potential IPW user” revealed characteristics of PWUs that would benefit from IPW use. Findings indicate how IPW use may help overcome PWC difficulties and confirm the importance of user input in the ongoing development of IPWs. PMID:24566051

Acid transformation of bauxite residue: Conversion of its alkaline characteristics.

PubMed

Kong, Xiangfeng; Li, Meng; Xue, Shengguo; Hartley, William; Chen, Chengrong; Wu, Chuan; Li, Xiaofei; Li, Yiwei

2017-02-15

Bauxite residue (BR) is a highly alkaline solid hazardous waste produced from bauxite processing for alumina production. Alkaline transformation appears to reduce the environmental risk of bauxite residue disposal areas (BRDAs) whilst potentially providing opportunities for the sustainable reuse and on-going management of BR. Mineral acids, a novel citric acid and a hybrid combination of acid-gypsum treatments were investigated for their potential to reduce residue pH and total alkalinity and transform the alkaline mineral phase. XRD results revealed that with the exception of andradite, the primary alkaline solid phases of cancrinite, grossular and calcite were transformed into discriminative products based on the transformation used. Supernatants separated from BR and transformed bauxite residue (TBR) displayed distinct changes in soluble Na, Ca and Al, and a reduction in pH and total alkalinity. SEM images suggest that mineral acid transformations promote macro-aggregate formation, and the positive promotion of citric acid, confirming the removal or reduction in soluble and exchangeable Na. NEXAFS analysis of Na K-edge revealed that the chemical speciation of Na in TBRs was consistent with BR. Three acid treatments and gypsum combination had no effect on Na speciation, which affects the distribution of Na revealed by sodium STXM imaging. Copyright © 2016 Elsevier B.V. All rights reserved.

Exploring powered wheelchair users and their caregivers' perspectives on potential intelligent power wheelchair use: a qualitative study.

PubMed

Kairy, Dahlia; Rushton, Paula W; Archambault, Philippe; Pituch, Evelina; Torkia, Caryne; El Fathi, Anas; Stone, Paula; Routhier, François; Forget, Robert; Demers, Louise; Pineau, Joelle; Gourdeau, Richard

2014-02-21

Power wheelchairs (PWCs) can have a positive impact on user well-being, self-esteem, pain, activity and participation. Newly developed intelligent power wheelchairs (IPWs), allowing autonomous or collaboratively-controlled navigation, could enhance mobility of individuals not able to use, or having difficulty using, standard PWCs. The objective of this study was to explore the perspectives of PWC users (PWUs) and their caregivers regarding if and how IPWs could impact on current challenges faced by PWUs, as well as inform current development of IPWs. A qualitative exploratory study using individual interviews was conducted with PWUs (n = 12) and caregivers (n = 4). A semi-structured interview guide and video were used to facilitate informed discussion regarding IPWs. Thematic analysis revealed three main themes: (1) "challenging situations that may be overcome by an IPW" described how the IPW features of obstacle avoidance, path following, and target following could alleviate PWUs' identified mobility difficulties; (2) "cautious optimism concerning IPW use revealed participants" addresses concerns regarding using an IPW as well as technological suggestions; (3) "defining the potential IPW user" revealed characteristics of PWUs that would benefit from IPW use. Findings indicate how IPW use may help overcome PWC difficulties and confirm the importance of user input in the ongoing development of IPWs.

Synchrotron-radiation-based X-ray micro-computed tomography reveals dental bur debris under dental composite restorations.

PubMed

Hedayat, Assem; Nagy, Nicole; Packota, Garnet; Monteith, Judy; Allen, Darcy; Wysokinski, Tomasz; Zhu, Ning

2016-05-01

Dental burs are used extensively in dentistry to mechanically prepare tooth structures for restorations (fillings), yet little has been reported on the bur debris left behind in the teeth, and whether it poses potential health risks to patients. Here it is aimed to image dental bur debris under dental fillings, and allude to the potential health hazards that can be caused by this debris when left in direct contact with the biological surroundings, specifically when the debris is made of a non-biocompatible material. Non-destructive micro-computed tomography using the BioMedical Imaging & Therapy facility 05ID-2 beamline at the Canadian Light Source was pursued at 50 keV and at a pixel size of 4 µm to image dental bur fragments under a composite resin dental filling. The bur's cutting edges that produced the fragment were also chemically analyzed. The technique revealed dental bur fragments of different sizes in different locations on the floor of the prepared surface of the teeth and under the filling, which places them in direct contact with the dentinal tubules and the dentinal fluid circulating within them. Dispersive X-ray spectroscopy elemental analysis of the dental bur edges revealed that the fragments are made of tungsten carbide-cobalt, which is bio-incompatible.

