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Comparative genomics

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https://www.readbyqxmd.com/read/28749355/hardware-accelerator-for-the-multifractal-analysis-of-dna-sequences
#1
Jorge E Duarte-Sanchez, Jaime Velasco-Medina, Pedro A Moreno
The multifractal analysis has allowed to quantify the genetic variability and non-linear stability along the human genome sequence. It has some implications in explaining several genetic diseases given by some chromosome abnormalities, among other genetic particularities. The multifractal analysis of a genome is carried out by dividing the complete DNA sequence in smaller fragments and calculating the generalized dimension spectrum of each fragment using the chaos game representation and the box-counting method...
July 24, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28749036/advantages-of-rna-seq-compared-to-rna-microarrays-for-transcriptome-profiling-of-anterior-cruciate-ligament-tears
#2
Muhammad Farooq Rai, Eric D Tycksen, Linda J Sandell, Robert H Brophy
Microarrays and RNA-seq are at the forefront of high throughput transcriptome analyses. Since these methodologies are based on different principles there are concerns about the concordance of data between the two techniques. The concordance of RNA-seq and microarrays for genome-wide analysis of differential gene expression has not been rigorously assessed in clinically derived ligament tissues. To demonstrate the concordance between RNA-seq and microarrays and to assess potential benefits of RNA-seq over microarrays, we assessed differences in transcript expression in anterior cruciate ligament (ACL) tissues based on time-from-injury...
July 27, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28748856/the-short-isoform-of-nuclear-mitotic-apparatus-protein-1-functions-as-a-putative-tumor-suppressor
#3
Wang-Sen Qin, Jin Wu, Yang Chen, Fa-Cai Cui, Fu-Ming Zhang, Guan-Ting Lyu, Hong-Mei Zhang
BACKGROUND: Nuclear mitotic apparatus protein 1 (NuMA1) had been reported to produce three groups of isoforms categorized as long, middle, and short groups, of which short NuMA displayed distinct localization patterns compared to long and middle isoforms. However, the function of short NuMA was not clear in the progress of cancer formation. This study aimed to unveil the role of short NuMA in cancer pathogenesis. METHODS: The expression levels of short isoforms were explored in paired gastric carcinoma (GC) samples and different cell lines...
August 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28748670/whole-genome-detection-of-signature-of-positive-selection-in-african-cattle-reveals-selection-for-thermotolerance
#4
Mengistie Taye, Wonseok Lee, Kelsey Caetano-Anolles, Tadelle Dessie, Olivier Hanotte, Okeyo Ally Mwai, Stephen Kemp, Seoae Cho, Sung Jong Oh, Hak-Kyo Lee, Heebal Kim
As African indigenous cattle evolved in a hot tropical climate, they have developed an inherent thermotolerance; survival mechanisms include a light-colored and shiny coat, increased sweating, and cellular and molecular mechanisms to cope with high environmental temperature. Here, we report the positive selection signature of genes in African cattle breeds which contribute for their heat tolerance mechanisms. We compared the genomes of five indigenous African cattle breeds with the genomes of four commercial cattle breeds using cross-population composite likelihood ratio (XP-CLR) and cross-population extended haplotype homozygosity (XP-EHH) statistical methods...
July 27, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28748565/evaluating-mechanisms-of-diversification-in-a-guineo-congolian-tropical-forest-frog-using-demographic-model-selection
#5
Daniel M Portik, Adam D Leaché, Danielle Rivera, Michael F Barej, Marius Burger, Mareike Hirschfeld, Mark-Oliver Rödel, David C Blackburn, Matthew K Fujita
The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers, and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses...
July 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28748554/estimation-of-inbreeding-depression-on-female-fertility-in-the-finnish-ayrshire-population
#6
K Martikainen, A M Tyrisevä, K Matilainen, J Pösö, P Uimari
Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (FPH ), runs of homozygosity (FROH ) and pedigree (FPED ). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows...
