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Genomics

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https://www.readbyqxmd.com/read/29432978/classification-of-pathogenic-microbes-using-a-minimal-set-of-single-nucleotide-polymorphisms-derived-from-whole-genome-sequences
#1
Tanmoy Roychowdhury, Vinod Kumar Singh, Alok Bhattacharya
In a context specific manner, Intra-species genomic variation plays an important role in phenotypic diversity observed among pathogenic microbes. Efficient classification of these pathogens is important for diagnosis and treatment of several infectious diseases. NGS technologies have provided access to wealth of data that can be utilized to discover important markers for pathogen classification. In this paper, we described three different approaches (Jensen-Shanon divergence, random forest and Shewhart control chart) for identification of a minimal set of SNPs that can be used for classification of organisms...
February 9, 2018: Genomics
https://www.readbyqxmd.com/read/29432977/unknown-facet-of-next-gen-dna-sequencing-history
#2
LETTER
Steve Upton, Edd Gent
No abstract text is available yet for this article.
February 9, 2018: Genomics
https://www.readbyqxmd.com/read/29432976/epigenomic-and-genomic-landscape-of-drosophila-melanogaster-heterochromatic-genes
#3
Parna Saha, Divya Tej Sowpati, Rakesh K Mishra
Heterochromatin is associated with transcriptional repression. In contrast, several genes in the pericentromeric regions of Drosophila melanogaster are dependent on this heterochromatic environment for their expression. Here we present a comprehensive analysis of the epigenetic landscape of heterochromatic genes across all the developmental stages of Drosophila using the available histone modification and expression data from modENCODE. We find that heterochromatic genes exhibit combinations of active and inactive histone marks that correspond to their level of expression during development...
February 9, 2018: Genomics
https://www.readbyqxmd.com/read/29432975/sequencing-and-analysis-of-the-whole-genome-of-indian-gujarati-male
#4
Suhani Almal, Sungwon Jeon, Milee Agarwal, Sweta Patel, Shivangi Patel, Youngjune Bhak, JeHoon Jun, Jong Bhak, Harish Padh
The article presents the analysis of whole genome sequence of a Gujarati Indian individual (IHGP01) that was sequenced at 23.05× coverage with a total of 74.93 Gb of sequence data generated using Illumina HiSeq 2000 platform. Variant analysis revealed over 3.9 million single nucleotide variants (SNVs) and about 393,000 small insertions and deletions (InDels) including novel variants. The known variants were analyzed for their health and disease relevance and pharmacogenomic profile. Mitochondrial and Y-chromosome haplogroup analysis clearly indicated arrival on the continent not more than 20,000-25,000 years ago, following the route out of Africa to central Europe, then into Asian continent and subsequent migration to West part of the Indian subcontinent...
February 9, 2018: Genomics
https://www.readbyqxmd.com/read/29427639/genotyping-by-sequencing-performance-in-selected-livestock-species
#5
Artur Gurgul, Anna Miksza-Cybulska, Tomasz Szmatoła, Igor Jasielczuk, Agata Piestrzyńska-Kajtoch, Agnieszka Fornal, Ewelina Semik-Gurgul, Monika Bugno-Poniewierska
Application of next generation sequencing for large scale genotyping in livestock is limited by high costs and challenging data analysis process. However, available restriction enzyme-based enrichment techniques like e.g. genotyping-by-sequencing (GBS) are promising tools allowing reduction of financial outlies by a high sample multiplexing and narrowing down the sequenced genome areas to the randomly distributed read tags. In this study, we tested the performance of standard, PstI endonuclease-adapted GBS protocol for population genetics in cattle, horse and sheep with application of different, including low-depth sequencing setups...
February 7, 2018: Genomics
https://www.readbyqxmd.com/read/29395657/compositional-dynamics-and-codon-usage-pattern-of-brca1-gene-across-nine-mammalian-species
#6
Supriyo Chakraborty, Tarikul Huda Mazumder, Arif Uddin
The BRCA1 gene is located on the human chromosome 17q21.31 and plays important role in biological processes. The aminoacyl-tRNA synthetases (AARS) are a family of heterogenous enzymes responsible protein synthesis and whose secondary functions include a role in autoimmune myositis. Our findings reveal that the compositional constraint and the preference of more A/T -ending codons determine the codon usage patterns in BRCA1 gene while more G/C-ending codons influence the codon usage pattern of AARS gene among mammals...
