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https://www.readbyqxmd.com/read/27919242/reducing-child-abuse-amongst-adolescents-in-low-and-middle-income-countries-a-pre-post-trial-in-south-africa
#1
Lucie Cluver, Franziska Meinck, Alexa Yakubovich, Jenny Doubt, Alice Redfern, Catherine Ward, Nasteha Salah, Sachin De Stone, Tshiamo Petersen, Phelisa Mpimpilashe, Rocio Herrero Romero, Lulu Ncobo, Jamie Lachman, Sibongile Tsoanyane, Yulia Shenderovich, Heidi Loening, Jasmina Byrne, Lorraine Sherr, Lauren Kaplan, Frances Gardner
BACKGROUND: No known studies have tested the effectiveness of child abuse prevention programmes for adolescents in low- or middle-income countries. 'Parenting for Lifelong Health' ( http://tiny.cc/whoPLH ) is a collaborative project to develop and rigorously test abuse-prevention parenting programmes for free use in low-resource contexts. Research aims of this first pre-post trial in South Africa were: i) to identify indicative effects of the programme on child abuse and related outcomes; ii) to investigate programme safety for testing in a future randomised trial, and iii) to identify potential adaptations...
July 13, 2016: BMC Public Health
https://www.readbyqxmd.com/read/27918579/a-graph-centric-approach-for-metagenome-guided-peptide-and-protein-identification-in-metaproteomics
#2
Haixu Tang, Sujun Li, Yuzhen Ye
Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27912021/grazers-structure-the-bacterial-and-algal-diversity-of-aquatic-metacommunities
#3
Julia Birtel, Blake Matthews
Consumers can have strong effects on the biotic and abiotic dynamics of spatially-structured ecosystems. In metacommunities, dispersing consumers can alter local assembly dynamics either directly through trophic interactions or indirectly by modifying local environmental conditions. In aquatic systems, very little is known about how key grazers, such as Daphnia, structure the microbial diversity of metacommunities and influence bacterial-mediated ecosystem functions. In an outdoor mesocosm experiment with replicate metacommunities (two 300 L mesocosms), we tested how the presence and absence of Daphnia and the initial density of the microbial community (manipulated via dilution) influenced the diversity and community structure of algae and bacteria, and several ecosystem properties (e...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911736/the-multiple-assemblies-of-vdac-from-conformational-heterogeneity-to-%C3%AE-aggregation-and-amyloid-formation
#4
REVIEW
Alexandre Boulbrima, Davina Temple, Georgios Psakis
From their cellular localisation, to their atomic structure and their involvement in mitochondrial-driven cell death, voltage-dependent anion channels (VDACs) have challenged the scientific community with enigmas and paradoxes for over four decades. VDACs form active monomer channels in lipid bilayers, but they can also organise in multimeric assemblies. What induces, regulates and/or controls the monomer-multimer dynamics at the cellular level is not known. However, these state transitions appear to be relevant for mitochondria in making life or death decisions and for driving developmental processes...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27909817/phylogenetic-structure-of-arbuscular-mycorrhizal-fungal-communities-along-an-elevation-gradient
#5
Cameron P Egan, Ragan M Callaway, Miranda M Hart, Jason Pither, John Klironomos
Despite the importance of arbuscular mycorrhizal (AM) fungi within terrestrial ecosystems, we know little about how natural AM fungal communities are structured. To date, the majority of studies examining AM fungal community diversity have focused on single habitats with similar environmental conditions, with relatively few studies having assessed the diversity of AM fungi over large-scale environmental gradients. In this study, we characterized AM fungal communities in the soil along a high-elevation gradient in the North American Rocky Mountains...
