bluuebunny/crossref_metadata_2025_split huggingface dataset:
The detection of covariation of mRNA levels of large sets of genes across multiple human populations
Authors: Quan Yu , Xie Chao , Williams Rohan B. H. , Little Peter F. R 
Published: December 2016

AbstractIn this study, we analyse RNA-Seq data from panels of human lymphoblastoid cell lines (LCLs) to identify covariation in the mRNA levels of large numbers of genes. Such large scale covariation may have biological origin or be due to technical variation in analysis (generally referred to as batch effects). We show that batch effects cannot explain this covariation by demonstrating reproducibility across different human populations and across different methods of analysis. This view is also supported by enrichment of single and combinations of transcription factors (TFs) binding to cognate promoter regions, enrichment of genes shown to be sensitive to the knockdown of individual TFs, enrichment of functional pathways, and finally enrichment of protein-protein interactions in proteins encoded by groups of covarying genes. The properties of the groups of covarying genes are therefore most readily explained by the influence of cumulative variations in the effectors of gene expression that act intranson cognate genes. We suggest that covariation has functional outcomes by showing that covariation of 83 genes involved in the spliceosome pathway accounts for 8–16% of the variation in the alternative splicing patterns of genes expressed in human LCLs.
Cannabis use and risk of schizophrenia: a Mendelian randomization study
Authors: Vaucher Julien , Keating Brendan J. , Lasserre Aurélie M. , Gan Wei , Lyall Donald M. , Ward Joey , Smith Daniel J. , Pell Jill P. , Sattar Naveed , Paré Guillaume , Holmes Michael V. 
Published: December 2016

ABSTRACTCannabis use is observationally associated with an increased risk of schizophrenia, however whether the relationship is causal is not known. To determine the nature of the association between cannabis use on risk of schizophrenia using Mendelian randomization (MR) analysis, we used ten genetic variants previously identified to associate with cannabis use in 32,330 individuals. Genetic variants were used in a MR analyses of the association of genetically determined cannabis on risk of schizophrenia in 34,241 cases and 45,604 controls from predominantly European descent. Estimates from MR were compared to a metaanalysis of observational studies reporting effect estimates for ever use of cannabis and risk of schizophrenia or related disorders. Genetically determined use of cannabis was associated with increased risk of schizophrenia (OR of schizophrenia for users vs. non-users of cannabis: 1.37; 95%CI, 1.09 to 1.67; P-value=0.007). The corresponding estimate from observational analysis was 1.50 (95% CI, 1.10 to 2.00; P-value for heterogeneity = 0.88). The genetic instrument did not show evidence of pleiotropy on MR-Egger (Egger test, P-value=0.292) nor on multivariable MR accounting for tobacco exposure (OR of schizophrenia for users vs. nonusers of cannabis, adjusted for ever vs. never smoker: 1.41; 95% CI, 1.09-1.83). Furthermore, the causal estimate remained robust to sensitivity analyses. These findings strongly support a causal association between genetically determined use of cannabis and risk of schizophrenia. Such robust evidence may inform public health message about the risks of cannabis use, especially regarding its potential mental health consequences.
Review: Population Structure in Genetic Studies: Confounding Factors and Mixed Models
Authors: Martin Lana S. , Eskin Eleazar 
Published: December 2016

AbstractA genome-wide association study (GWAS) seeks to identify genetic variants that contribute to the development and progression of a specific disease. Over the past 10 years, new approaches using mixed models have emerged to mitigate the deleterious effects of population structure and relatedness in association studies. However, developing GWAS techniques to effectively test for association while correcting for population structure is a computational and statistical challenge. Using laboratory mouse strains as an example, our review characterizes the problem of population structure in association studies and describes how it can cause false positive associations. We then motivate mixed models in the context of unmodeled factors.
Ras/ERK-signalling promotes tRNA synthesis and growth via the RNA polymerase III repressor Maf1 inDrosophila
Authors: Sriskanthadevan-Pirahas Shrivani , Deshpande Rujuta , Lee Byoungchun , Grewal Savraj S. 
Published: December 2016

