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Genomics

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https://www.readbyqxmd.com/read/29031638/dbgaps-a-comprehensive-database-of-genes-and-genetic-markers-associated-with-psoriasis-and-its-subtypes
#1
Shweta Aggarwal, Arnab Nayek, Dibyabhaba Pradhan, Rashi Verma, Monika Yadav, Kalaiarasan Ponnusamy, Arun Kumar Jain
Psoriasis is a systemic hyperproliferative inflammatory skin disorder, although rarely fatal but significantly reduces quality of life. Understanding the full genetic component of the disease association may provide insight into biological pathways as well as targets and biomarkers for diagnosis, prognosis and therapy. Studies related to psoriasis associated genes and genetic markers are scattered and not easily amendable to data-mining. To alleviate difficulties, we have developed dbGAPs an integrated knowledgebase representing a gateway to psoriasis associated genomic data...
October 11, 2017: Genomics
https://www.readbyqxmd.com/read/28989035/ploc-mgneg-predict-subcellular-localization-of-gram-negative-bacterial-proteins-by-deep-gene-ontology-learning-via-general-pseaac
#2
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
Information of the proteins' subcellular localization is crucially important for revealing their biological functions in a cell, the basic unit of life. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop computational tools for timely identifying their subcellular locations based on the sequence information alone. The current study is focused on the Gram-negative bacterial proteins. Although considerable efforts have been made in protein subcellular prediction, the problem is far from being solved yet...
October 6, 2017: Genomics
https://www.readbyqxmd.com/read/28982639/characterisation-of-the-complete-mitochondrial-genome-of-helice-wuana-grapsoidea-varunidae-and-comparison-with-other-brachyuran-crabs
#3
Bo-Ping Tang, Yu Liu, Zhao-Zhe Xin, Dai-Zhen Zhang, Zheng-Fei Wang, Xiao-Yu Zhu, Ying Wang, Hua-Bin Zhang, Chun-Lin Zhou, Xin-Yue Chai, Qiu-Ning Liu
The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an A+T-rich control region. The genome composition is highly A+T biased 68.42%, and exhibits a negative AT-skew (-0...
October 2, 2017: Genomics
https://www.readbyqxmd.com/read/28970049/tri-allelic-heteroplasmies-dna-rna-differences-and-their-polynucleotide-tract-associations-in-the-mitochondrial-genome
#4
Shilin Zhao, David C Samuels, Ying-Yong Zhao, Yan Guo
The human mitochondrial genome has been extensively studied for its function and disease associations. Utilizing five types of high-throughput sequencing data on ten breast cancer patients (total N=50), we examined several aspects of the mitochondrial genome that have not been thoroughly studied, including the occurrence of tri-allelic heteroplasmy, the difference between DNA and RNA, and the variants association with polynucleotide tracts. We validated four previously reported and identified 23 additional tri-allelic positions...
September 29, 2017: Genomics
https://www.readbyqxmd.com/read/28970048/comparative-transcriptomics-of-pleurotus-eryngii-reveals-blue-light-regulation-of-carbohydrate-active-enzymes-cazymes-expression-at-primordium-differentiated-into-fruiting-body-stage
#5
Chunliang Xie, Wenbing Gong, Zuohua Zhu, Li Yan, Zhenxiu Hu, Yuande Peng
Blue light is an important environmental factor which could induce mushroom primordium differentiation and fruiting body development. However, the mechanisms of Pleurotus eryngii primordium differentiation and development induced by blue light are still unclear. The CAZymes (carbohydrate-active enzymes) play important roles in degradation of renewable lignocelluloses to provide carbohydrates for fungal growth, development and reproduction. In the present research, the expression profiles of genes were measured by comparison between the Pleurotus eryngii at primordium differentiated into fruiting body stage after blue light stimulation and dark using high-throughput sequencing approach...
September 29, 2017: Genomics
https://www.readbyqxmd.com/read/28966045/transcriptome-analysis-reveals-potential-genes-involved-in-flower-pigmentation-in-a-red-flowered-mutant-of-white-clover-trifolium-repens-l
#6
Heshan Zhang, Hong Tian, Mingxin Chen, Junbo Xiong, Hua Cai, Yang Liu
White clover (Trifolium repens L.) has been cultivated for ornamental use because of its flowers, leaf marks and creeping habit. Although a mutation in flower color is very infrequent in this species, the red-flowered mutant of white clover was a novel germplasm for ornamental white clover breeding. The mechanism of flower pigmentation in white clover is still limited because of the rarity of mutation materials and the lack of genomic data. In this study, two cDNA libraries from red-flowered white clover mutant between sunlight-exposed plants and shade-treated plants, respectively, were used for transcriptome sequencing...
September 28, 2017: Genomics
https://www.readbyqxmd.com/read/28943389/single-step-genome-wide-association-studies-based-on-genotyping-by-sequence-data-reveals-novel-loci-for-the-litter-traits-of-domestic-pigs
#7
Pingxian Wu, Qiang Yang, Kai Wang, Jie Zhou, Jideng Ma, Qianzhi Tang, Long Jin, Weihang Xiao, Anan Jiang, Yanzhi Jiang, Li Zhu, Xuewei Li, Guoqing Tang
In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level...