Molecular Inversion Probe Analysis of Gene Copy Alterations Reveals Distinct Categories of Colorectal Carcinoma

PubMed Central

Ji, Hanlee; Kumm, Jochen; Zhang, Michael; Farnam, Kyle; Salari, Keyan; Faham, Malek; Ford, James M.; Davis, Ronald W.

2006-01-01

Genomic instability is a major feature of neoplastic development in colorectal carcinoma and other cancers. Specific genomic instability events, such as deletions in chromosomes and other alterations in gene copy number, have potential utility as biologically relevant prognostic biomarkers. For example, genomic deletions on chromosome arm 18q are an indicator of colorectal carcinoma behavior and potentially useful as a prognostic indicator. Adapting a novel genomic technology called molecular inversion probes which can determine gene copy alterations, such as genomic deletions, we designed a set of probes to interrogate several hundred individual exons of >200 cancer genes with an overall distribution covering all chromosome arms. In addition, >100 probes were designed in close proximity of microsatellite markers on chromosome arm 18q. We analyzed a set of colorectal carcinoma cell lines and primary colorectal tumor samples for gene copy alterations and deletion mutations in exons. Based on clustering analysis, we distinguished the different categories of genomic instability among the colorectal cancer cell lines. Our analysis of primary tumors uncovered several distinct categories of colorectal carcinoma, each with specific patterns of 18q deletions and deletion mutations in specific genes. This finding has potential clinical ramifications given the application of 18q loss of heterozygosity events as a potential indicator for adjuvant treatment in stage II colorectal carcinoma. PMID:16912164

Comment on 'Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets' by Lam et al.

PubMed

Hill, W David

2018-04-01

Intelligence and educational attainment are strongly genetically correlated. This relationship can be exploited by Multi-Trait Analysis of GWAS (MTAG) to add power to Genome-wide Association Studies (GWAS) of intelligence. MTAG allows the user to meta-analyze GWASs of different phenotypes, based on their genetic correlations, to identify association's specific to the trait of choice. An MTAG analysis using GWAS data sets on intelligence and education was conducted by Lam et al. (2017). Lam et al. (2017) reported 70 loci that they described as 'trait specific' to intelligence. This article examines whether the analysis conducted by Lam et al. (2017) has resulted in genetic information about a phenotype that is more similar to education than intelligence.

An application of statistics to comparative metagenomics

PubMed Central

Rodriguez-Brito, Beltran; Rohwer, Forest; Edwards, Robert A

2006-01-01

Background Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments. Results Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified. Conclusion The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems. PMID:16549025

An application of statistics to comparative metagenomics.

PubMed

Rodriguez-Brito, Beltran; Rohwer, Forest; Edwards, Robert A

2006-03-20

Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments. Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified. The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.

Geothermal Play-Fairway Analysis of the Tatun Volcano Group, Taiwan

NASA Astrophysics Data System (ADS)

Chen, Yan-Ru; Song, Sheng-Rong

2017-04-01

Geothermal energy is a sustainable and low-emission energy resource. It has the advantage of low-cost and withstanding nature hazards. Taiwan is located on the western Ring of Fire and characteristic of widespread hot spring and high surface heat flows, especially on the north of Taiwan. Many previous studies reveal that the Tatun Volcano Group (TVG) has great potential to develop the geothermal energy. However, investment in geothermal development has inherent risk and how to reduce the exploration risk is the most important. The exploration risk can be lowered by using the play-fairway analysis (PFA) that integrates existing data representing the composite risk segments in the region in order to define the exploration strategy. As a result, this study has adapted this logic for geothermal exploration in TVG. There are two necessary factors in geothermal energy, heat and permeability. They are the composite risk segments for geothermal play-fairway analysis. This study analyzes existing geologic, geophysical and geochemical data to construct the heat and permeability potential models. Heat potential model is based on temperature gradient, temperature of hot spring, proximity to hot spring, hydrothermal alteration zones, helium isotope ratios, and magnetics. Permeability potential model is based on fault zone, minor fault, and micro-earthquake activities. Then, these two potential models are weighted by using the Analytical Hierarchy Process (AHP) and combined to rank geothermal favorability. Uncertainty model is occurred by the quality of data and spatial accuracy of data. The goal is to combine the potential model with the uncertainty model as a risk map to find the best drilling site for geothermal exploration in TVG. Integrated results indicate where geothermal potential is the highest and provide the best information for those who want to develop the geothermal exploration in TVG.