July 27, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28748222/an-improved-plasmodium-cynomolgi-genome-assembly-reveals-an-unexpected-methyltransferase-gene-expansion
#7
Erica M Pasini, Ulrike Böhme, Gavin G Rutledge, Annemarie Voorberg-Van der Wel, Mandy Sanders, Matt Berriman, Clemens Hm Kocken, Thomas Dan Otto
BACKGROUND: Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of P. cynomolgi to the closely related, but less tractable, human malaria parasite P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to P. vivax malaria. Molecular and genome-scale studies of P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28747766/dna-methylation-signatures-of-chronic-alcohol-dependence-in-purified-cd3-t-cells-of-patients-undergoing-alcohol-treatment
#8
Christof Brückmann, Sumaiya A Islam, Julia L MacIsaac, Alexander M Morin, Kathrin N Karle, Adriana Di Santo, Richard Wüst, Immanuel Lang, Anil Batra, Michael S Kobor, Vanessa Nieratschker
Several studies have shown an association of alcohol dependence with DNA methylation (DNAm), suggesting that environmentally-induced changes on epigenomic variation may play an important role in alcohol dependence. In the present study, we analysed genome-wide DNAm profiles of purified CD3(+) T-cells from pre- and post-treatment alcohol dependent patients, as well as closely matched healthy controls. We identified 59 differentially methylated CpG sites comparing patients prior to treatment with healthy controls and were able to confirm 8 of those sites in additional analyses for differentially methylated regions...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747666/comparative-analysis-of-four-buckwheat-species-based-on-morphology-and-complete-chloroplast-genome-sequences
#9
Cheng-Long Wang, Meng-Qi Ding, Chen-Yan Zou, Xue-Mei Zhu, Yu Tang, Mei-Liang Zhou, Ji-Rong Shao
Buckwheat is a nutritional and economically crop belonging to Polygonaceae, Fagopyrum. To better understand the mutation patterns and evolution trend in the chloroplast (cp) genome of buckwheat, and found sufficient number of variable regions to explore the phylogenetic relationships of this genus, two complete cp genomes of buckwheat including Fagopyrum dibotrys (F. dibotrys) and Fagopyrum luojishanense (F. luojishanense) were sequenced, and other two Fagopyrum cp genomes were used for comparative analysis...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747543/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#10
Zhan Zhou, Yangyun Zou, Gangbiao Liu, Jingqi Zhou, Jingcheng Wu, Shimin Zhao, Zhixi Su, Xun Gu
Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN/CS) and normal populations (pN/pS). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels...
July 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28747508/mutations-in-the-e2-glycoprotein-and-the-3-untranslated-region-enhance-chikungunya-virus-virulence-in-mice
#11
David W Hawman, Kathryn S Carpentier, Julie M Fox, Nicholas A May, Wes Sanders, Stephanie A Montgomery, Nathaniel J Moorman, Michael S Diamond, Thomas E Morrison
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes debilitating musculoskeletal pain and inflammation and can persist for months to years after acute infection. Although studies in humans and experimentally-infected animals suggest that CHIKV infection persists in musculoskeletal tissues, the mechanisms for this remain poorly understood. To evaluate this further, we isolated CHIKV from the serum of persistently infected Rag1(-/-) mice at day 28. When inoculated into naïve WT mice, this persistently circulating CHIKV strain displayed a capacity for earlier dissemination and greater pathogenicity compared with the parental virus...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28747507/roles-of-cellular-nsf-protein-in-entry-and-nuclear-egress-of-budded-virions-of-autographa-californica-multiple-nucleopolyhedrovirus
#12
Ya Guo, Qi Yue, Jinli Gao, Zhe Wang, Yun-Ru Chen, Gary W Blissard, Tong-Xian Liu, Zhaofei Li
In eukaryotic cells, the soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE) proteins comprise the minimal machinery that triggers fusion of transport vesicles with their target membranes. Comparative studies revealed that genes encoding the components of the SNARE system are highly conserved in yeast, insect, and human genomes. Upon infection of insect cells by the virus AcMNPV, the transcript levels of most SNARE genes were initially up-regulated. We found that overexpression of dominant-negative (DN) forms of NSF or knock-down of the expression of NSF, the key regulator of the SNARE system, significantly affected the infectious AcMNPV production...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28747497/the-genetic-stability-of-piv5-vectored-rsv-vaccine-candidates-after-in-vitro-and-in-vivo-passage
