bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevotella copri, a potential indicator for high feed efficiency in western steers
Authors: Brooke Charles G. , Najafi Negeen , Dykier Katherine C. , Hess Matthias 
Published: October 2018

AbstractThere has been a great interest to identify a microbial marker that can be used to predict feed efficiency of beef cattle. Such a marker, specifically one that would allow an early identification of animals with high feed efficiency for future breeding efforts, would facilitate increasing the profitability of cattle operations and simultaneously render them more sustainable by reducing their methane footprint. The work presented here suggests that Prevotella copri might be an ideal microbial marker for identifying beef cattle with high feed efficiency early in their life span and in the production cycle. Developing more refined quantification techniques that allow correlation of P. copri to feed efficiency of beef cattle that can be applied by lay people in the field holds great promise to improve the economy of cattle operations while simultaneously reducing their environmental impact by mitigating methane production from enteric fermentation.
Zika Virus Subverts Stress Granules to Promote and Restrict Viral Gene Expression
Authors: Bonenfant Gaston , Williams Nina , Netzband Rachel , Schwarz Megan C. , Evans Matthew J. , Pager Cara T. 
Published: October 2018

AbstractFlaviviruses limit the cell stress response by preventing the formation of stress granules and modulate viral gene expression by subverting different proteins involved in the stress granule pathway. In this study, we investigated the formation of stress granules during Zika virus (ZIKV) infection and the role stress granule proteins play during the viral life cycle. Using immunofluorescence and confocal microscopy, we determined that ZIKV disrupted the formation of arsenite-induced stress granules and changed the subcellular distribution, but not the abundance or integrity, of stress granule proteins. We also investigated the role of different stress granule proteins in ZIKV infection by using target-specific siRNAs to deplete Ataxin2, G3BP1, HuR, TIA-1, TIAR and YB1. Knock-down of TIA-1 and TIAR affected ZIKV protein and RNA levels, but not viral titers. Conversely, depletion of Ataxin2 and YB1 decreased virion production despite having only a small effect on ZIKV protein expression. Notably, however, depletion of G3BP1 and HuR decreased and increased ZIKV gene expression and virion production, respectively. Using an MR766Gaussialuciferase reporter genome together with knockdown and overexpression assays, G3BP1 and HuR were found to modulate ZIKV replication. These data indicate that ZIKV disrupts the formation of stress granules by sequestering stress granule proteins required for replication, where G3BP1 functions to promote ZIKV infection, while HuR exhibits an antiviral effect. The consequence of ZIKV re-localizing and subverting select stress granule proteins might have broader consequences on cellular RNA homeostasis and contribute to cellular gene dysregulation and ZIKV pathogenesis.ImportanceMany viruses inhibit stress granules (SGs). In this study, we observed that ZIKV restricts SG assembly likely by re-localizing and subverting specific SG proteins to modulate ZIKV replication. This ZIKV-SG protein interaction is interesting, as many SG proteins are also known to function in neuronal granules, which are critical in neural development and function. Moreover, dysregulation of different SG proteins in neurons has been shown to play a role in the progression of neurodegenerative diseases. The likely consequences of ZIKV modulating SG assembly and subverting specific SG proteins are alterations to cellular mRNA transcription, splicing, stability, and translation. Such changes in cellular ribostasis could profoundly affect neural development and contribute to the devastating developmental and neurological anomalies observed following intrauterine ZIKV infection. Our study provides new insights into virus-host interactions and the identification of the SG proteins that may contribute to the unusual pathogenesis associated with this re-emerging arbovirus.
Longitudinal plasma metabolomics of aging and sex
Authors: Darst Burcu F. , Koscik Rebecca L. , Hogan Kirk J. , Johnson Sterling C. , Engelman Corinne D. 
Published: October 2018