ABSTRACTThe small G-protein Ras is a conserved regulator of cell and tissue growth. These effects of Ras are mediated largely through activation of a canonical RAF-MEK-ERK kinase cascade. An important challenge is to identify how this Ras/ERK pathway alters cellular metabolism to drive growth. Here we report on stimulation of RNA polymerase III (Pol III)-mediated tRNA synthesis as a growth effector of Ras/ERK signalling inDrosophila. We find that activation of Ras/ERK signalling promotes tRNA synthesis both in vivo and in culturedDrosophilaS2 cells. We also show that Pol III function is required for Ras/ERK signalling to drive proliferation in both epithelial and stem cells inDrosophilatissues. We find that the transcription factor Myc is required but not sufficient for Ras-mediated stimulation of tRNA synthesis. Instead we show that the main way that Ras promotes Pol III function and tRNA synthesis is by inhibiting the nuclear localization and function of the Pol III repressor Maf1. We propose that inhibition of Maf1 and stimulation of tRNA synthesis is one way by which Ras signalling enhances protein synthesis to promote cell and tissue growth.
Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing
Authors: Neparáczki Endre , Kocsy Klaudia , Tóth Gábor Endre , Maróti Zoltán , Kalmár Tibor , Bihari Péter , Nagy István , Pálfi György , Molnár Erika , Raskó István , Török Tibor 
Published: December 2016

AbstractAs part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination.
An Estradiol-Inducible Promoter Enables Fast, Graduated Control of Gene Expression in Fission Yeast
Authors: Ohira Makoto J. , Hendrickson David G. , Scott McIsaac R. , Rhind Nicholas 
Published: December 2016

ABSTRACTThe fission yeastSchizosaccharomyces pombelacks a diverse toolkit of inducible promoters for experimental manipulation. Available inducible promoters suffer from slow induction kinetics, limited control of expression levels and/or a requirement for defined growth medium. In particular, noS. pombeinducible promoter systems exhibit a linear dose response, which would allow expression to be tuned to specific levels. We have adapted a fast, orthogonal promoter system with a large dynamic range and a linear dose response, based on β-estradiol-regulated function of the human estrogen receptor, for use inS. pombe. We show that this promoter system, termed Z3EV, turns on quickly, can reach a maximal induction of 20 fold, and exhibits a linear dose response over its entire induction range, with few off target effects. We demonstrate the utility of this system by regulating the mitotic inhibitor Wee1 to create a strain in which cell size is regulated by β-estradiol concentration. This promoter system will be of great utility for experimentally regulating gene expression in fission yeast.
A synthesis of over 9,000 mass spectrometry experiments reveals the core set of human protein complexes
Authors: Drew Kevin , Lee Chanjae , Huizar Ryan L. , Tu Fan , Borgeson Blake , McWhite Claire D. , Ma Yun , Wallingford John B. , Marcotte Edward M. 
Published: December 2016

AbstractMacromolecular protein complexes carry out many of the essential functions of cells, and many genetic diseases arise from disrupting the functions of such complexes. Currently there is great interest in defining the complete set of human protein complexes, but recent published maps lack comprehensive coverage. Here, through the synthesis of over 9,000 published mass spectrometry experiments, we present hu.MAP, the most comprehensive and accurate human protein complex map to date, containing >4,600 total complexes, >7,700 proteins and >56,000 unique interactions, including thousands of confident protein interactions not identified by the original publications. hu.MAP accurately recapitulates known complexes withheld from the learning procedure, which was optimized with the aid of a new quantitative metric (k-cliques) for comparing sets of sets. The vast majority of complexes in our map are significantly enriched with literature annotations and the map overall shows improved coverage of many disease-associated proteins, as we describe in detail for ciliopathies. Using hu.MAP, we predicted and experimentally validated candidate ciliopathy disease genesin vivoin a model vertebrate, discovering CCDC138, WDR90, and KIAA1328 to be new cilia basal body/centriolar satellite proteins, and identifying ANKRD55 as a novel member of the intraflagellar transport machinery. By offering significant improvements to the accuracy and coverage of human protein complexes, hu.MAP (http://proteincomplexes.org) serves as a valuable resource for better understanding the core cellular functions of human proteins and helping to determine mechanistic foundations of human disease.
Complete fold annotation of the human proteome using a novel structural feature space
Authors: Middleton Sarah A. , Illuminati Joseph , Kim Junhyong 
Published: December 2016

ABSTRACTRecognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 96% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into biological function, including the prediction of functional motifs relevant to human diseases. Our method can be applied tode novofold prediction of entire proteomes and identify candidate novel fold families.
Systematic morphological profiling of human gene and allele function reveals Hippo-NF-κB pathway connectivity
Authors: Rohban Mohammad H , Singh Shantanu , Wu Xiaoyun , Berthet Julia B , Bray Mark-Anthony , Shrestha Yashaswi , Varelas Xaralabos , Boehm Jesse S , Carpenter Anne E 
Published: December 2016