December 1, 2016: Mycorrhiza
https://www.readbyqxmd.com/read/27907259/spectral-diversity-area-relationships-for-assessing-biodiversity-in-a%C3%A2-wildland-agriculture-matrix
#6
Kyla Marie Dahlin
Species-area relationships have long been used to assess patterns of species diversity across scales. Here, this concept is extended to spectral diversity using hyperspectral data collected by NASA's Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over western Michigan. This mixture of mesic forest and agricultural lands offers two end-points on the local-scale diversity continuum; one set of well-mixed forest patches and one set of highly homogeneous agricultural patches. Using the sum of the first three principal component values and the principal components' convex hull volume, spectral diversity was compared within and among these plots and to null expectations for perfectly random and perfectly patchy landscapes...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27905533/five-key-attributes-can-increase-marine-protected-areas-performance-for-small-scale-fisheries-management
#7
Antonio Di Franco, Pierre Thiriet, Giuseppe Di Carlo, Charalampos Dimitriadis, Patrice Francour, Nicolas L Gutiérrez, Alain Jeudy de Grissac, Drosos Koutsoubas, Marco Milazzo, María Del Mar Otero, Catherine Piante, Jeremiah Plass-Johnson, Susana Sainz-Trapaga, Luca Santarossa, Sergi Tudela, Paolo Guidetti
Marine protected areas (MPAs) have largely proven to be effective tools for conserving marine ecosystem, while socio-economic benefits generated by MPAs to fisheries are still under debate. Many MPAs embed a no-take zone, aiming to preserve natural populations and ecosystems, within a buffer zone where potentially sustainable activities are allowed. Small-scale fisheries (SSF) within buffer zones can be highly beneficial by promoting local socio-economies. However, guidelines to successfully manage SSFs within MPAs, ensuring both conservation and fisheries goals, and reaching a win-win scenario, are largely unavailable...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902806/orthology-guided-transcriptome-assembly-of-italian-ryegrass-and-meadow-fescue-for-single-nucleotide-polymorphism-discovery
#8
Štěpán Stočes, Tom Ruttink, Jan Bartoš, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, Isabel Roldán-Ruiz, Tomasz Książczyk, Elodie Rey, Jaroslav Doležel, David Kopecký
Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and map-based cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue ( Huds.) and Italian ryegrass ( Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902365/the-oral-cavities-of-healthy-infants-harbor-high-proportions-of-streptococcus-salivarius-strains-with-phenotypic-and-genotypic-resistance-to-multiple-classes-of-antibiotics
#9
Thaís H Palma, Erika Harth-Chú, Jodie Scott, Rafael N Stipp, Heike Boisvert, Mariana F Salomão, Jéssica D Theobaldo, Rosana F Possobon, Leandro C Nascimento, Jonathan W McCafferty, Lina Faller, Margaret J Duncan, Renata O Mattos-Graner
Emerging antibiotic resistance in the oropharyngeal microbiota, of which Streptococcus salivarius is a prominent species, represents a challenge for treating pediatric populations. In this study, we investigated the role of S. salivarius as a reservoir for antibiotic resistance genes (ARG) in the oral microbiota by analyzing 95 S. salivarius isolates from 22 healthy infants (2 to 16 months of age). Minimum inhibitory concentrations (MIC) of penicillin G, amoxicillin, erythromycin, tetracycline, doxycycline and streptomycin were determined...
October 24, 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#10
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27899642/the-ucsc-genome-browser-database-2017-update
#11
Cath Tyner, Galt P Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clayton M Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo, Maximilian Haeussler, Steve Heitner, Angie S Hinrichs, Donna Karolchik, Brian T Lee, Christopher M Lee, Parisa Nejad, Brian J Raney, Kate R Rosenbloom, Matthew L Speir, Chris Villarreal, John Vivian, Ann S Zweig, David Haussler, Robert M Kuhn, W James Kent
Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899630/european-nucleotide-archive-in-2016
#12
Ana Luisa Toribio, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra Ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rosello, Nicole Silvester, Dmitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898054/refined-experimental-annotation-reveals-conserved-corrinoid-autotrophy-in-chloroform-respiring-dehalobacter-isolates
#13
Po-Hsiang Wang, Shuiquan Tang, Kayla Nemr, Robert Flick, Jun Yan, Radhakrishnan Mahadevan, Alexander F Yakunin, Frank E Löffler, Elizabeth A Edwards
Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional...