AbstractUnderstanding how metabolites are longitudinally influenced by age and sex could facilitate the identification of metabolomic profiles and trajectories that indicate disease risk. We investigated the metabolomics of age and sex using longitudinal plasma samples from the Wisconsin Registry for Alzheimer’s Prevention (WRAP), a cohort of participants who were dementia free at enrollment. Metabolomic profiles were quantified for 2,316 fasting plasma samples among 1,187 participants, each with up to three study visits. Of 1,097 metabolites tested, 608 (55.4%) were associated with age and 680 (62.0%) with sex after correcting for multiple testing. Approximately twice as many metabolites were associated with age in stratified analyses of women versus men, and 63 metabolite trajectories significantly differed by sex, most notably including sphingolipids, which tended to increase in women and decrease in men with age. Using genome-wide genotyping, we also report the heritabilities of metabolites investigated, which ranged dramatically (0.2-99.2%); however, the median heritability of 36.2% suggests that many metabolites are highly influenced by a complex combination of genomic and environmental influences. These findings offer a more profound description of the aging process and may inform many new hypotheses regarding the role metabolites play in healthy and accelerated aging.
Deep Convolutional Network for Animal Sound Classification and Source Attribution using Dual Audio Recordings
Authors: Oikarinen Tuomas , Srinivasan Karthik , Meisner Olivia , Hyman Julia B. , Parmar Shivangi , Desimone Robert , Landman Rogier , Feng Guoping 
Published: October 2018

ABSTRACTWe introduce an end-to-end feedforward convolutional neural network that is able to reliably classify the source and type of animal calls in a noisy environment using two streams of audio data after being trained on a dataset of modest size and imperfect labels. The data consists of audio recordings from captive marmoset monkeys housed in pairs, with several other cages nearby. Our network can classify both the call type and which animal made it with a single pass through a single network using raw spectrogram images as input. The network vastly increases data analysis capacity for researchers interested in studying marmoset vocalizations, and allows data collection in the home cage, in group housed animals.
Combining Gene Ontology with Deep Neural Networks to Enhance the Clustering of Single Cell RNA-Seq Data
Authors: Peng Jiajie , Wang Xiaoyu , Shang Xuequn 
Published: October 2018

AbstractBackgroundSingle cell RNA sequencing (scRNA-seq) is applied to assay the individual transcriptomes of large numbers of cells. The gene expression at single-cell level provides an opportunity for better understanding of cell function and new discoveries in biomedical areas. To ensure that the single-cell based gene expression data are interpreted appropriately, it is crucial to develop new computational methods.ResultsIn this article, we try to construct the structure of neural networks based on the prior knowledge of Gene Ontology (GO). By integrating GO with both unsupervised and supervised models, two novel methods are proposed, named GOAE (Gene Ontology AutoEncoder) and GONN (Gene Ontology Neural Network) respectively, for clustering of scRNA-seq data.ConclusionsThe evaluation results show that the proposed models outperform some state-of-the-art approaches. Furthermore, incorporating with GO, we provide an opportunity to interpret the underlying biological mechanism behind the neural network-based model.
FT/FD-GRF5 repression loop directs growth to increase soybean yield
Authors: Xu Kun , Zhang Xiao-Mei , Yu Guolong , Lu Mingyang , Liu Chunyan , Chen Haifeng , Zhu Jinlong , Chen Fulu , Cheng Zhiyuan , Huang Penghui , Zhou Xinan , Chen Qingshan , Feng Xianzhong , Miao Yuchen , Liu Liangyu , Searle Iain , Fu Yong-Fu 
Published: October 2018

