bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium
Authors: Ramstein Guillaume P , Evans Joseph , Kaeppler Shawn M , Mitchell Robert B , Vogel Kenneth P , Buell C Robin , Casler Michael D 
Published: March 2016

Abstract
Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.
Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici
Authors: McDonald Megan C , McGinness Lachlan , Hane James K , Williams Angela H , Milgate Andrew , Solomon Peter S 
Published: March 2016

Abstract
Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates, for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ∼10% had an effect on the coding regions of the genome. Furthermore, we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method, we have identified &lt; 100 candidate effector genes whose gene sequence correlates with virulence toward a wheat cultivar carrying a major resistance gene.
Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome
Authors: Gu Junchen , Stevens Michael , Xing Xiaoyun , Li Daofeng , Zhang Bo , Payton Jacqueline E , Oltz Eugene M , Jarvis James N , Jiang Kaiyu , Cicero Theodore , Costello Joseph F , Wang Ting 
Published: March 2016

AbstractDNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation, and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. Here, we present an in-depth analysis of 54 single-CpG-resolution DNA methylomes of normal human cell types by integrating high-throughput sequencing-based methylation data. We found that the ratio of methylated to unmethylated CpGs is relatively constant regardless of cell type. However, which CpGs made up the unmethylated complement was cell-type specific. We categorized the 26,000,000 human autosomal CpGs based on their methylation levels across multiple cell types to identify variably methylated CpGs and found that 22.6% exhibited variable DNA methylation. These variably methylated CpGs formed 660,000 variably methylated regions (VMRs), encompassing 11% of the genome. By integrating a multitude of genomic data, we found that VMRs enrich for histone modifications indicative of enhancers, suggesting their role as regulatory elements marking cell type specificity. VMRs enriched for transcription factor binding sites in a tissue-dependent manner. Importantly, they enriched for GWAS variants, suggesting that VMRs could potentially be implicated in disease and complex traits. Taken together, our results highlight the link between CpG methylation variation, genetic variation, and disease risk for many human cell types.
Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains ofSaccharomyces cerevisiae
Authors: Borneman Anthony R , Forgan Angus H , Kolouchova Radka , Fraser James A , Schmidt Simon A 
Published: March 2016

AbstractHumans have been consuming wines for more than 7000 yr . For most of this time, fermentations were presumably performed by strains of Saccharomyces cerevisiae that naturally found their way into the fermenting must . In contrast, most commercial wines are now produced by inoculation with pure yeast monocultures, ensuring consistent, reliable and reproducible fermentations, and there are now hundreds of these yeast starter cultures commercially available. In order to thoroughly investigate the genetic diversity that has been captured by over 50 yr of commercial wine yeast development and domestication, whole genome sequencing has been performed on 212 strains of S. cerevisiae, including 119 commercial wine and brewing starter strains, and wine isolates from across seven decades. Comparative genomic analysis indicates that, despite their large numbers, commercial strains, and wine strains in general, are extremely similar genetically, possessing all of the hallmarks of a population bottle-neck, and high levels of inbreeding. In addition, many commercial strains from multiple suppliers are nearly genetically identical, suggesting that the limits of effective genetic variation within this genetically narrow group may be approaching saturation.
Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes
Authors: Fu Yong-Bi , Peterson Gregory W , Dong Yibo 
Published: March 2016

Abstract
Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7–6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0–16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications.
Drak Is Required for Actomyosin Organization DuringDrosophilaCellularization
Authors: Chougule Ashish B , Hastert Mary C , Thomas Jeffrey H 
Published: March 2016

AbstractThe generation of force by actomyosin contraction is critical for a variety of cellular and developmental processes. Nonmuscle myosin II is the motor that drives actomyosin contraction, and its activity is largely regulated by phosphorylation of the myosin regulatory light chain. During the formation of the Drosophila cellular blastoderm, actomyosin contraction drives constriction of microfilament rings, modified cytokinesis rings. Here, we find that Drak is necessary for most of the phosphorylation of the myosin regulatory light chain during cellularization. We show that Drak is required for organization of myosin II within the microfilament rings. Proper actomyosin contraction of the microfilament rings during cellularization also requires Drak activity. Constitutive activation of myosin regulatory light chain bypasses the requirement for Drak, suggesting that actomyosin organization and contraction are mediated through Drak’s regulation of myosin activity. Drak is also involved in the maintenance of furrow canal structure and lateral plasma membrane integrity during cellularization. Together, our observations suggest that Drak is the primary regulator of actomyosin dynamics during cellularization.
Neurofibromin Loss of Function Drives Excessive Grooming in Drosophila
Authors: King Lanikea B , Koch Marta , Murphy Keith R , Velazquez Yoheilly , Ja William W , Tomchik Seth M 
Published: March 2016

