bluuebunny/crossref_metadata_2025_split huggingface dataset:
AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation inPopulus tremula
Authors: Sundell David , Street Nathaniel R. , Kumar Manoj , Mellerowicz Ewa J. , Kucukoglu Melis , Johnsson Christoffer , Kumar Vikash , Mannapperuma Chanaka , Delhomme Nicolas , Nilsson Ove , Tuominen Hannele , Pesquet Edouard , Fischer Urs , Niittylä Totte , Sundberg Bjöern , Hvidsten Torgeir R. 
Published: December 2016

AbstractTrees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer new, elite varieties will benefit from an improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA Sequencing data spanning the secondary phloem, vascular cambium and wood forming tissues. The transcriptome comprised 28,294 expressed, previously annotated genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from theSalicaceaewhole genome duplication were found to have diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. Co-expression network analysis revealed that the regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. The high spatial resolution enabled identification of novel roles for characterised genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. The associated web resource (AspWood,http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the expression profiles and co-expression network.
Histone gene expression is regulated by histone H2B ubiquitylation in fission yeast
Authors: Pagé Viviane , Grabowski David , Allis C. David , Tanny Jason C. 
Published: December 2016

AbstractCell cycle-regulated expression of histone genes is vital for coordination of DNA replication with chromatin assembly. In yeast, histone genes are regulated by transcriptional activation in S phase and transcriptional repression in other phases of the cell cycle, although the mechanisms are poorly understood. Here we describe a role for histone H2B monoubiquitylation (H2Bub1), a histone mark that is linked to RNA polymerase II transcription elongation, in the activation of replication-dependent histone genes in the fission yeastSchizosaccharomyces pombe. Loss of H2Bub1 is also associated with a delay in S phase progression and reduced expression of the replication initiation factor Cdc18 (ortholog of Cdc6). We provide evidence that H2Bub1 impacts histone gene transcription and acts through a mechanism that involves the 3’UTR. Consistent with our previous finding that H2Bub1 is functionally opposed to the elongation factor Cdk9, we also find that the effects of H2Bub1 on histone genes are suppressed by reduction in the activity of Cdk9. Our data suggest that H2Bub1 promotes cell growth by activating cell cycle-regulated genes.
Variable penetrance of the 15q11.2 BP1–BP2 microduplication in a family with cognitive and language impairment
Authors: Benítez-Burraco Antonio , Barcos-Martínez Montserrat , Espejo-Portero Isabel , Jiménez-Romero Ma Salud 
Published: December 2016

ABSTRACTThe 15q11.2 BP1–BP2 region is found duplicated or deleted in people with cognitive, language, and behavioral impairment.Case presentation. We report on a family (the father and three male twin siblings) who presents with a duplication of the 15q11.2 BP1-BP2 region and a variable phenotype: whereas the father and the fraternal twin are normal carriers, the monozygotic twins exhibit severe language and cognitive delay and behavioral disturbances. The genes located within the duplicated region are involved in brain development and function, and some of them are related to language processing.Conclusions. The probands’ phenotype may result from changes in the expression level of some of these genes important for cognitive development.
Sex matters in Massive Parallel Sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems
Authors: Benestan Laura , Moore Jean-Sébastien , Sutherland Ben J. G. , Le Luyer Jérémy , Maaroufi Halim , Rougeux Clément , Normandeau Eric , Rycroft Nathan , Atema Jelle , Harris Les N. , Tallman Ross F. , Greenwood Spencer J. , Clark K. Fraser , Bernatchez Louis 
Published: December 2016

AbstractUsing massively parallel sequencing data from two species with different life history traits -- American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus) -- we highlighted how an unbalanced sex ratio in the samples combined with a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Multivariate analyses revealed two genetic clusters that separated males and females instead of showing the expected pattern of genetic differentiation among ecologically divergent (inshore vs. offshore in lobster) or geographically distant (east vs. west in Arctic Char) sampling locations. We created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups, and then demonstrated that significant genetic differentiation could be observed despite panmixia for lobster, and that Fstvalues were overestimated for Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to nonsignificant genetic structure (lobster) and a more accurate estimation of Fst(Arctic Char). We further characterized the putative functions of sex-linked markers. Given that only 9.6% of all marine/diadromous population genomic studies to date reported sex information, we urge researchers to collect and consider individual sex information. In summary, we argue that sex information is useful to (i) control sex ratio in sampling, (ii) overcome “sex-ratio bias” that can lead to spurious genetic differentiation signals and (iii) fill knowledge gaps regarding sex determining systems.
Looking at my own Face: Visual Processing Strategies in Physical Self-representation
Authors: Chakraborty Anya , Chakrabarti Bhismadev 
Published: December 2016