AbstractMajor advances in crop yield are eternally needed to cope with population growth. To balance vegetative and reproductive growth plays an important role in agricultural yield. To extend vegetative phase can increase crop yield, however, this strategy risks loss of yield in the field as crops may not mature in time before winter come. Here, we identified a repression feedback loop between GmFTL/GmFDL and GmGRF5-1 (Glycine-max-Flowering-Locus-T/Glycine-max-FDL and Glycine-max-GROWTH-REGULATING-FACTOR5-1), which functions as a pivotal regulator in balancing vegetative and reproductive phases in soybean. GmFTL/GmFDL and GmGRF5-1 directly repress gene expression each other. Additionally, GmGRF5-1 enhances vegetative growth by directly enhancing expression of photosynthesis- and auxin synthesis-related genes. To modulate the loop, such as fine-tuning GmFTL expression to trade-off vegetative and reproductive growth, increases substantially soybean yield in the field. Our findings not only uncover the mechanism balancing vegetative and reproductive growth, but open a new window to improve crop yield.
A Novel Denitrification Regulator, Adr, Mediates Denitrification Under Aerobic Conditions inSinorhizobium meliloti
Authors: Slape Coreen M. , Patankar Arati V. , GonzáLez Juan E. 
Published: October 2018

AbstractSinorhizobium melilotiis a soil dwelling bacteria capable of forming a symbiotic relationship with several legume hosts. Once symbiosis is established,S. melilotifixes atmospheric nitrogen into nitrogenated compounds, thus carrying out an important step in the nitrogen cycle.S. melilotiis also capable of the reverse process, denitrification, the reduction of nitrate and nitrite to nitrogen gas. In this study we have identified a novel regulator of denitrification inS. meliloti, Adr, which affects the expression of the denitrification genes in aerobically grown cultures. Analysis of the Adr sequence reveals a LuxR-like quorum sensing regulator, however, it does not respond to the known quorum sensing signals produced byS. meliloti. Additionally, we show that FixJ, the major regulator of denitrification and microaerobic respiration inS. meliloti, is active under our growth conditions. Comparison of the FixJ microarray to our Adr microarray shows a significant overlap between the two regulons. We also show that while Adr is not necessary for symbiotic nitrogen fixation, a functional copy of this regulator confers a competitive advantage toS. melilotiduring host invasion. Our findings suggest that Adr is a new type of denitrification regulator and that it acts at the same regulatory level as FixJ.ImportanceRhizobia contribute to the nitrogen cycle by fixing atmospheric nitrogen to nitrogenated compounds and by denitrification, the reduction nitrate and nitrite to nitrogen gas. Denitrification enhances the survival ofSinorhizobium melilotiin the various environments it may encounter, such as free-living conditions in the rhizosphere, during invasion of the plant host, and after a symbiotic relationship has been established. Oxygen concentration is the typical signal for denitrification gene expression. Recent studies of low oxygen cultures ofS. melilotihave outlined the regulation structure for denitrification. In this study, we examine the regulation of denitrification in aerobically grownS. meliloticultures. Understanding howS. melilotiresponds to various oxygen concentrations will result in a more complete picture of denitrification regulation in this agriculturally important organism and the impact of denitrification on the soil microbiome as a whole.
Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs
Authors: Gómez-Godínez Lorena Jacqueline , Ormeño-Orrillo Ernesto , Martínez-Romero Esperanza 
Published: October 2018

ABSTRACTThe free-living soil bacteria that are beneficial for the growth of plants are known as plant growth-promoting rhizobacteria (PGPR). In this work, a multi-species of PGPR bacteria inoculant was designed, which included nitrogen-fixing strains such as Rhizobium phaseoli, Sinorhizobium americanum and Azospirillum brasilense, as well as other plant growth promoting bacteria such as Bacillus subtillis and Methylobacterium extorquens. The multi-species community exerted a beneficial effect on plant seedlings when it was inoculated, greater than the effect observed when inoculating each bacteria individually. Acetylene reduction of maize roots was recorded with the multi-species inoculant, which suggests that nitrogen fixation occurred under these conditions. To analyze the contributions of the different nitrogen-fixing bacteria that were inoculated, a metatranscriptomic analysis was performed. The differential expression analysis revealed that the predominantly nif transcripts of Azospirillum are overexpressed, suggesting that it was responsible for nitrogen fixation in maize. Overall, we analyzed the interaction of a synthetic community, suggesting it as an option, for future formulations of biofertilizers.IMPORTANCEWhile nodulation processes and nitrogen fixation by rhizobia have been well studied, little is known about the interaction between rhizobia and non-leguminous plants such as maize, which is used as a model for this study. Nitrogen fixation in cereals is a long searched goal. Instead of single species inoculants, multi-species inoculation may be more efficient to promote plant growth and fix nitrogen. Metatrascriptomes allowed us to recognize the bacteria responsible for nitrogen fixation in plant rootlets. The study of the function of certain genes may help to understand how microorganisms interact with the root plant, as well as allow a better use of microorganisms for the generation of novel biofertilizers using microbial consortia.
A statistical simulator scDesign for rational scRNA-seq experimental design
Authors: Li Wei Vivian , Li Jingyi Jessica 
Published: October 2018