January 27, 2018: Genomics
https://www.readbyqxmd.com/read/29366861/functional-network-analysis-reveals-biological-roles-of-lncrnas-and-mrnas-in-mog35-55-specific-cd4-t-helper-cells
#7
Zhaoying Li, Pixia Gong, Wen Wang, Siying Qu, Xi Wang, Zhongze He, Guangyou Wang, Qingfei Kong, Lili Mu, Jinghua Wang, Shaohong Fang, Wei Zhao, Bo Sun, Hulun Li
Long non-coding RNAs have the potential to regulate immune responses. Their impact on multiple sclerosis has remained elusive. For illustrating their roles in experimental autoimmune encephalomyelitis (EAE) pathogenesis, we investigated the differential expression of lncRNAs and mRNAs in CD4+Th cells obtained from myelin oligodendrocytic glycoprotein35-55(MOG35-55)-induced EAE and complete Freund's adjuvant (CFA) controls. We observed differential expression of 1112 lncRNAs and 519 mRNAs in CD4+Th cells. The functional network showed lncRNAs had the capacity to modulate EAE pathogenesis via regulating many known EAE regulators such as Ptpn6...
January 20, 2018: Genomics
https://www.readbyqxmd.com/read/29366860/bioinformatic-analysis-of-regulation-of-natural-antisense-transcripts-by-transposable-elements-in-human-mrna
#8
Jaeeun Jung, Sugi Lee, Hyun-Soo Cho, Kunhyang Park, Jea-Woon Ryu, Minah Jung, Jeongkil Kim, HyeRan Kim, Dae-Soo Kim
Non-coding RNA is no longer considered to be "junk" DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletely understood. It is well-known that the insertion of transposable elements (TEs) can affect gene transcription. Using a bioinformatics approach, we identified NATs using human mRNA sequences from the UCSC Genome Browser Database...
January 20, 2018: Genomics
https://www.readbyqxmd.com/read/29366530/identification-and-characterization-of-long-non-coding-rna-in-prenatal-and-postnatal-skeletal-muscle-of-sheep
#9
Cun-Yuan Li, Xiaoyue Li, Zhijin Liu, Wei Ni, Xiangyu Zhang, Wureli Hazi, Qiman Ma, Yunfeng Zhang, Yang Cao, Jiangjiao Qi, Yang Yao, Lin Feng, Dawei Wang, Xiaoxu Hou, Shuting Yu, Li Liu, Mengdan Zhang, Shengwei Hu
lncRNAs are a class of transcriptional RNA molecules of >200 nucleotides in length. However, the overall expression pattern and function of lncRNAs in sheep muscle is not clear. Here, we identified 1566 lncRNAs and 404 differentially expressed lncRNAs in sheep muscle from prenatal (110 days of fetus) and postnatal (2 to 3 years old of adult sheep) developmental stages by using RNA-seq technology. Several lncRNAs were identified by using RT-PCR and DNA sequencing. The expression levels of several lncRNAs were confirmed by qRT-PCR...
January 20, 2018: Genomics
https://www.readbyqxmd.com/read/29360500/idna6ma-pseknc-identifying-dna-n6-methyladenosine-sites-by-incorporating-nucleotide-physicochemical-properties-into-pseknc
#10
Pengmian Feng, Hui Yang, Hui Ding, Hao Lin, Wei Chen, Kuo-Chen Chou
N6-methyladenine (6mA) is one kind of post-replication modification (PTM or PTRM) occurring in a wide range of DNA sequences. Accurate identification of its sites will be very helpful for revealing the biological functions of 6mA, but it is time-consuming and expensive to determine them by experiments alone. Unfortunately, so far, no bioinformatics tool is available to do so. To fill in such an empty area, we have proposed a novel predictor called iDNA6mA-PseKNC that is established by incorporating nucleotide physicochemical properties into Pseudo K-tuple Nucleotide Composition (PseKNC)...