AbstractWe live in an age of ‘selfies’. Yet, how we look at our own faces has seldom been systematically investigated. In this study we test if visual processing of self-faces is different from other faces, using psychophysics and eye-tracking. Specifically, the association between the psychophysical properties of self-face representation and visual processing strategies involved in self-face recognition was tested. Thirty-three adults performed a self-face recognition task from a series of self-other face morphs with simultaneous eye-tracking. Participants were found to look at lower part of the face for longer duration for self-face compared to other-face. Participants with a reduced overlap between self and other face representations, as indexed by a steeper slope of the psychometric response curve for self-face recognition, spent a greater proportion of time looking at the upper regions of faces identified as self. Additionally, the association of autism-related traits with self-face processing metrics was tested, since autism has previously been associated with atypical self-processing, particularly in the psychological domain. Autistic traits were associated with reduced looking time to both self and other faces. However, no self-face specific association was noted with autistic traits, suggesting that autism-related features may be related to self-processing in a domain specific manner.
Associations of coffee genetic risk scores with coffee, tea and other beverages in the UK Biobank
Authors: Taylor Amy E. , Munafò Marcus R. 
Published: December 2016

AbstractBackgroundGenetic variants which determine amount of coffee consumed have been identified in genome-wide association studies (GWAS) of coffee consumption; these may help to further understanding of the effects of coffee on health outcomes. However, there is limited information about how these variants relate to caffeinated beverage consumption more generally.AimsTo improve phenotype definition for coffee consumption related genetic risk scores by testing their association with coffee, tea and other beverages.MethodsWe tested the associations of genetic risk scores for coffee consumption with beverage consumption in 114,316 individuals of European ancestry from the UK Biobank. Drinks were self-reported in a baseline questionnaire and in detailed 24 dietary recall questionnaires in a subset.ResultsGenetic risk scores including two and eight single nucleotide polymorphisms (SNPs) explained up to 0.39%, 0.19% and 0.77% of the variance in coffee, tea and combined coffee and tea consumption respectively. A one standard deviation increase in the 8 SNP genetic risk score was associated with a 0.13 cup per day (95% CI: 0.12, 0.14), 0.12 cup per day (95%CI: 0.11, 0.14) and 0.25 cup per day (95% CI: 0.24, 0.27) increase in coffee, tea and combined tea and coffee consumption, respectively. Genetic risk scores also demonstrated positive associations with both caffeinated and decaffeinated coffee and tea consumption. In 48,692 individuals with dietary recall data, the genetic risk scores were positively associated with coffee and tea, (apart from herbal teas) consumption, but did not show clear evidence for positive associations with other beverages. However, there was evidence that the genetic risk scores were associated with lower daily water consumption and lower overall drink consumption.ConclusionsGenetic risk scores created from variants identified in coffee consumption GWAS associate more broadly with caffeinated beverage consumption and also with decaffeinated coffee and tea consumption.
ASAP: A web-based platform for the analysis and interactive visualization of single-cell RNA-seq data
Authors: Gardeux Vincent , David Fabrice , Shajkofci Adrian , Schwalie Petra C , Deplancke Bart 
Published: December 2016

AbstractMotivationSingle-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research groups in the world, yet, these groups often lack the expertise to handle complex scRNA-seq data sets.ResultsWe developed a fully integrated, web-based platform aimed at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment. This Automated Single-cell Analysis Pipeline (ASAP) combines a wide range of commonly used algorithms with sophisticated visualization tools. Compared with existing scRNA-seq analysis platforms, researchers (including those lacking computational expertise) are able to interact with the data in a straightforward fashion and in real time. Furthermore, given the overlap between scRNA-seq and bulk RNA-seq analysis workflows, ASAP should conceptually be broadly applicable to any RNA-seq dataset. As a validation, we demonstrate how we can use ASAP to simply reproduce the results from a single-cell study of 91 mouse cells involving five distinct cell types.AvailabilityThe tool is freely available athttp://asap.epfl.chContactbart.deplancke@epfl.ch
Sequence and structural diversity of mouse Y chromosomes
Authors: Morgan Andrew P , de Villena Fernando Pardo-Manuel 
Published: December 2016