AbstractMotivationSingle-cell RNA-sequencing (scRNA-seq) has revolutionized biological sciences by revealing genome-wide gene expression levels within individual cells. However, a critical challenge faced by researchers is how to optimize the choices of sequencing platforms, sequencing depths, and cell numbers in designing scRNA-seq experiments, so as to balance the exploration of the depth and breadth of transcriptome information.ResultsHere we present a flexible and robust simulator, scDesign, the first statistical framework for researchers to quantitatively assess practical scRNA-seq experimental design in the context of differential gene expression analysis. In addition to experimental design, scDesign also assists computational method development by generating high-quality synthetic scRNA-seq datasets under customized experimental settings. In an evaluation based on 17 cell types and six different protocols, scDesign outperformed four state-of-the-art scRNA-seq simulation methods and led to rational experimental design. In addition, scDesign demonstrates reproducibility across biological replicates and independent studies. We also discuss the performance of multiple differential expression and dimension reduction methods based on the protocol-dependent scRNA-seq data generated by scDesign. scDesign is expected to be an effective bioinformatic tool that assists rational scRNA-seq experiment design based on specific research goals and compares various scRNA-seq computational methods.AvailabilityWe have implemented our method in the R package scDesign, which is freely available at https://github.com/Vivianstats/scDesign.Contactjli@stat.ucla.edu
Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird
Authors: Kim Kang-Wook , Jackson Benjamin C. , Zhang Hanyuan , Toews David P. L. , Taylor Scott A. , Greig Emma I. , Lovette Irby J. , Liu Mengning M. , Davison Angus , Griffith Simon C. , Zeng Kai , Burke Terry 
Published: October 2018

AbstractColour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finchErythrura gouldiaethat is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region forfollistatin, an antagonist of theTGF-βsuperfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.
IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization
Authors: Kang Kyuho , Park Sung Ho , Kang Keunsoo , Ivashkiv Lionel B. 
Published: October 2018

AbstractComplete polarization of macrophages towards an M1-like proinflammatory and antimicrobial state requires combined action of IFN-γ and LPS. Synergistic activation of canonical inflammatory NF-κB target genes by IFN-γ and LPS is well appreciated, but less is known about whether IFN-γ negatively regulates components of the LPS response, and how this affects polarization. A combined transcriptomic and epigenomic approach revealed that IFN-γ selectively abrogates LPS-induced feedback and select metabolic pathways by suppressing TLR4-mediated activation of gene enhancers. In contrast to superinduction of inflammatory genesviaenhancers that harbor IRF sequences and bind STAT1, IFN-γ-mediated repression targeted enhancers with STAT sequences that bound STAT3. TLR4-activated IFN-γ-suppressed enhancers comprised two subsets distinguished by differential regulation of histone acetylation and recruitment of STAT3, CDK8 and cohesin, and were functionally inactivated by IFN-γ. These findings reveal that IFN-γ suppresses feedback inhibitory and metabolic components of the TLR response to achieve full M1 polarization, and provide insights into mechanisms by which IFN-γ selectively inhibits TLR4-induced transcription.
Reporter Ion Data Analysis Reduction (R.I.D.A.R) for isobaric proteomics quantification studies
Authors: Jenkins Conor , Norris Alexis L. , O’Neill Maura , Das Sudipto , Andresson Thorkell , Orsburn Ben 
Published: October 2018