Abstract
Neurofibromatosis I is a common genetic disorder that results in tumor formation, and predisposes individuals to a range of cognitive/behavioral symptoms, including deficits in attention, visuospatial skills, learning, language development, and sleep, and autism spectrum disorder-like traits. The nf1-encoded neurofibromin protein (Nf1) exhibits high conservation, from the common fruit fly, Drosophila melanogaster, to humans. Drosophila provides a powerful platform to investigate the signaling cascades upstream and downstream of Nf1, and the fly model exhibits similar behavioral phenotypes to mammalian models. In order to understand how loss of Nf1 affects motor behavior in flies, we combined traditional activity monitoring with video analysis of grooming behavior. In nf1 mutants, spontaneous grooming was increased up to 7x. This increase in activity was distinct from previously described dopamine-dependent hyperactivity, as dopamine transporter mutants exhibited slightly decreased grooming. Finally, we found that relative grooming frequencies can be compared in standard activity monitors that measure infrared beam breaks, enabling the use of activity monitors as an automated method to screen for grooming phenotypes. Overall, these data suggest that loss of nf1 produces excessive activity that is manifested as increased grooming, providing a platform to dissect the molecular genetics of neurofibromin signaling across neuronal circuits.
The Stress Granule RNA-Binding Protein TIAR-1 Protects Female Germ Cells from Heat Shock inCaenorhabditis elegans
Authors: Huelgas-Morales Gabriela , Silva-García Carlos Giovanni , Salinas Laura S , Greenstein David , Navarro Rosa E 
Published: March 2016

AbstractIn response to stressful conditions, eukaryotic cells launch an arsenal of regulatory programs to protect the proteome. One major protective response involves the arrest of protein translation and the formation of stress granules, cytoplasmic ribonucleoprotein complexes containing the conserved RNA-binding proteins TIA-1 and TIAR. The stress granule response is thought to preserve mRNA for translation when conditions improve. For cells of the germline—the immortal cell lineage required for sexual reproduction—protection from stress is critically important for perpetuation of the species, yet how stress granule regulatory mechanisms are deployed in animal reproduction is incompletely understood. Here, we show that the stress granule protein TIAR-1 protects the Caenorhabditis elegans germline from the adverse effects of heat shock. Animals containing strong loss-of-function mutations in tiar-1 exhibit significantly reduced fertility compared to the wild type following heat shock. Analysis of a heat-shock protein promoter indicates that tiar-1 mutants display an impaired heat-shock response. We observed that TIAR-1 was associated with granules in the gonad core and oocytes during several stressful conditions. Both gonad core and oocyte granules are dynamic structures that depend on translation; protein synthesis inhibitors altered their formation. Nonetheless, tiar-1 was required for the formation of gonad core granules only. Interestingly, the gonad core granules did not seem to be needed for the germ cells to develop viable embryos after heat shock. This suggests that TIAR-1 is able to protect the germline from heat stress independently of these structures.
Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis
Authors: Markert Matthew J , Zhang Ying , Enuameh Metewo S , Reppert Steven M , Wolfe Scot A , Merlin Christine 
Published: March 2016

Abstract
The eastern North American monarch butterfly, Danaus plexippus, is an emerging model system to study the neural, molecular, and genetic basis of animal long-distance migration and animal clockwork mechanisms. While genomic studies have provided new insight into migration-associated and circadian clock genes, the general lack of simple and versatile reverse-genetic methods has limited in vivo functional analysis of candidate genes in this species. Here, we report the establishment of highly efficient and heritable gene mutagenesis methods in the monarch butterfly using transcriptional activator-like effector nucleases (TALENs) and CRISPR-associated RNA-guided nuclease Cas9 (CRISPR/Cas9). Using two clock gene loci, cryptochrome 2 and clock (clk), as candidates, we show that both TALENs and CRISPR/Cas9 generate high-frequency nonhomologous end-joining (NHEJ)-mediated mutations at targeted sites (up to 100%), and that injecting fewer than 100 eggs is sufficient to recover mutant progeny and generate monarch knockout lines in about 3 months. Our study also genetically defines monarch CLK as an essential component of the transcriptional activation complex of the circadian clock. The methods presented should not only greatly accelerate functional analyses of many aspects of monarch biology, but are also anticipated to facilitate the development of these tools in other nontraditional insect species as well as the development of homology-directed knock-ins.
Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution
Authors: Chiang Charleston W K , Ralph Peter , Novembre John 
Published: March 2016