AbstractOver the 180 million years since their origin, the sex chromosomes of mammals have evolved a gene repertoire highly specialized for function in the male germline. The mouse Y chromosome is unique among mammalian Y chromosomes characterized to date in that it is large, gene-rich and euchromatic. Yet little is known about its diversity in natural populations. Here we take advantage of published whole-genome sequencing data to survey the diversity of sequence and copy number of sex-linked genes in three subspecies of house mice. Copy number of genes on the repetitive long arm of both sex chromosomes is highly variable, but sequence diversity in non-repetitive regions is decreased relative to expectations based on autosomes. We use simulations and theory to show that this reduction in sex-linked diversity is incompatible with neutral demographic processes alone, but is consistent with recent positive selection on genes active during spermatogenesis. Our results support the hypothesis that the mouse sex chromosomes are engaged in ongoing intragenomic conflict.
Quantification of subclonal selection in cancer from bulk sequencing data
Authors: Williams Marc J. , Werner Benjamin , Curtis Christina , Barnes Chris P , Sottoriva Andrea , Graham Trevor A 
Published: December 2016

AbstractRecent studies have identified prevalent subclonal architectures within many cancer types. However, the temporal evolutionary dynamics that produce these subclonal architectures remain unknown. Here we measure evolutionary dynamics in primary human cancers using computational modelling of clonal selection applied to high throughput sequencing data. Our approach simultaneously determines the subclonal architecture of a tumour sample, and measures the mutation rate, the selective advantage, and the time of appearance of subclones. Simulations demonstrate the accuracy of the method, and revealed the degree to which evolutionary dynamics are recorded in the genome. Application of our method to high-depth sequencing data from gastric and lung cancers revealed that detectable subclones consistently emerged early during tumour growth and had considerably large fitness advantages (>20% growth advantage). Our quantitative platform provides new insight into the evolutionary history of cancers by facilitating the measurement of fundamental evolutionary parameters in individual patients.
The DOE Systems Biology Knowledgebase (KBase)
Authors: Arkin Adam P , Stevens Rick L , Cottingham Robert W , Maslov Sergei , Henry Christopher S , Dehal Paramvir , Ware Doreen , Perez Fernando , Harris Nomi L , Canon Shane , Sneddon Michael W , Henderson Matthew L , Riehl William J , Gunter Dan , Murphy-Olson Dan , Chan Stephen , Kamimura Roy T , Brettin Thomas S , Meyer Folker , Chivian Dylan , Weston David J , Glass Elizabeth M , Davison Brian H , Kumari Sunita , Allen Benjamin H , Baumohl Jason , Best Aaron A , Bowen Ben , Brenner Steven E , Bun Christopher C , Chandonia John-Marc , Chia Jer-Ming , Colasanti Ric , Conrad Neal , Davis James J , DeJongh Matthew , Devoid Scott , Dietrich Emily , Drake Meghan M , Dubchak Inna , Edirisinghe Janaka N , Fang Gang , Faria José P , Frybarger Paul M , Gerlach Wolfgang , Gerstein Mark , Gurtowski James , Haun Holly L , He Fei , Jain Rashmi , Joachimiak Marcin P , Keegan Kevin P , Kondo Shinnosuke , Kumar Vivek , Land Miriam L , Mills Marissa , Novichkov Pavel , Oh Taeyun , Olsen Gary J , Olson Bob , Parrello Bruce , Pasternak Shiran , Pearson Erik , Poon Sarah S , Price Gavin A , Ramakrishnan Srividya , Ranjan Priya , Ronald Pamela C , Schatz Michael C , Seaver Samuel M D , Shukla Maulik , Sutormin Roman A , Syed Mustafa H , Thomason James , Tintle Nathan L , Wang Daifeng , Xia Fangfang , Yoo Hyunseung , Yoo Shinjae 
Published: December 2016

AbstractThe U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology — predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing infrastructure; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities that currently include genome assembly, annotation, ontology assignment, comparative genomics, transcriptomics, and metabolic modeling; (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software development kit allowing the community to add functionality to the system.
Quantitative mRNA Imaging Throughout the EntireDrosophilaBrain
Authors: Long Xi , Colonell Jennifer , Wong Allan M , Singer Robert H , Lionnet Timothée 
Published: December 2016

AbstractWe describe a fluorescence in situ hybridization method that permits detection of the localization and abundance of single mRNAs (smFISH) in cleared whole-mount adultDrosophilabrains. The approach is rapid, multiplexable and does not require molecular amplification; it allows facile mRNA expression quantification with subcellular resolution on a standard confocal microscope. Using a custom Bessel Beam-Structured Illumination microscope (BB-SIM), we further demonstrate single-mRNA detection across the entire brain sample.
Isotopic niches support the resource breadth hypothesis
Authors: Rader Jonathan A. , Newsome Seth D. , Sabat Pablo , Chesser R. Terry , Dillon Michael E. , Martínez del Rio Carlos 
Published: December 2016