November 29, 2016: ISME Journal
https://www.readbyqxmd.com/read/27897341/adaptive-self-assembly-behaviour-restrained-by-supramolecular-crystallization-and-molecular-recognition
#14
Seiji Shinkai, Bappaditya Roy, Takao Noguchi, Daisuke Yoshihara, Junji Sakamoto, Tatsuhiro Yamamoto
Recently, the supramolecular community is integrating different approaches to find converging ideas towards understanding the 'origin of life'. In this report, we have found an interesting adaptation trait, as like in Darwin's theory, in a bolaamphiphile molecule and established an environment friendly behaviour under non-covalent forces leading to evolve diverse assembly structures and interesting photo-physical properties. The perylene diimide (PDI)-based bolaamphiphile is used as a promising scaffold with great potential for the development of emerging supramolecular system...
November 29, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27893703/generation-of-genome-scale-metabolic-reconstructions-for-773-members-of-the-human-gut-microbiota
#15
Stefanía Magnúsdóttir, Almut Heinken, Laura Kutt, Dmitry A Ravcheev, Eugen Bauer, Alberto Noronha, Kacy Greenhalgh, Christian Jäger, Joanna Baginska, Paul Wilmes, Ronan M T Fleming, Ines Thiele
Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria. Using this resource, we identified a defined growth medium for Bacteroides caccae ATCC 34185. We also showed that interactions among modeled species depend on both the metabolic potential of each species and the nutrients available...
November 28, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27889387/diet-microbiome-interactions-in-health-are-controlled-by-intestinal-nitrogen-source-constraints
#16
Andrew J Holmes, Yi Vee Chew, Feyza Colakoglu, John B Cliff, Eline Klaassens, Mark N Read, Samantha M Solon-Biet, Aisling C McMahon, Victoria C Cogger, Kari Ruohonen, David Raubenheimer, David G Le Couteur, Stephen J Simpson
Diet influences health and patterns of disease in populations. How different diets do this and why outcomes of diets vary between individuals are complex and involve interaction with the gut microbiome. A major challenge for predicting health outcomes of the host-microbiome dynamic is reconciling the effects of different aspects of diet (food composition or intake rate) on the system. Here we show that microbial community assembly is fundamentally shaped by a dichotomy in bacterial strategies to access nitrogen in the gut environment...
November 15, 2016: Cell Metabolism
https://www.readbyqxmd.com/read/27886869/frailty-and-the-prediction-of-negative-health-outcomes-a-meta-analysis
#17
REVIEW
Sofie Vermeiren, Roberta Vella-Azzopardi, David Beckwée, Ann-Katrin Habbig, Aldo Scafoglieri, Bart Jansen, Ivan Bautmans
INTRODUCTION: Frailty is one of the most important concerns regarding our aging population. Evidence grows that the syndrome is linked to several important health outcomes. A general overview of frailty concepts and a comprehensive meta-analysis of their relation with negative health outcomes still lacks in literature, making it difficult for health care professionals and researchers to recognize frailty and the related health risks on the one hand and on the other hand to appropriately follow up the frailty process and take substantiated action...
December 1, 2016: Journal of the American Medical Directors Association
https://www.readbyqxmd.com/read/27885862/an-automated-curation-procedure-for-addressing-chemical-errors-and-inconsistencies-in-public-datasets-used-in-qsar-modelling
#18
K Mansouri, C M Grulke, A M Richard, R S Judson, A J Williams
The increasing availability of large collections of chemical structures and associated experimental data provides an opportunity to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experimental data. Here we describe the development of an automated KNIME workflow to curate and correct errors in the structure and identity of chemicals using the publicly available PHYSPROP physicochemical properties and environmental fate datasets...
November 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27882551/fitness-gains-in-guppies-support-evolution-s-role-in-coexistence
#19
Kelsey Lyberger
Understanding processes that drive the assembly of communities is not a new goal in ecology; researchers have long studied what leads to the coexistence of species. However, the study of rapid evolution as a driving process of community assembly is an emerging frontier in evolutionary-ecology research. This article is protected by copyright. All rights reserved.
November 24, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27879004/plant-domestication-and-the-assembly-of-bacterial-and-fungal-communities-associated-with-strains-of-the-common-sunflower-helianthus-annuus
#20
Jonathan W Leff, Ryan C Lynch, Nolan C Kane, Noah Fierer
Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and fungal communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and fungal communities. We also assessed fungal communities in the sunflower seeds to investigate the degree to which root and rhizosphere communities were influenced by vertical transmission of the microbiome through seeds...
November 23, 2016: New Phytologist
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