AbstractWe hypothesized that human genes and disease-associated alleles might be systematically functionally annotated using morphological profiling of cDNA constructs, via a microscopy-based Cell Painting assay. Indeed, 50% of the 220 tested genes yielded detectable morphological profiles, which grouped into biologically meaningful gene clusters consistent with known functional annotation (e.g., the RAS-RAF-MEK-ERK cascade). We used novel subpopulation-based visualization methods to interpret the morphological changes for specific clusters. This unbiased morphologic map of gene function revealed TRAF2/C-REL negative regulation of YAP 1/WWTR1-responsive pathways. We confirmed this discovery of functional connectivity between theNF-κBpathway and Hippo pathway effectors at the transcriptional level, thereby expanding knowledge of these two signaling pathways that critically regulate tumor initiation and progression. We make the images and raw data publicly available, providing an initial morphological map of major biological pathways for future study.
Paired CRISPR/Cas9 guide-RNAs enable high-throughput deletion scanning (ScanDel) of a Mendelian disease locus for functionally critical non-coding elements
Authors: Gasperini Molly , Findlay Gregory M. , McKenna Aaron , Milbank Jennifer H. , Lee Choli , Zhang Melissa D. , Cusanovich Darren A. , Shendure Jay 
Published: December 2016

AbstractThe extent to which distal non-coding mutations contribute to Mendelian disease remains a major unknown in human genetics. Given that a gene’s in vivo function can be appropriately modeled in vitro, CRISPR/Cas9 genome editing enables the large-scale perturbation of distal non-coding regions to identify functional elements in their native context. However, early attempts at such screens have relied on one individual guide RNA (gRNA) per cell, resulting in sparse mutagenesis with minimal redundancy across regions of interest. To address this, we developed a system that uses pairs of gRNAs to program thousands of kilobase-scale deletions that scan across a targeted region in a tiling fashion (“ScanDel”). As a proof-of-concept, we applied ScanDel to program 4,342 overlapping 1- and 2- kilobase (Kb) deletions that tile a 206 Kb region centered onHPRT1, the gene underlying Lesch-Nyhan syndrome, with median 27-fold redundancy per base. Programmed deletions were functionally assayed by selecting for loss ofHPRT1function with 6-thioguanine.HPRT1exons served as positive controls, and all were successfully identified as functionally critical by the screen. Remarkably,HPRT1function appeared robust to deletion of any intergenic or deeply intronic non-coding region across the 206 Kb locus, indicating that proximal regulatory sequences are sufficient for its expression. A sparser mutagenesis screen of the same 206 Kb with individual gRNAs also failed to identify critical distal regulatory elements. Although our screen did find programmed deletions and individual gRNAs with putative functional consequences that targeted exon-proximal non-coding sequences (e.g. the promoter), long-read sequencing revealed that this signal was driven almost entirely by rare, unexpected deletions that extended into exonic sequence. These targeted validation experiments defined a small region surrounding the transcriptional start site as the only non-coding sequence essential toHPRT1function. Overall, our results suggest that distal regulatory elements are not critical forHPRT1expression, and underscore the necessity of comprehensive edited-locus genotyping for validating the results of CRISPR screens. The application of ScanDel to additional loci will enable more insight into the extent to which the disruption of distal non-coding elements contributes to Mendelian diseases. In addition, dense, redundant, large-scale deletion scanning with gRNA pairs will facilitate a deeper understanding of endogenous gene regulation in the human genome.
Detection and characterization of low and high genome coverage regions using an efficient running median and a double threshold approach
Authors: Desvillechabrol Dimitri , Bouchier Christiane , Kennedy Sean , Cokelaer Thomas 
Published: December 2016

AbstractMotivationNext Generation Sequencing (NGS) provides researchers with powerful tools to investigate both prokaryotic and eukaryotic genetics. An accurate assessment of reads mapped to a specific genome consists of inspecting thegenome coverageas number of reads mapped to a specific genome location. Most current methods use the average of the genome coverage (sequencing depth) to summarize the overall coverage. This metric quickly assess the sequencing quality but ignores valuable biological information like the presence of repetitive regions or deleted genes. The detection of such information may be challenging due to a wide spectrum of heterogeneous coverage regions, a mixture of underlying models or the presence of a non-constant trend along the genome. Using robust statistics to systematically identify genomic regions with unusual coverage is needed to characterize these regions more precisely.ResultsWe implemented an efficient running median algorithm to estimate the genome coverage trend. The distribution of the normalized genome coverage is then estimated using a Gaussian mixture model. Az-score statistics is then assigned to each base position and used to separate the central distribution from the regions of interest (ROI) (i.e., under and over-covered regions). Finally, a double threshold mechanism is used to cluster the genomic ROIs. HTML reports provide a summary with interactive visual representations of the genomic ROIs.AvailabilityAn implementation of the genome coverage characterization is available within theSequanaproject. The standalone application is calledsequana_coverage. The source code is available onGitHub(http://github.com/sequana/sequana), and documentation onReadTheDocs(http://sequana.readtheodcs.org). An example of HTML report is provided onhttp://sequana.github.io.Contactdimitri.desvillechabrol@pasteur.fr,thomas.cokelaer@pasteur.fr
New single-molecule imaging of the eisosome BAR domain protein Pil1p reveals filament-like dynamics
Authors: Lacy Michael M. , Baddeley David , Berro Julien 
Published: December 2016