Disruption of TCA Cycle and Glutamate Metabolism Identified by Metabolomics in an In Vitro Model of Amyotrophic Lateral Sclerosis.

PubMed

Veyrat-Durebex, Charlotte; Corcia, Philippe; Piver, Eric; Devos, David; Dangoumau, Audrey; Gouel, Flore; Vourc'h, Patrick; Emond, Patrick; Laumonnier, Frédéric; Nadal-Desbarats, Lydie; Gordon, Paul H; Andres, Christian R; Blasco, Hélène

2016-12-01

This study aims to develop a cellular metabolomics model that reproduces the pathophysiological conditions found in amyotrophic lateral sclerosis in order to improve knowledge of disease physiology. We used a co-culture model combining the motor neuron-like cell line NSC-34 and the astrocyte clone C8-D1A, with each over-expressing wild-type or G93C mutant human SOD1, to examine amyotrophic lateral sclerosis (ALS) physiology. We focused on the effects of mutant human SOD1 as well as oxidative stress induced by menadione on intracellular metabolism using a metabolomics approach through gas chromatography coupled with mass spectrometry (GC-MS) analysis. Preliminary non-supervised analysis by Principal Component Analysis (PCA) revealed that cell type, genetic environment, and time of culture influenced the metabolomics profiles. Supervised analysis using orthogonal partial least squares discriminant analysis (OPLS-DA) on data from intracellular metabolomics profiles of SOD1 G93C co-cultures produced metabolites involved in glutamate metabolism and the tricarboxylic acid cycle (TCA) cycle. This study revealed the feasibility of using a metabolomics approach in a cellular model of ALS. We identified potential disruption of the TCA cycle and glutamate metabolism under oxidative stress, which is consistent with prior research in the disease. Analysis of metabolic alterations in an in vitro model is a novel approach to investigation of disease physiology.

Potential proinflammatory effects of hydroxyapatite nanoparticles on endothelial cells in a monocyte–endothelial cell coculture model

PubMed Central

Liu, Xin; Sun, Jiao

2014-01-01

Currently, synthetic hydroxyapatite nanoparticles (HANPs) are used in nanomedicine fields. The delivery of nanomedicine to the bloodstream exposes the cardiovascular system to a potential threat. However, the possible adverse cardiovascular effects of HANPs remain unclear. Current observations using coculture models of endothelial cells and monocytes with HANPs to mimic the complex physiological functionality of the vascular system demonstrate that monocytes could play an important role in the mechanisms of endothelium dysfunction induced by the exposure to HANPs. Our transmission electron microscopy analysis revealed that both monocytes and endothelial cells could take up HANPs. Moreover, our findings demonstrated that at a subcytotoxic dose, HANPs alone did not cause direct endothelial cell injury, but they did induce an indirect activation of endothelial cells, resulting in increased interleukin-6 production and elevated adhesion molecule expression after coculture with monocytes. The potential proinflammatory effect of HANPs is largely mediated by the release of soluble factors from the activated monocytes, leading to an inflammatory response of the endothelium, which is possibly dependent on p38/c-Jun N-terminal kinase, and nuclear factor-kappa B signaling activation. The use of in vitro monocyte–endothelial cell coculture models for the biocompatibility assessment of HANPs could reveal their potential proinflammatory effects on endothelial cells, suggesting that exposure to HANPs possibly increases the risk of cardiovascular disease. PMID:24648726

Functional Movement ScreenTM and history of injury in assessment of potential risk of injury among team handball players.

PubMed

Slodownik, Robert; Ogonowska-Slodownik, Anna; Morgulec-Adamowicz, Natalia

2017-09-29

Handball is known to be one of the team sports representing the highest risk of injury. Several investigators have tried to identify injury risk factors in team sports including handball and suggested the need to develop an optimal tool to capture and quantify the potential risk of injury. The aim of the study was to evaluate potential risk of injury among handball players. It was a mixed design study. Handball players from 1st and 2nd division were evaluated (n = 30) using the Functional Movement ScreenTM (FMSTM). Additionally, self-reported history of injury was collected during FMSTM evaluation and after 6 months. Competitive level, training experience, playing position, anthropometric features, symmetry of movement patterns and history of previous injury were analysed while assessing the potential risk of injury. Significant difference between the right and left side (upper limb) was revealed for Shoulder Mobility Test (U = 308.5, p = 0.014). Odds Ratio analysis revealed that having previous injury in the last 12 months is the only statistically significant injury risk factor (OR = 13.71, p = 0.02). Based on this study we can assume that previous injury history reports are crucial in predicting injuries. FMSTM can help in identifying a typical adaptation in throwing shoulder among handball players, but should not be used alone to assess injury risk.

