Genes with common functions often exhibit correlated expression levels, which can be used to identify sets of interacting genes from microarray data. Microarrays typically measure across genomic space, creating a massive matrix co-expression that must mined extract only the most relevant gene interactions. We describe graph theoretical approach extracting co-expressed genes, based on computation cliques. Unlike results traditional clustering algorithms, cliques are not disjoint and allow...

Abstract Background MicroRNAs are small non-coding RNAs that regulate gene expression and thus play important roles in mammalian development. However, the comprehensive lists of microRNAs, as well as, molecular mechanisms by which microRNAs during gamete embryo development poorly defined. The objectives this study were to determine bull sperm predict their functions. Methods To accomplish our we isolated miRNAs from high low fertility bulls, conducted microRNA microarray experiments...

Aeromonas veronii is a gram-negative species abundant in aquatic environments that causes disease humans as well terrestrial and animals. In the current study, 41 publicly available A. genomes were compared to investigate distribution of putative virulence genes, global dissemination pathotypes, potential mechanisms virulence. The complete genome strain ML09-123 from an outbreak motile aeromonas septicemia farm-raised catfish southeastern United States was included. Dissemination types...

Gene co-expression networks are often constructed by computing some measure of similarity between expression levels gene transcripts and subsequently applying a high-pass filter to remove all but the most likely biologically-significant relationships. The selection this threshold necessarily has significant effect on any conclusions derived from resulting network. Many approaches have been taken choose an appropriate threshold, among them statistical significance, accepting only top one...

A wealth of clustering algorithms has been applied to gene co-expression experiments. These cover a broad range approaches, from conventional techniques such as k-means and hierarchical clustering, graphical approaches k-clique communities, weighted networks (WGCNA) paraclique. Comparison these methods evaluate their relative effectiveness provides guidance algorithm selection, development implementation. Most prior work on comparative evaluation focused parametric methods. Graph theoretical...

Aflatoxin is a potent carcinogen that can contaminate grain infected with the fungus Aspergillus flavus. However, resistance to aflatoxin accumulation in maize complex trait low heritability. Here, two complementary analyses were performed better understand mechanisms involved. The first coupled results of genome-wide association study (GWAS) accounted for linkage disequilibrium among single nucleotide polymorphisms (SNPs) gene-set enrichment pathway-based approach. rationale was cumulative...

Summary Epigenetic modifications in histones are crucial for proper sperm physiology, egg activation and reproductive development of males. The objectives this study were to determine the conservation interactomes histone three (H3) ascertain expression dynamics acetylated methylated H3 lysine 27 (H3K27ac H3K27me3) spermatozoa from Holstein bulls with different fertility. Methods immunocytochemistry flow cytometry used evaluate H3K27ac H3K27me3 10 vivo Computational biology methods including...

Bovine respiratory disease (BRD) is a multifactorial complex and the leading infectious in post-weaned beef cattle. Clinical manifestations of BRD are recognized calves within high-risk setting, commonly associated with weaning, shipping, novel feeding housing environments. However, understanding host immune interactions genomic mechanisms involved susceptibility remain elusive. Utilizing high-throughput RNA-sequencing, we contrasted at-arrival blood transcriptomes 6 cattle that ultimately...

ABSTRACT Contamination of maize ( Zea mays L.) with aflatoxin, produced by the fungus Aspergillus flavus Link, has severe health and economic consequences. Efforts to reduce aflatoxin accumulation in have focused on identifying selecting germplasm natural host resistance factors, several lines significantly reduced been identified. Past linkage mapping studies identified quantitative trait loci (QTL) that consistently levels maize. In addition, an association panel 300 inbred was previously...

The liver is the primary site for metabolism of nutrients, drugs, and chemical agents. Although metabolic pathways are complex tightly regulated, genetic variation among individuals, reflected in variations gene expression levels, introduces complexity into research on disease. This study dissected networks that control through combination large-scale quantitative mRNA analysis with mapping a reference population BXD recombinant inbred mouse strains which extensive single-nucleotide...

ABSTRACT High-throughput transcriptomics was used to identify Fibroporia radiculosa genes that were differentially regulated during colonization of wood treated with a copper-based preservative. The transcriptome profiled at two time points while the fungus growing on micronized copper quat (MCQ). A total 917 transcripts expressed. Fifty-eight these more highly expressed when MCQ protecting from strength loss and had putative functions related oxalate production/degradation, laccase...

The identification of novel genes by high-throughput studies complex diseases is complicated the large number potential genes. However, since disease-associated tend to interact, one solution arrange them in modules based on co-expression data and known gene interactions. hypothesis this study was that such a module could be a) found validated allergic disease b) used find validate ore more To test these hypotheses integrated analysis expression microarray experiments from different forms...

ABSTRACT The feasibility of short-read sequencing for genomic analysis was demonstrated Fibroporia radiculosa , a copper-tolerant fungus that causes brown rot decay wood. effect read quality on assembly assessed by filtering Illumina GAIIx reads from single run paired-end library (75-nucleotide length and 300-bp fragment size) at three different stringency levels then assembling each data set with Velvet. A simple approach devised to determine which filter “best.” Venn diagrams identified...

Aspergillus flavus is a pathogenic fungus infecting maize and producing aflatoxins that are health hazards to humans animals. Characterizing host defense mechanism prioritizing candidate resistance genes important the development of resistant germplasm. We investigated methods amenable for analysis significance relations among based on empirical gene expression data obtained by RT-qPCR technique from inbred lines. optimized pipeline tools chosen various programs provide rigorous statistical...

Tools of molecular biology and the evolving tools genomics can now be exploited to study genetic regulatory mechanisms that control cellular responses a wide variety stimuli. These are highly complex, involve many genes gene products. The main objectives this paper describe novel research program centered on understanding these by i.developing powerful graph algorithms exploit innovative principles fixed parameter tractability in order generate distilled sets; ii.producing scalable, high...

Intestinal microbiota contributes health of living organisms. Florfenicol is an approved antimicrobial (AM) prescribed for several bacterial fish diseases. The present study investigated the extent to which florfenicol modulates intestinal microbial populations channel catfish (Ictalurus punctatus). was administered orally at a standard therapeutic dose (10–15 mg/kg body weight 10 days), and contents were collected 16S rRNA subjected Illumina sequencing. Alpha diversity analysis indicated...

Abstract Microsatellites are common in genomes of most eukaryotic species. Due to their high mutability, an adaptive role for microsatellites has been considered. However, little is known concerning the contribution towards phenotypic variation. We used populations sunflower ( Helianthus annuus ) at two latitudes quantify effect microsatellite allele length on phenotype level gene expression. conducted a garden experiment with seed collected from Kansas and Oklahoma followed by RNA‐Seq 95...

Bull fertility is the degree of sperm’s ability to fertilize and activate egg support embryo development, this critical for herd reproductive performance. We used bull as a unique model organism study male because cattle genetics physiology similar those other mammals including humans. Moreover, reliable data along with well-established in vitro systems are available bovine. The objective original was ascertain evolutionary diversification expression dynamics Testis Specific Histone 2B...

Decreasing mammalian fertility and sperm quality have created an urgent need to find effective methods distinguish non-viable from viable fertilising spermatozoa. The aims of the present study were evaluate expression levels β-tubulin 2C (TUBB2C), heat shock protein 10 (HSP10), hexokinase 1 (HXK1) superoxide dismutase (SOD1) in spermatozoa Holstein bulls with varying using western blotting analyse biological networks these key proteins a bioinformatics software (Metacore; Thomson-Reuters,...