January 19, 2018: Genomics
https://www.readbyqxmd.com/read/29357303/single-step-genomic-evaluation-improves-accuracy-of-breeding-value-predictions-for-resistance-to-infectious-pancreatic-necrosis-virus-in-rainbow-trout
#11
Grazyella M Yoshida, Roberto Carvalheiro, Francisco H Rodriguez, Jean P Lhorente, José M Yáñez
The aim of this study was to compare the accuracy of breeding values (EBVs) predicted using the traditional pedigree based Best Linear Unbiased Prediction (PBLUP) and the single-step genomic Best Linear Unbiased Prediction (ssGBLUP) for resistance against infectious pancreatic necrosis virus (IPNV) in rainbow trout. A total of 2278 animals were challenged against IPNV and 768 individuals were genotyped using 57 K single nucleotide polymorphism for rainbow trout. Accuracies for both methods were assessed using five-fold cross-validation...
January 18, 2018: Genomics
https://www.readbyqxmd.com/read/29355597/elucidating-the-gene-regulatory-networks-modulating-cancer-stem-cells-and-non-stem-cancer-cells-in-high-grade-serous-ovarian-cancer
#12
Sibun Parida, Sohini Chakraborty, Ranjan Kumar Maji, Zhumur Ghosh
The origin and pathogenesis of epithelial ovarian cancer have perplexed investigators for decades. The most prevalent type of it is the high-grade serous ovarian carcinoma (HGSOv) which is a highly aggressive disease with high relapse rates and insurgence of chemo-resistance at later stages of treatment. These are driven by a rare population of stem cell like cancer cells called cancer stem cells (CSCs). We have taken up a systems approach to find out the common gene interaction paths between non-stem cancer cells and CSCs in HGSOv...
January 17, 2018: Genomics
https://www.readbyqxmd.com/read/29331610/pseudomonas-putida-modulates-the-expression-of-mirnas-and-their-target-genes-in-response-to-drought-and-salt-stresses-in-chickpea-cicer-arietinum-l
#13
Ram Jatan, Puneet Singh Chauhan, Charu Lata
MicroRNAs are small non-coding regulatory RNA molecules that play an important role in the modulation of gene expression during various environmental stresses. Pseudomonas putida RA, a plant growth promoting rhizobacteria (PGPR) colonizes the root surface of plants improving their growth and development during abiotic stresses modulating the expression of stress-responsive genes; however, the impact of RA on stress responsive-miRNA remains elusive. The present study was an attempt to delineate the role of PGPR in modulating stress responsive-miRNAs in a tolerant desi chickpea genotype exposed to drought and salt stresses...
January 10, 2018: Genomics
https://www.readbyqxmd.com/read/29325965/genome-wide-association-mapping-for-seed-protein-and-oil-contents-using-a-large-panel-of-soybean-accessions
#14
Dongmei Li, Xue Zhao, Yingpeng Han, Wenbin Li, Futi Xie
Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0...
January 8, 2018: Genomics
https://www.readbyqxmd.com/read/29317305/investigation-of-putative-invasion-determinants-of-actinobacillus-species-using-comparative-genomics
#15
Adina R Bujold, Andrew E Shure, Rui Liu, Andrew M Kropinski, Janet I MacInnes
Actinobacillus spp. are Gram-negative bacteria associated with mucosal membranes. While some are commensals, others can cause important human and animal diseases. A. pleuropneumoniae causes severe fibrinous hemorrhagic pneumonia in swine but not systemic disease whereas other species invade resulting in septicemia and death. To understand the invasive phenotype of Actinobacillus spp., complete genomes of eight isolates were obtained and pseudogenomes of five isolates were assembled and annotated. Phylogenetically, A...