An integrative systems genetics approach reveals potential causal genes and pathways related to obesity.

PubMed

Kogelman, Lisette J A; Zhernakova, Daria V; Westra, Harm-Jan; Cirera, Susanna; Fredholm, Merete; Franke, Lude; Kadarmideen, Haja N

2015-10-20

Obesity is a multi-factorial health problem in which genetic factors play an important role. Limited results have been obtained in single-gene studies using either genomic or transcriptomic data. RNA sequencing technology has shown its potential in gaining accurate knowledge about the transcriptome, and may reveal novel genes affecting complex diseases. Integration of genomic and transcriptomic variation (expression quantitative trait loci [eQTL] mapping) has identified causal variants that affect complex diseases. We integrated transcriptomic data from adipose tissue and genomic data from a porcine model to investigate the mechanisms involved in obesity using a systems genetics approach. Using a selective gene expression profiling approach, we selected 36 animals based on a previously created genomic Obesity Index for RNA sequencing of subcutaneous adipose tissue. Differential expression analysis was performed using the Obesity Index as a continuous variable in a linear model. eQTL mapping was then performed to integrate 60 K porcine SNP chip data with the RNA sequencing data. Results were restricted based on genome-wide significant single nucleotide polymorphisms, detected differentially expressed genes, and previously detected co-expressed gene modules. Further data integration was performed by detecting co-expression patterns among eQTLs and integration with protein data. Differential expression analysis of RNA sequencing data revealed 458 differentially expressed genes. The eQTL mapping resulted in 987 cis-eQTLs and 73 trans-eQTLs (false discovery rate < 0.05), of which the cis-eQTLs were associated with metabolic pathways. We reduced the eQTL search space by focusing on differentially expressed and co-expressed genes and disease-associated single nucleotide polymorphisms to detect obesity-related genes and pathways. Building a co-expression network using eQTLs resulted in the detection of a module strongly associated with lipid pathways. Furthermore, we detected several obesity candidate genes, for example, ENPP1, CTSL, and ABHD12B. To our knowledge, this is the first study to perform an integrated genomics and transcriptomics (eQTL) study using, and modeling, genomic and subcutaneous adipose tissue RNA sequencing data on obesity in a porcine model. We detected several pathways and potential causal genes for obesity. Further validation and investigation may reveal their exact function and association with obesity.

In silico analysis of the polygalacturonase inhibiting protein 1 from apple, Malus domestica.

PubMed

Matsaunyane, Lerato Bt; Oelofse, Dean; Dubery, Ian A

2015-03-11

The Malus domestica polygalacturonase inhibiting protein 1 (MdPGIP1) gene, encoding the M. domestica polygalacturonase inhibiting protein 1 (MdPGIP1), was isolated from the Granny Smith apple cultivar (GenBank accession no. DQ185063). The gene was used to transform tobacco and potato for enhanced resistance against fungal diseases. Analysis of the MdPGIP1 nucleotide sequence revealed that the gene comprises 993 nucleotides that encode a 330 amino acid polypeptide. In silico characterization of the MdPGIP1 polypeptide revealed domains typical of PGIP proteins, which include a 24 amino acid putative signal peptide, a potential cleavage site [Alanine-Leucine-Serine (ALS)] for the signal peptide, a 238 amino acid leucine-rich repeat (LRR) domain, a 46 amino acid N-terminal domain and a 22 amino acid C-terminal domain. The hydropathic evaluation of MdPGIP1 indicated a repetitive hydrophobic motif in the LRR domain and a hydrophilic surface area consistent with a globular protein. The typical consensus glycosylation sequence of Asn-X-Ser/Thr was identified in MdPGIP1, indicating potential N-linked glycosylation of MdPGIP1. The molecular mass of non-glycosylated MdPGIP1 was calculated as 36.615 kDa and the theoretical isoelectric point as 6.98. Furthermore, the secondary and tertiary structure of MdPGIP1 was modelled, and revealed that MdPGIP1 is a curved and elongated molecule that contains sheet B1, sheet B2 and 310-helices on its LRR domain. The overall properties of the MdPGIP1 protein is similar to that of the prototypical Phaseolus vulgaris PGIP 2 (PvPGIP2), and the detected differences supported its use in biotechnological applications as an inhibitor of targeted fungal polygalacturonases (PGs).

Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River.