AbstractIsobaric labeling-based relative quantification techniques such as iTRAQ and TMT were introduced 15 years ago and are now nearly ubiquitous in shotgun proteomics labs around the world. The methods for data processing in these experiments has changed little since inception, with peptide database searching of all MS/MS spectra occurring concurrent or asynchronous to the quantification of the reporter fragment regions. In this study we present an alternative method for data processing whereby the reporter ion region of all MS/MS spectra are first examined and spectra that are not quantitatively interesting to the end user are discarded. The remaining MS/MS spectra that are retained can then be more rapidly searched for computationally expensive database alterations such as post-translational modifications and single amino acid variations in more practical time. We have termed this method Reporter Ion Data Analysis Reduction (RIDAR). To demonstrate the application of RIDAR, we reprocess a recent CPTAC 2 study containing approximately 7.8 million MS/MS spectra. Post RIDAR processing we can search this public dataset versus a human canonical FASTA database and a compiled proteogenomic database of over 875,000 known cancer mutations in a single day on a standard desktop computer, a time reduction of 85% compared to the conventional workflow. With the rapidly increasing size and density of shotgun proteomics data files, RIDAR facilitates rapid analysis of large proteomics datasets for researchers without access to high performance computational resources.Abstract Graphic
Single-cell virus sequencing of influenza infections that trigger innate immunity
Authors: Russell Alistair B. , Kowalsky Jacob R. , Bloom Jesse D. 
Published: October 2018

SUMMARYThe outcome of viral infection is extremely heterogeneous, with infected cells only sometimes activating innate immunity. Here we develop a new approach to assess how the genetic variation inherent in viral populations contributes to this heterogeneity. We do this by determining both the transcriptome and full-length sequences of all viral genes in single influenza-infected cells. Most cells are infected by virions with defects such as amino-acid mutations, internal deletions, or failure to express a gene. We identify instances of each type of defect that increase the likelihood that a cell activates an innate-immune response. However, immune activation remains stochastic in cells infected by virions with these defects, and sometimes occurs even when a cell is infected by a virion that expresses unmutated copies of all genes. Our work shows that viral genetic variation substantially contributes to but does not fully explain the heterogeneity in single influenza-infected cells.
GrgA as a potential target of selective antichlamydials
Authors: Zhang Huirong , Vellappan Sangeevan , Tang M. Matt , Bao Xiaofeng , Fan Huizhou 
Published: October 2018

ABSTRACTChlamydiais a common pathogen that can causes serious complications in the reproductive system and eyes. Lack of vaccine and other effective prophylactic measures coupled with the largely asymptomatic nature and unrare clinical treatment failure calls for development of new antichlamydials, particularly selective antichlamydials without adverse effects on humans and the beneficial microbiota. We previously reported that benzal-N-acylhydrazones (BAH) can inhibit chlamydiae without detectable adverse effects on host cells and beneficial lactobacilli that dominate the human vaginal microbiota among reproductive-age women. However, the antichlamydial mechanism of BAH is not known. Whereas 4 single nucleotide polymorphisms (i.e., SNP1-4) were identified in a rareChlamydiavariant with a low level of BAH resistance, termed MCR, previous studies failed to establish a causal effect of any particular SNP(s). In the present work, we performed recombination to segregate the four SNPs. Susceptibility tests indicate that the R51G GrgA allele is both necessary and sufficient for the low level of BAH resistance. Thus, theChlamydia-specific transcription factor GrgA either is a direct target of BAH or regulates BAH susceptibility. We further confirm an extremely low rate of BAH resistance inChlamydia. Our findings warrant exploration of GrgA as a therapeutic and prophylactic target for chlamydial infections.