September 21, 2017: Genomics
https://www.readbyqxmd.com/read/28941638/applying-mssim-combined-chaos-game-representation-to-genome-sequences-analysis
#8
Hai Ming Ni, Da Wei Qi, Hongbo Mu
Converting DNA sequence to image by using chaos game representation (CGR) is an effective genome sequence pretreatment technology, which provides the basis for further analysis between the different genes. In this paper, we have constructed 10 mammal species, 48 hepatitis E virus (HEV), and 10 kinds of bacteria genetic CGR images, respectively, to calculate the mean structural similarity (MSSIM) coefficient between every two CGR images. From our analysis, the MSSIM coefficient of gene CGR images can accurately reflect the similarity degrees between different genomes...
September 20, 2017: Genomics
https://www.readbyqxmd.com/read/28935392/transcriptome-analysis-of-paecilomyces-hepiali-at-different-growth-stages-and-culture-additives-to-reveal-putative-genes-in-cordycepin-biosynthesis
#9
Fang Pang, Linping Wang, Yu Jin, Lanping Guo, Lipu Song, Guiming Liu, Chengqiang Feng
Paecilomyces hepialid (PH) is an endoparasitic fungus of Cordyceps sinensis (CS) and has become a substitute for CS due to their similar pharmacological activities. Because the market demand for CS is difficult to satisfy, and cordycepin, the effective compound of CS, is difficult to industrially produce, we produced 5 samples of PH by culturing for different durations and adding different additives to the culture broth, and detected their cordycepin content with UPLC ESI MS/MS. Then we grouped these cultures into five transcriptome comparisons containing 3 time variable groups and 2 additive variable groups...
September 18, 2017: Genomics
https://www.readbyqxmd.com/read/28917635/evolutionary-analysis-of-nucleosome-positioning-sequences-based-on-new-symmetric-relative-entropy
#10
Hu Meng, Hong Li, Yan Zheng, Zhenhua Yang, Yun Jia, Suling Bo
New Symmetric Relative Entropy (NSRE) was applied innovatively to analyze the nucleosome sequences in S. cerevisiae, S. pombe and Drosophila. NSRE distributions could well reflect the characteristic differences of nucleosome sequences among three organisms, and the differences indicate a concerted evolution in the sequence usage of nucleosome. Further analysis about the nucleosomes around TSS shows that the constitutive property of +1/-1 nucleosomes in S. cerevisiae is different from that in S. pombe and Drosophila, which indicates that S...
September 14, 2017: Genomics
https://www.readbyqxmd.com/read/28917637/diversity-of-copy-number-variation-in-a-worldwide-population-of-sheep
#11
Liu Yang, Lingyang Xu, Yang Zhou, Mei Liu, Lei Wang, James W Kijas, Hongping Zhang, Li Li, George E Liu
Copy number variation (CNV) represents a major source of genomic variation. We investigated the diversity of CNV distribution using SNP array data collected from a comprehensive collection of geographically dispersed sheep breeds. We identified 24,558 putative CNVs, which can be merged into 619 CNV regions, spanning 197Mb of total length and corresponding to ~6.9% of the sheep genome. Our results reveal a population differentiation in CNV between different geographical areas, including Africa, America, Asia, Southwestern Asia, Central Europe, Northern Europe and Southwestern Europe...
September 13, 2017: Genomics
https://www.readbyqxmd.com/read/28917636/parallel-approach-on-sorting-of-genes-in-search-of-optimal-solution
#12
Pranav Kumar, G Sahoo
An important tool for comparing genome analysis is the rearrangement event that can transform one given genome into other. For finding minimum sequence of fission and fusion, we have proposed here an algorithm and have shown a transformation example for converting the source genome into the target genome. The proposed algorithm comprises of circular sequence i.e. "cycle graph" in place of mapping. The main concept of algorithm is based on optimal result of permutation. These sorting processes are performed in constant running time by showing permutation in the form of cycle...
September 13, 2017: Genomics
https://www.readbyqxmd.com/read/28911975/selection-shapes-the-patterns-of-codon-usage-in-three-closely-related-species-of-genus-misgurnus
#13
Shaokui Yi, Yanhe Li, Weimin Wang
Neutrality plots revealed that selection probably dominates codon bias, whereas mutation plays only a minor role, in shaping the codon bias in three loaches, Misgurnus anguillicaudatus, M. mohoity, and M. bipartitus. These three species also clearly showed similar tendencies in the preferential usage of codons. Nineteen, nine, and 14 preferred codon pairs and 179, 182, and 173 avoided codon pairs were also detected in M. anguillicaudatus, M. bipartitus, and M. mohoity, respectively, and the most frequently avoided type of cP3-cA1 dinucleotide in these species was nnUAnn...