Abstract
Identity-by-descent (IBD) is a fundamental concept in genetics with many applications. In a common definition, two haplotypes are said to share an IBD segment if that segment is inherited from a recent shared common ancestor without intervening recombination. Segments several cM long can be efficiently detected by a number of algorithms using high-density SNP array data from a population sample, and there are currently efforts to detect shorter segments from sequencing. Here, we study a problem of identifiability: because existing approaches detect IBD based on contiguous segments of identity-by-state, inferred long segments of IBD may arise from the conflation of smaller, nearby IBD segments. We quantified this effect using coalescent simulations, finding that significant proportions of inferred segments 1–2 cM long are results of conflations of two or more shorter segments, each at least 0.2 cM or longer, under demographic scenarios typical for modern humans for all programs tested. The impact of such conflation is much smaller for longer (&gt; 2 cM) segments. This biases the inferred IBD segment length distribution, and so can affect downstream inferences that depend on the assumption that each segment of IBD derives from a single common ancestor. As an example, we present and analyze an estimator of the de novo mutation rate using IBD segments, and demonstrate that unmodeled conflation leads to underestimates of the ages of the common ancestors on these segments, and hence a significant overestimate of the mutation rate. Understanding the conflation effect in detail will make its correction in future methods more tractable.
The Genetic Basis of Baculum Size and Shape Variation in Mice
Authors: Schultz Nicholas G , Ingels Jesse , Hillhouse Andrew , Wardwell Keegan , Chang Peter L , Cheverud James M , Lutz Cathleen , Lu Lu , Williams Robert W , Dean Matthew D 
Published: March 2016

AbstractThe rapid divergence of male genitalia is a preeminent evolutionary pattern. This rapid divergence is especially striking in the baculum, a bone that occurs in the penis of many mammalian species. Closely related species often display diverse baculum morphology where no other morphological differences can be discerned. While this fundamental pattern of evolution has been appreciated at the level of gross morphology, nearly nothing is known about the genetic basis of size and shape divergence. Quantifying the genetic basis of baculum size and shape variation has been difficult because these structures generally lack obvious landmarks, so comparing them in three dimensions is not straightforward. Here, we develop a novel morphometric approach to quantify size and shape variation from three-dimensional micro-CT scans taken from 369 bacula, representing 75 distinct strains of the BXD family of mice. We identify two quantitative trait loci (QTL) that explain ∼50% of the variance in baculum size, and a third QTL that explains more than 20% of the variance in shape. Together, our study demonstrates that baculum morphology may diverge relatively easily, with mutations at a few loci of large effect that independently modulate size and shape. Based on a combination of bioinformatic investigations and new data on RNA expression, we prioritized these QTL to 16 candidate genes, which have hypothesized roles in bone morphogenesis and may enable future genetic manipulation of baculum morphology.
Genomic Bayesian Prediction Model for Count Data with Genotype × Environment Interaction
Authors: Montesinos-López Abelardo , Montesinos-López Osval A , Crossa José , Burgueño Juan , Eskridge Kent M , Falconi-Castillo Esteban , He Xinyao , Singh Pawan , Cichy Karen 
Published: March 2016