PubMed

Suriya, Jayaraman; Chandra Shekar, Mootapally; Nathani, Neelam Mustakali; Suganya, Thangaiyan; Bharathiraja, Subramanian; Krishnan, Muthukalingan

2017-01-01

Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. Recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the Cauvery River has significantly increased the concentration of uranium (U) and other heavy metals. To perceive the impact of uranium on bacterial diversity in Cauvery River, sediment samples collected from polluted (UP) site with 32.4 Bq/K of U concentration and control (UNP) site were scrutinized for bacterial diversity through metagenomic analysis of the V3 region of 16S rDNA by Illumina sequencing. Taxonomic assignment revealed that the unpolluted sample was dominated by Bacteroidetes (27.7 %), and Firmicutes (25.9 %), while sediment sample from the highly polluted site revealed abundance of Proteobacteria (47.5 %) followed by Bacteroidetes (22.4 %) and Firmicutes (14.6 %). Among Proteobacteria, Gammaproteobacteria was the most prevalent group followed by alpha, delta, epsilon, and beta in the uranium-polluted sample. Rare and abundant species analysis revealed that species like Idiomarina loihiensis was abundant in the pollutant sample; however, it was rare (<0.1 %) in the sample from pristine environment. Similarly, the species distribution in both the samples varied, with the bacteria potentially active in redox activity and biosorption potential dominating in the polluted sample. Outcomes of the present study demonstrated the impact of uranium and metal accumulation on the bacterial communities and further confirmed the promising candidature of specific bacterial species as bioindicators of contamination.

Circular RNA hsa_circ_0003575 regulates oxLDL induced vascular endothelial cells proliferation and angiogenesis.

PubMed

Li, Chen-Ye; Ma, Lan; Yu, Bo

2017-11-01

Circular RNAs (circRNAs) are a novel class of RNAs generated from back-splicing and characterized by covalently closed continuous loops. Recently, circRNAs have recently shown large regulation on cardiovascular system, including atherosclerosis. The present study aims to investigate the circRNA expression profile and identify their roles on vascular endothelial cells induced by oxLDL. Human circRNA microarray analysis revealed that total 943 differently expressed circRNAs were screened with 2 fold change. Hsa_circ_0003575 was validated to be significantly up-regulated in oxLDL induced HUVECs. Loss-of-function experiments indicated that hsa_circ_0003575 silencing promoted the proliferation and angiogenesis ability of HUVECs. Bioinformatics online programs predicted the potential circRNA-miRNA-mRNA network for hsa_circ_0003575. In summary, circRNA microarray analysis reveals the expression profiles of HUVECs and verifies the role of hsa_circ_0003575 on HUVECs, providing a therapeutic strategy for vascular endothelial cell injury of atherosclerosis. Copyright © 2017. Published by Elsevier Masson SAS.

Screening circular RNA related to chemotherapeutic resistance in breast cancer.

PubMed

Gao, Danfeng; Zhang, Xiufen; Liu, Beibei; Meng, Dong; Fang, Kai; Guo, Zijian; Li, Lihua

2017-09-01

We aimed to identify circular RNAs (circRNAs) associated with breast cancer chemoresistance. CircRNA microarray expression profiles were obtained from Adriamycin (ADM) resistant MCF-7 breast cancer cells (MCF-7/ADM) and parental MCF-7 cells and were validated using quantitative real-time reverse transcription PCR. The expression data were analyzed bioinformatically. We detected 3093 circRNAs and identified 18 circRNAs that are differentially expressed between MCF-7/ADM and MCF-7 cells; after validating by quantitative real-time reverse transcription PCR, we predicted the possible miRNAs and potential target genes of the seven upregulated circRNAs using TargetScan and miRanda. The bioinformatics analysis revealed several target genes related to cancer-related signaling pathways. Additionally, we discovered a regulatory role of the circ_0006528-miR-7-5p-Raf1 axis in ADM-resistant breast cancer. These results revealed that circRNAs may play a role in breast cancer chemoresistance and that hsa_circ_0006528 might be a promising candidate for further functional analysis.

Employee impact and attitude analysis for GHS implementation in Taiwan.