AbstractMolecular assemblies can have highly heterogeneous dynamics within the cell, but the limitations of conventional fluorescence microscopy can mask nanometer-scale features. We have developed a novel, broadly applicable, fluorescent labeling and imaging protocol, called Single-molecule Recovery After Photobleaching (SRAP), which allowed us to reveal the heterogeneous dynamics of the eisosome, a multi-protein structure on the cytoplasmic face of the plasma membrane in fungi. By fluorescently labeling only a small fraction of cellular Pil1p, the core eisosome BAR domain protein in fission yeast, we visualized whole eisosomes and, after photobleaching, recorded the binding of individual Pil1p molecules with ~20 nm precision. Further analysis of these dynamic structures and comparison to computer simulations allowed us to show that Pil1p exchange is spatially heterogeneous, supporting a new model of the eisosome as a dynamic filament.Abbreviations usedBARBin/Amphiphysin/Rvs domainFRAPFluorescence Recovery After PhotobleachingmEGFPmonomeric Enhanced Green Fluorescent ProteinSiR647silicon-rhodamine 647TIRFTotal Internal Reflection Fluorescence
Resolving the Functional Significance ofBRCA1RING Domain Missense Substitutions
Authors: Paquette Andrew , Tao Kayoko , Clark Kathleen A , Stark Alex W , Rosenthal Judith , Snow Angela K , Bell Russell , Thompson Bryony A , Unger Joshua , Milash Brett A , Pappas Lisa , Gertz Jason , Varley Katherine E , Thomas Alun , Boucher Ken , Foulkes William D , Goldgar David E , Tavtigian Sean V 
Published: December 2016

ABSTRACTPart 1Development and calibration of suitably accurate functional assays forBRCA1RING domain and BRCT domain missense substitutions could dramatically accelerate clinical classification of rare missense substitutions observed in that gene. Leveraging data from 68,000 full sequence tests ofBRCA1andBRCA2, plus data from the limited number of already classifiedBRCA1RING domain missense substitutions, we used logistic regression and related techniques to evaluate threeBRCA1RING domain assays. These were recently described high throughput yeast 2-hybrid and E3 ubiquitin ligase assays, plus a newly developed mammalian 2-hybrid assay. While there were concerns about the accuracy of the yeast 2-hybrid assay and the indirect nature of the ubiquitin ligase assay, the mammalian 2-hybrid assay had excellent correlation with existing missense substitution classifications. After calibration, this assay contributed to classification of one newly reportedBRCA1missense substitution. In principal, the mammalian 2-hybrid assay could be converted to a high-throughput format that would likely retain suitable accuracy.Part 2How does one achieve clinically applicable classification of the vast majority of all possible sequence variants in disease susceptibility genes? BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino-terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a Mammalian 2-hybrid (M2H) assay. Downstream of the M2H laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that about 20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of about 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 47 with concordant computational and functional assay evidence in favor of pathogenicity; these are particularly likely to be classified as Likely Pathogenic once human observational data become available.
Evaluating the outcomes of VCA-led improvement projects
Authors: Johns Craig Michael , Kimber Nathan , Howieson Janet , Lawley Meredith 
Published: December 2016

Purpose
The purpose of this paper is to describe the potential benefits of value chain analysis (VCA) improvement projects by evaluating their effectiveness for all chain members.

Design/methodology/approach
The study uses an action research approach to extend VCA methodology by implementing an improvement project developed through the VCA process, and the subsequent evaluation of this project using a combination of techniques.

Findings
The paper addressed a key research gap around the evaluation of improvement projects and has shown that the implementation of VCA, both as a guiding framework for developing interventions and a basis for evaluating their effectiveness, can provide significant benefits to all industry stakeholders.

Research limitations/implications
The research focussed on evaluating the outcomes of a single project within an industry case study. While the diversity in different industry structures and the range of improvement projects possible makes it difficult to generalise the findings, the methodology and evaluation options make a valuable practical and theoretical contribution.

Practical implications
The case study highlights the advantages of improvement projects guided by VCA and offers a variety of evaluation options for both private and public sector VCA practitioners.

Originality/value
This study is one of the very few to evaluate the implementation of activities identified during the diagnostic phase of an agribusiness VCA.