September 11, 2017: Genomics
https://www.readbyqxmd.com/read/28911974/molecular-genetics-of-the-transcription-factor-glis3-identifies-its-dual-function-in-beta-cells-and-neurons
#14
Sophie Calderari, Massimiliano Ria, Christelle Gérard, Tatiane C Nogueira, Olatz Villate, Stephan C Collins, Helen Neil, Nicolas Gervasi, Christophe Hue, Nicolas Suarez-Zamorano, Cécilia Prado, Miriam Cnop, Marie-Thérèse Bihoreau, Pamela J Kaisaki, Jean-Baptiste Cazier, Cécile Julier, Mark Lathrop, Michel Werner, Decio L Eizirik, Dominique Gauguier
The GLIS family zinc finger 3 isoform (GLIS3) is a risk gene for Type 1 and Type 2 diabetes, glaucoma and Alzheimer's disease endophenotype. We identified GLIS3 binding sites in insulin secreting cells (INS1) (FDR q<0.05; enrichment range 1.40-9.11 fold) sharing the motif wrGTTCCCArTAGs, which were enriched in genes involved in neuronal function and autophagy and in risk genes for metabolic and neuro-behavioural diseases. We confirmed experimentally Glis3-mediated regulation of the expression of genes involved in autophagy and neuron function in INS1 and neuronal PC12 cells...
September 11, 2017: Genomics
https://www.readbyqxmd.com/read/28890207/whole-genome-dna-methylation-profiling-of-oral-cancer-in-ethnic-population-of-meghalaya-north-east-india-reveals-novel-genes
#15
Shngainlang Khongsti, Frederick A Lamare, Neizekhotuo Brian Shunyu, Sahana Ghosh, Arindam Maitra, Srimoyee Ghosh
Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal...
September 7, 2017: Genomics
https://www.readbyqxmd.com/read/28890206/unraveling-the-nuclear-and-chloroplast-genomes-of-an-agar-producing-red-macroalga-gracilaria-changii-rhodophyta-gracilariales
#16
Chai-Ling Ho, Wei-Kang Lee, Ee-Leen Lim
Agar and agarose have wide applications in food and pharmaceutical industries. Knowledge on the genome of red seaweeds that produce them is still lacking. To fill the gap in genome analyses of these red algae, we have sequenced the nuclear and organellar genomes of an agarophyte, Gracilaria changii. The partial nuclear genome sequence of G. changii has a total length of 35.8Mb with 10,912 predicted protein coding sequences. Only 39.4% predicted proteins were found to have significant matches to protein sequences in SwissProt...
September 7, 2017: Genomics
https://www.readbyqxmd.com/read/28882736/gene-centric-metegenome-analysis-reveals-diversity-of-pseudomonas-aeruginosa-biofilm-gene-orthologs-in-fresh-water-ecosystem
#17
Rani Anupama, Amitava Mukherjee, Subramanian Babu
Metagenomic analysis of biofilm forming bacteria in environmental samples remains challenging due to the non-availability of gene sequences of most of the uncultivable bacteria. Sequences of Pseudomonas aeruginosa PAO1-UW genes involved either directly or indirectly in biofilm formation were analyzed using BLASTn to obtain matching sequences from different strain, species and genus. Conserved regions in the functional domain of the amino acid sequences were used to design common primers for direct PCR analysis of freshwater metagenomes...
September 4, 2017: Genomics
https://www.readbyqxmd.com/read/28882735/integrative-factor-analysis-an-unsupervised-method-for-quantifying-cross-study-consistency-of-gene-expression-data
#18
Xin Victoria Wang, Giovanni Parmigiani
Integrative analyses of multiple gene expression studies are frequently performed. In the setting of two studies, integrative correlation (IGC) can be used to assess the consistency of co-expression of a given gene. For three or more studies, an extension of IGC gives a global score per gene. We propose to extend IGC and use factor analysis to assess the study-specific consistency of co-expression of genes when there are three or more studies, possibly on different platforms. Our method is able to identify studies whose expression patterns are different from others...
September 4, 2017: Genomics
https://www.readbyqxmd.com/read/28860085/first-de-novo-whole-genome-sequencing-and-assembly-of-the-pink-footed-goose
#19
J M Pujolar, L Dalén, R A Olsen, M M Hansen, J Madsen
Annotated genomes can provide new perspectives on the biology of species. We present the first de novo whole genome sequencing for the pink-footed goose. In order to obtain a high-quality de novo assembly the strategy used was to combine one short insert paired-end library with two mate-pair libraries. The pink-footed goose genome was assembled de novo using three different assemblers and an assembly evaluation was subsequently performed in order to choose the best assembler. For our data, ALLPATHS-LG performed the best, since the assembly produced covers most of the genome, while introducing the fewest errors...
August 30, 2017: Genomics
https://www.readbyqxmd.com/read/28843784/how-many-differentially-expressed-genes-a-perspective-from-the-comparison-of-genotypic-and-phenotypic-distances
#20
Bi Zhao, Aqeela Erwin, Bin Xue
Identifying differentially expressed genes is critical in microarray data analysis. Many methods have been developed by combining p-value, fold-change, and various statistical models to determine these genes. When using these methods, it is necessary to set up various pre-determined cutoff values. However, many of these cutoff values are somewhat arbitrary and may not have clear connections to biology. In this study, a genetic distance method based on gene expression level was developed to analyze eight sets of microarray data extracted from the GEO database...
August 24, 2017: Genomics
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