January 6, 2018: Genomics
https://www.readbyqxmd.com/read/29317304/lncrna-and-mrna-integration-network-reconstruction-reveals-novel-key-regulators-in-esophageal-squamous-cell-carcinoma
#16
Shervin Alaei, Balal Sadeghi, Ali Najafi, Ali Masoudi-Nejad
Many experimental and computational studies have identified key protein coding genes in initiation and progression of esophageal squamous cell carcinoma (ESCC). However, the number of researches that tried to reveal the role of long non-coding RNAs (lncRNAs) in ESCC has been limited. LncRNAs are one of the important regulators of cancers which are transcribed dominantly in the genome and in various conditions. The main goal of this study was to use a systems biology approach to predict novel lncRNAs as well as protein coding genes associated with ESCC and assess their prognostic values...
January 6, 2018: Genomics
https://www.readbyqxmd.com/read/29309842/diseases-and-their-clinical-heterogeneity-are-we-ignoring-the-snipers-and-micromanagers-an-illustration-using-beta-thalassemia-clinical-spectrum-and-fetal-hemoglobin-levels
#17
Sankha Subhra Das, Anik Mitra, Nishant Chakravorty
Diseases and pathological ailments are known to perplex clinicians and researchers with their varied clinical manifestations. Such variations are mostly attributed to the complex interplays between numerous molecular players and their modifiers. This complexity in turn baffles scientists further to tweak multiple players together when attempting to identify definitive therapeutic interventions. In this pursuit, researchers often tend to ignore one of the commonest known genetic variations - single nucleotide polymorphisms (SNPs) in non-coding genetic regions...
January 5, 2018: Genomics
https://www.readbyqxmd.com/read/29309841/dmrfusion-a-differentially-methylated-region-detection-tool-based-on-the-ranked-fusion-method
#18
Maryam Yassi, Ehsan Shams Davodly, Afsaneh Mojtabanezhad Shariatpanahi, Mehdi Heidari, Mahdieh Dayyani, Alireza Heravi-Moussavi, Mohammad Hossein Moattar, Mohammad Amin Kerachian
DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Computational analysis of differentially methylated regions (DMRs) could explore the underlying reasons of methylation. DMRFusion is presented as a useful tool for comprehensive DNA methylation analysis of DMRs on methylation sequencing data. This tool is designed base on the integration of several ranking methods; Information gain, Between versus within Class scatter ratio, Fisher ratio, Z-score and Welch's t-test...
January 5, 2018: Genomics
https://www.readbyqxmd.com/read/29288711/whole-genome-sequence-of-auricularia-heimuer-basidiomycota-fungi-the-third-most-important-cultivated-mushroom-worldwide
#19
Yuan Yuan, Fang Wu, Jing Si, Yi-Fan Zhao, Yu-Cheng Dai
Heimuer, Auricularia heimuer, is one of the most famous traditional Chinese foods and medicines, and it is the third most important cultivated mushroom worldwide. The aim of this study is to develop genomic resources for A. heimuer to furnish tools that can be used to study its secondary metabolite production capability, wood degradation ability and biosynthesis of polysaccharides. The genome was obtained from single spore mycelia of the strain Dai 13782 by using combined high-throughput Illumina HiSeq 4000 system with the PacBio RSII long-read sequencing platform...
December 27, 2017: Genomics
https://www.readbyqxmd.com/read/29277352/comparative-genomic-analysis-of-lactobacillus-mucosae-lm1-identifies-potential-niche-specific-genes-and-pathways-for-gastrointestinal-adaptation
#20
Valerie Diane V Valeriano, Ju Kyoung Oh, Bernadette B Bagon, Heebal Kim, Dae-Kyung Kang
Lactobacillus mucosae is currently of interest as putative probiotics due to their metabolic capabilities and ability to colonize host mucosal niches. L. mucosae LM1 has been studied in its functions in cell adhesion and pathogen inhibition, etc. It demonstrated unique abilities to use energy from carbohydrate and non-carbohydrate sources. Due to these functions, we report the first complete genome sequence of an L. mucosae strain, L. mucosae LM1. Analysis of the pan-genome in comparison with closely-related Lactobacillus species identified a complete glycogen metabolism pathway, as well as folate biosynthesis, complementing previous proteomic data on the LM1 strain...
December 22, 2017: Genomics
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