AbstractGenomic tools allow the study of the whole genome, and facilitate the study of genotype-environment combinations and their relationship with phenotype. However, most genomic prediction models developed so far are appropriate for Gaussian phenotypes. For this reason, appropriate genomic prediction models are needed for count data, since the conventional regression models used on count data with a large sample size (nT) and a small number of parameters (p) cannot be used for genomic-enabled prediction where the number of parameters (p) is larger than the sample size (nT). Here, we propose a Bayesian mixed-negative binomial (BMNB) genomic regression model for counts that takes into account genotype by environment (G×E) interaction. We also provide all the full conditional distributions to implement a Gibbs sampler. We evaluated the proposed model using a simulated data set, and a real wheat data set from the International Maize and Wheat Improvement Center (CIMMYT) and collaborators. Results indicate that our BMNB model provides a viable option for analyzing count data.
OS SENTIMENTOS GERADOS NOS (AS) PROFISSIONAIS ENFERMEIROS (AS) DIANTE O PROCESSO MORTE/ MORRER DO PACIENTE
Authors: Silveira Larissa De Carvalho , Brito Maiara Brandão de , Portella Sandra Dutra Cabral 
Published: March 2016

As atitudes de negação da finitude humana na sociedade ocidental atualmente constituem-se como reflexo de uma construção sociocultural e histórica. A influência cultural e a visão de uma enfermagem curativista dificultam a elaboração do luto durante o enfrentamento da morte do paciente provocando nos enfermeiros(as) sentimentos de fracasso, incapacidade e incompetência. O trabalho desenvolvido pela enfermagem revela-se cansativo desgastante, devido a convivência com a dor, sofrimento e morte dos clientes. Tais questões contribuem para o desgaste emocional – provocando o estresse. Desgaste no humor e desmotivação acompanhado de sintomas físicos e psíquicos acarretam um processo gradual para o agravamento do estresse entre outros sentimentos que podem evoluir para um desgaste emocional crônico, a Síndrome de Burnout. Este estudo tem por objetivo analisar as produções científicas que abordam os sentimentos gerados nos enfermeiros (as) durante o processo morte/morrer do paciente. Trata-se de uma pesquisa do tipo revisão integrativa de caráter exploratório. Os artigos analisados encontram-se indexados nas bases de dados do Sciello e Lilacs. O período de estudo circunscreveu entre os anos 2001 a 2011. Os principais achados deste estudo possibilitaram uma análise sobre a produção científica em seis categorias: negação da morte e os sentimentos em relação ao fim da vida, desconforto durante o preparo do corpo, relação dos avanços tecnológicos com a obstinação terapêutica, dor incontrolável do paciente, despreparo do enfermeiro no enfrentamento da morte e sofrimento psíquico. Constatou-se que o despreparo do enfermeiro (a) reflete em um cuidado deficitário que gera situações (des)humanas e prejudiciais ao cuidado humano no fim da vida, revelando-se um “descuidado” do profissional que cuida.
ASSISTÊNCIA DE ENFERMAGEM NO PRÉ-OPERATÓRIO E SUA INFLUÊNCIA NO PÓS-OPERATÓRIO: UMA PERCEPÇÃO DO CLIENTE
Authors: Rocha Débora Rodrigues da , Pereira Ivo Olguimar 
Published: March 2016

Este trabalho teve como objetivo geral identificar a percepção dos clientes no período pré-operatório sobre a assistência de enfermagem e sua influência no pós-operatório. Foi realizada uma pesquisa de caráter descritivo e natureza quantitativa devido à utilização de dados numéricos. O instrumento para coleta dos dados foi por meio do questionário de múltipla escolha. Os dados foram coletados na enfermaria, na fase pós-operatória de um hospital privado localizado na cidade de Vitória da Conquista, Bahia- Brasil. A análise de dados é estatística descritiva. Os resultados foram, a prevalência do sexo feminino (69,23%), e o ensino fundamental incompleto (30,77%) entre os participantes. Os que souberam o nome da sua terminologia cirúrgica (51,28%). Os clientes que receberam orientações no pré-operatório sobre a cirurgia, constatou-se (64,10%) e os que compreenderam o que foi falado foram (66,67%). Os sentimentos mais evidenciados pelos clientes foram a ansiedade ( 43,60%). O técnico de enfermagem, enfermeiro e médico (25,64%) e apenas o médico (20,51%) foram os profissionais que mais orientaram alguns dos clientes participantes. A qualificação da equipe de enfermagem avaliado pelos clientes foram prevalentes o bom e o ótimo (38,46%). O estudo mostrou que, a carência de informações/orientações prestadas pelo enfermeiro na fase pré operatória dificulta o entendimento e provocam equívocos, neste sentido há uma necessidade de implementação de novas práticas, como a prescrição de enfermagem, visando um atendimento qualificado e minimizando possíveis complicações.