PubMed

Chang, Yi-Kuo; Su, Teh-Sheng; Ouyang, Yun; Tseng, Jo-Ming

2013-01-01

The employee impact and attitude analysis for GHS implementation in Taiwan was investigated in this study. An impact assessment on the new regulations or changes in regulations for government, potential costs, benefits, and the global trade in chemicals to industries and hazard communication program for workers was studied by the methods of the questionnaire design and Delphi expert method. A survey was conducted using questionnaires and taking 200 experts from government's expert database and 500 selected respondents from case company. Results from present study revealed that the barrier associated with GHS implementation is existed; it is feasible to overcome. Both experts and employees think that business entities are insufficient to test and classify chemicals on their own, and the technical guidance from the government is needed. Data analyzed by the logistic regression revealed that more hours an employee spends on education and trainings of new GHS systems; the employee thinks implementation of GHS will improve hazard awareness for transporters. The weak labeling ability affects deployment of the new GHS system.

Metagenomic and metabolomic analysis of the toxic effects of trichloroacetamide-induced gut microbiome and urine metabolome perturbations in mice.

PubMed

Zhang, Yan; Zhao, Fuzheng; Deng, Yongfeng; Zhao, Yanping; Ren, Hongqiang

2015-04-03

Disinfection byproducts (DBPs) in drinking water have been linked to various diseases, including colon, colorectal, rectal, and bladder cancer. Trichloroacetamide (TCAcAm) is an emerging nitrogenous DBP, and our previous study found that TCAcAm could induce some changes associated with host-gut microbiota co-metabolism. In this study, we used an integrated approach combining metagenomics, based on high-throughput sequencing, and metabolomics, based on nuclear magnetic resonance (NMR), to evaluate the toxic effects of TCAcAm exposure on the gut microbiome and urine metabolome. High-throughput sequencing revealed that the gut microbiome's composition and function were significantly altered after TCAcAm exposure for 90 days in Mus musculus mice. In addition, metabolomic analysis showed that a number of gut microbiota-related metabolites were dramatically perturbed in the urine of the mice. These results may provide novel insight into evaluating the health risk of environmental pollutants as well as revealing the potential mechanism of TCAcAm's toxic effects.

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

Emms, David M.; Covshoff, Sarah; Hibberd, Julian M.

C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort revealed that the set of parallel duplicated and retained genes ismore » enriched for genes that are preferentially expressed in bundle sheath cells, the cell type in which photosynthesis was activated during C4 evolution. Moreover, functional analysis of the cohort of parallel duplicated genes identified SWEET-13 as a potential key transporter in the evolution of C4 photosynthesis in grasses, and provides new insight into the mechanism of phloem loading in these C4 species.« less

Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins.

PubMed

Waks, Zeev; Weissbrod, Omer; Carmeli, Boaz; Norel, Raquel; Utro, Filippo; Goldschmidt, Yaara

2016-12-23

Compiling a comprehensive list of cancer driver genes is imperative for oncology diagnostics and drug development. While driver genes are typically discovered by analysis of tumor genomes, infrequently mutated driver genes often evade detection due to limited sample sizes. Here, we address sample size limitations by integrating tumor genomics data with a wide spectrum of gene-specific properties to search for rare drivers, functionally classify them, and detect features characteristic of driver genes. We show that our approach, CAnceR geNe similarity-based Annotator and Finder (CARNAF), enables detection of potentially novel drivers that eluded over a dozen pan-cancer/multi-tumor type studies. In particular, feature analysis reveals a highly concentrated pool of known and putative tumor suppressors among the <1% of genes that encode very large, chromatin-regulating proteins. Thus, our study highlights the need for deeper characterization of very large, epigenetic regulators in the context of cancer causality.

A cluster analysis of service utilization and incarceration among homeless youth

PubMed Central

Kort-Butler, Lisa A.; Tyler, Kimberly A.

2012-01-01

Our paper examines service usage (e.g., shelter) as well as a typology of individuals who are most likely to use groupings of services among 249 homeless youth. Our results revealed that the majority of homeless young people have used food programs (66%) and street outreach (65%) on at least one occasion within the past year. Cluster analysis of services revealed four distinct groups: (1) basic survival service use, characterized by above average shelter, food, and outreach service use, but below average on counseling, substance abuse/ mental health services, and incarceration; (2) multiple service use, which included above average use of all six services; (3) incarceration experience, characterized by above average incarceration experience, but below average use of all other five services; and (4) minimal service use, which included slightly above average use of counseling, but below average use of all other services. These findings have the potential to provide important information that may assist with targeting services to homeless youth. PMID:23017796

Novel microscopy-based screening method reveals regulators of contact-dependent intercellular transfer

PubMed Central

Michael Frei, Dominik; Hodneland, Erlend; Rios-Mondragon, Ivan; Burtey, Anne; Neumann, Beate; Bulkescher, Jutta; Schölermann, Julia; Pepperkok, Rainer; Gerdes, Hans-Hermann; Kögel, Tanja