SummaryBecause a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges.We investigated isotopic niche width in a small radiation of South American birds in the genusCinclodes. We analysed feathers of 12 species ofCinclodesto test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology.We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology.Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies.
Fermentation of glycerol by Anaerobium acetethylicum and its potential use in biofuel production
Authors: Patil Yogita , Junghare Madan , Müller Nicolai 
Published: December 2016

SummaryGrowth of biodiesel industries resulted in increased coproduction of crude glycerol which is therefore becoming a waste product instead of a valuable ‘coproduct’. Glycerol can be used for the production of valuable chemicals, e.g. biofuels, to reduce glycerol waste disposal. In this study, a novel bacterial strain is described which converts glycerol mainly to ethanol and hydrogen with very little amounts of acetate, formate and 1,2‐propanediol as coproducts. The bacterium offers certain advantages over previously studied glycerol‐fermenting microorganisms. Anaerobium acetethylicum during growth with glycerol produces very little side products and grows in the presence of maximum glycerol concentrations up to 1500 mM and in the complete absence of complex organic supplements such as yeast extract or tryptone. The highest observed growth rate of 0.116 h−1 is similar to that of other glycerol degraders, and the maximum concentration of ethanol that can be tolerated was found to be about 60 mM (2.8 g l−1) and further growth was likely inhibited due to ethanol toxicity. Proteome analysis as well as enzyme assays performed in cell‐free extracts demonstrated that glycerol is degraded via glyceraldehyde‐3‐phosphate, which is further metabolized through the lower part of glycolysis leading to formation of mainly ethanol and hydrogen. In conclusion, fermentation of glycerol to ethanol and hydrogen by this bacterium represents a remarkable option to add value to the biodiesel industries by utilization of surplus glycerol.
Effect of early allograft dysfunction on outcomes following liver transplantation
Authors: Hudcova Jana , Scopa Caitlin , Rashid Jawad , Waqas Ahsan , Ruthazer Robin , Schumann Roman 
Published: December 2016

AbstractEarly allograft dysfunction (EAD) following liver transplantation (LT) remains a challenge for patients and clinicians. We retrospectively analyzed the effect of pre‐defined EAD on outcomes in a 10‐year cohort of deceased‐donor LT recipients with clearly defined exclusion criteria. EAD was defined by at least one of the following: AST or ALT >2000 IU/L within first‐week post‐LT, total bilirubin ≥10 mg/dL, and/or INR ≥1.6 on post‐operative day 7. Ten patients developed primary graft failure and were analyzed separately. EAD occurred in 86 (36%) recipients in a final cohort of 239 patients. In univariate and multivariate analyses, EAD was significantly associated with mechanical ventilation ≥2 days or death on days 0, 1, PACU/SICU stay >2 days or death on days 0‐2 and renal failure (RF) at time of hospital discharge (all P<.05). EAD was also significantly associated with higher one‐year graft loss in both uni‐ and multivariate Cox hazard analyses (P=.0203 and .0248, respectively). There was no difference in patient mortality between groups in either of the Cox proportional hazard models. In conclusion, we observed significant effects of EAD on short‐term post‐LT outcomes and lower graft survival.
Plant defence induced by PGPR against Spodoptera litura in tomato (Solanum lycopersicum L.)
Authors: Bano A. , Muqarab R. 
Published: December 2016

Abstract

The research conducted including its rationale: Spodoptera litura is the major pest of tomato causing significant reduction in tomato yield. Application of Plant growth promoting rhizobacteria(PGPR) prevent use of chemical fertilizer and synthetic pesticides through enhancement of plant growth and yield and induction of systemic resistance. Present investigation is an attempt to evaluate the role of PGPR, Pseudomonas putida and Rothia sp. on the physiology and yield of tomato fruit infested with the S. litura.

Central methods applied: The surface sterilized seeds of tomato were inoculated with 48 h culture of P. putida and Rothia sp. At 6–7 branching stage of the plant, the larvae of S. litura at 2nd in star was used to infect the tomato plant leaves.

Key results: The S. litura infestation decreased dry weight of shoots and roots by 46% and 22%, and significant reduction was recorded in tomato fruit yield. The P. putida and Rothia sp. inoculations alleviated the adverse effects of insect infestation and resulted in 60% increase in plant biomass and 40% increase in yield over infested plants.

Main conclusions including key points of discussion: PGPR: Defense appears to be mediated via increase in proline production, enhanced activities of antioxidant enzymes, stimulation in the activities of protease and polyphenol oxidases, increased contents of phenolics, protein and chlorophyll. The formulation of biopesticide involving PGPR comprise an environment friendly and sustainable approach to overcome insect infestation.