2015-01-01

Contact-dependent intercellular transfer (codeIT) of cellular constituents can have functional consequences for recipient cells, such as enhanced survival and drug resistance. Pathogenic viruses, prions and bacteria can also utilize this mechanism to spread to adjacent cells and potentially evade immune detection. However, little is known about the molecular mechanism underlying this intercellular transfer process. Here, we present a novel microscopy-based screening method to identify regulators and cargo of codeIT. Single donor cells, carrying fluorescently labelled endocytic organelles or proteins, are co-cultured with excess acceptor cells. CodeIT is quantified by confocal microscopy and image analysis in 3D, preserving spatial information. An siRNA-based screening using this method revealed the involvement of several myosins and small GTPases as codeIT regulators. Our data indicates that cellular protrusions and tubular recycling endosomes are important for codeIT. We automated image acquisition and analysis to facilitate large-scale chemical and genetic screening efforts to identify key regulators of codeIT. PMID:26271723

Genome analysis of crude oil degrading Franconibacter pulveris strain DJ34 revealed its genetic basis for hydrocarbon degradation and survival in oil contaminated environment.

PubMed

Pal, Siddhartha; Kundu, Anirban; Banerjee, Tirtha Das; Mohapatra, Balaram; Roy, Ajoy; Manna, Riddha; Sar, Pinaki; Kazy, Sufia K

2017-10-01

Franconibacter pulveris strain DJ34, isolated from Duliajan oil fields, Assam, was characterized in terms of its taxonomic, metabolic and genomic properties. The bacterium showed utilization of diverse petroleum hydrocarbons and electron acceptors, metal resistance, and biosurfactant production. The genome (4,856,096bp) of this strain contained different genes related to the degradation of various petroleum hydrocarbons, metal transport and resistance, dissimilatory nitrate, nitrite and sulfite reduction, chemotaxy, biosurfactant synthesis, etc. Genomic comparison with other Franconibacter spp. revealed higher abundance of genes for cell motility, lipid transport and metabolism, transcription and translation in DJ34 genome. Detailed COG analysis provides deeper insights into the genomic potential of this organism for degradation and survival in oil-contaminated complex habitat. This is the first report on ecophysiology and genomic inventory of Franconibacter sp. inhabiting crude oil rich environment, which might be useful for designing the strategy for bioremediation of oil contaminated environment. Copyright © 2017 Elsevier Inc. All rights reserved.

Fault Tree Analysis.

PubMed

McElroy, Lisa M; Khorzad, Rebeca; Rowe, Theresa A; Abecassis, Zachary A; Apley, Daniel W; Barnard, Cynthia; Holl, Jane L

The purpose of this study was to use fault tree analysis to evaluate the adequacy of quality reporting programs in identifying root causes of postoperative bloodstream infection (BSI). A systematic review of the literature was used to construct a fault tree to evaluate 3 postoperative BSI reporting programs: National Surgical Quality Improvement Program (NSQIP), Centers for Medicare and Medicaid Services (CMS), and The Joint Commission (JC). The literature review revealed 699 eligible publications, 90 of which were used to create the fault tree containing 105 faults. A total of 14 identified faults are currently mandated for reporting to NSQIP, 5 to CMS, and 3 to JC; 2 or more programs require 4 identified faults. The fault tree identifies numerous contributing faults to postoperative BSI and reveals substantial variation in the requirements and ability of national quality data reporting programs to capture these potential faults. Efforts to prevent postoperative BSI require more comprehensive data collection to identify the root causes and develop high-reliability improvement strategies.

2-Furaldehyde diethyl acetal from tender coconut water (Cocos nucifera) attenuates biofilm formation and quorum sensing-mediated virulence of Chromobacterium violaceum and Pseudomonas aeruginosa.

PubMed

Sethupathy, Sivasamy; Nithya, Chari; Pandian, Shunmugiah Karutha

2015-01-01

The aim of this study was to evaluate the anti-biofilm and quorum sensing inhibitory (QSI) potential of tender coconut water (TCW) against Chromobacterium violaceum and Pseudomonas aeruginosa. TCW significantly inhibited the QS regulated violacein, virulence factors and biofilm production without affecting their growth. qRT-PCR analysis revealed the down-regulation of autoinducer synthase, transcriptional regulator and virulence genes. Mass-spectrometric analysis of a petroleum ether extract of the TCW hydrolyte revealed that 2-furaldehyde diethyl acetal (2FDA) and palmitic acid (PA) are the major compounds. In vitro bioassays confirmed the ability of 2FDA to inhibit the biofilm formation and virulence factors. In addition, the combination of PA with 2FDA resulted in potent inhibition of biofilm formation and virulence factors. The results obtained strongly suggest that TCW can be exploited as a base for designing a novel antipathogenic drug formulation to treat biofilm mediated infections caused by P. aeruginosa.

Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation

PubMed Central

Cheng, Xin-Yue; Tian, Xue-Liang; Wang, Yun-Sheng; Lin, Ren-Miao; Mao, Zhen-Chuan; Chen, Nansheng; Xie, Bing-Yan

2013-01-01

Our recent research revealed that pinewood nematode (PWN) possesses few genes encoding enzymes for degrading α-pinene, which is the main compound in pine resin. In this study, we examined the role of PWN microbiome in xenobiotics detoxification by metagenomic and bacteria culture analyses. Functional annotation of metagenomes illustrated that benzoate degradation and its related metabolisms may provide the main metabolic pathways for xenobiotics detoxification in the microbiome, which is obviously different from that in PWN that uses cytochrome P450 metabolism as the main pathway for detoxification. The metabolic pathway of degrading α-pinene is complete in microbiome, but incomplete in PWN genome. Experimental analysis demonstrated that most of tested cultivable bacteria can not only survive the stress of 0.4% α-pinene, but also utilize α-pinene as carbon source for their growth. Our results indicate that PWN and its microbiome have established a potentially mutualistic symbiotic relationship with complementary pathways in detoxification metabolism. PMID:23694939

Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators.

PubMed

Clarke, Luka A; Botelho, Hugo M; Sousa, Lisete; Falcao, Andre O; Amaral, Margarida D

2015-11-01

A meta-analysis of 13 independent microarray data sets was performed and gene expression profiles from cystic fibrosis (CF), similar disorders (COPD: chronic obstructive pulmonary disease, IPF: idiopathic pulmonary fibrosis, asthma), environmental conditions (smoking, epithelial injury), related cellular processes (epithelial differentiation/regeneration), and non-respiratory "control" conditions (schizophrenia, dieting), were compared. Similarity among differentially expressed (DE) gene lists was assessed using a permutation test, and a clustergram was constructed, identifying common gene markers. Global gene expression values were standardized using a novel approach, revealing that similarities between independent data sets run deeper than shared DE genes. Correlation of gene expression values identified putative gene regulators of the CF transmembrane conductance regulator (CFTR) gene, of potential therapeutic significance. Our study provides a novel perspective on CF epithelial gene expression in the context of other lung disorders and conditions, and highlights the contribution of differentiation/EMT and injury to gene signatures of respiratory disease. Copyright © 2015 Elsevier Inc. All rights reserved.

Mechanism for the Excited-State Multiple Proton Transfer Process of Dihydroxyanthraquinone Chromophores.

PubMed

Zhou, Qiao; Du, Can; Yang, Li; Zhao, Meiyu; Dai, Yumei; Song, Peng

2017-06-22

The single and dual cooperated proton transfer dynamic process in the excited state of 1,5-dihydroxyanthraquinone (1,5-DHAQ) was theoretically investigated, taking solvent effects (ethanol) into account. The absorption and fluorescence spectra were simulated, and dual fluorescence exhibited, which is consistent with previous experiments. Analysis of the calculated IR and Raman vibration spectra reveals that the intramolecular hydrogen bonding interactions (O 20 -H 21 ···O 24 and O 22 -H 23 ···O 25 ) are strengthened following the excited proton transfer process. Finally, by constructing the potential energy surfaces of the ground state, first excited singlet state, and triplet state, the mechanism of the intramolecular proton transfer of 1,5-DHAQ can be revealed.

Fundamentals of negative refractive index optical trapping: forces and radiation pressures exerted by focused Gaussian beams using the generalized Lorenz-Mie theory

PubMed Central

Ambrosio, Leonardo A.; Hernández-Figueroa, Hugo E.

2010-01-01

Based on the generalized Lorenz-Mie theory (GLMT), this paper reveals, for the first time in the literature, the principal characteristics of the optical forces and radiation pressure cross-sections exerted on homogeneous, linear, isotropic and spherical hypothetical negative refractive index (NRI) particles under the influence of focused Gaussian beams in the Mie regime. Starting with ray optics considerations, the analysis is then extended through calculating the Mie coefficients and the beam-shape coefficients for incident focused Gaussian beams. Results reveal new and interesting trapping properties which are not observed for commonly positive refractive index particles and, in this way, new potential applications in biomedical optics can be devised. PMID:21258549