#13
Shannon I Phan, Carolyn M Adam, Zhenhai Chen, Michael Citron, Xiaoping Liang, Amy S Espeseth, Dai Wang, Biao He
Human respiratory syncytial virus (RSV) is the leading etiologic agent of lower respiratory tract infections in children, but no licensed vaccine exists. Previously, our laboratory developed two parainfluenza virus 5 (PIV5)-based RSV vaccine candidates that protect mice against RSV challenge. PIV5 was engineered to express either the RSV fusion protein (F) or the RSV major attachment glycoprotein (G) between the HN and L genes of the PIV5 genome [PIV5-RSV-F (HN-L) or PIV5-RSV-G (HN-L)]. To investigate the stability of the vaccine candidates in vitro, they were passaged in Vero cells at high and low multiplicities of infection (MOI) for eleven generations and the genome sequences, growth kinetics, and protein expression of the resulting viruses were compared with those of the parent viruses...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28747387/molecular-characteristics-of-the-kcnj5-mutated-aldosterone-producing-adenomas
#14
Masanori Murakami, Takanobu Yoshimoto, Kazuhiko Nakabayashi, Yujiro Nakano, Takahiro Fukaishi, Kyoichiro Tsuchiya, Isao Minami, Ryotaro Bouchi, Kohji Okamura, Yasuhisa Fujii, Koshi Hashimoto, Ken-Ichiro Hata, Kazunori Kihara, Yoshihiro Ogawa
The pathophysiology of aldosterone-producing adenomas (APAs) has been investigated via genetic approaches and the pathogenic significance of a series of somatic mutations, including KCNJ5, has been uncovered. However, how the mutational status of an APA is associated with its molecular characteristics, including its transcriptome and methylome, has not been fully understood. This study was undertaken to explore the molecular characteristics of APAs, specifically focusing on APAs with KCNJ5 mutations as opposed to those without KCNJ5 mutations, by comparing their transcriptome and methylome status...
July 26, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28747381/rapid-evolution-of-female-biased-genes-among-four-species-of-anopheles-malaria-mosquitoes
#15
Francesco Papa, Nikolai Windbichler, Robert M Waterhouse, Alessia Cagnetti, Rocco D'Amato, Tania Persampieri, Mara K N Lawniczak, Tony Nolan, Philippos A Papathanos
Understanding how phenotypic differences between males and females arise from the sex-biased expression of nearly identical genomes can reveal important insights into the biology and evolution of a species. Among Anopheles mosquito species, these phenotypic differences include vectorial capacity, as it is only females that blood feed and thus transmit human malaria. Here, we use RNA-seq data from multiple tissues of four vector species spanning the Anopheles phylogeny to explore the genomic and evolutionary properties of sex-biased genes...
July 26, 2017: Genome Research
https://www.readbyqxmd.com/read/28747380/identification-of-differentially-expressed-splice-variants-by-the-proteogenomic-pipeline-splicify
#16
Malgorzata A Komor, Thang Pham, Annemieke C Hiemstra, Sander R Piersma, Anne S Bolijn, Tim Schelfhorst, Pien M Delis-van Diemen, Marianne Tijssen, Robert P Sebra, Meredith Ashby, Gerrit A Meijer, Connie R Jimenez, Remond J A Fijneman
Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions...
July 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28747373/investigation-of-respiratory-syncytial-virus-outbreak-on-an-adult-stem-cell-transplant-unit-using-whole-genome-sequencing
#17
Yijun Zhu, Teresa R Zembower, Kristen E Metzger, Zhengdeng Lei, Stefan J Green, Chao Qi
A viral whole genome sequencing strategy, based on PCR amplification followed by Next-generation Sequencing, was used to investigate a nosocomial RSV-B outbreak in a hematology-oncology and stem cell transplant unit. RSV-B genomes from 16 patients and healthcare workers (HCWs) suspected to be involved in the outbreak were compared to RSV-B genomes acquired from outpatients during the same time period but epidemiologically unrelated to the outbreak. Phylogenetic analysis of the whole genome identified a cluster of 11 patients and HCWs with an identical RSV-B strain which were clearly distinct from strains recovered from individuals unrelated to the outbreak...
July 26, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28747165/increased-ercc1-expression-is-linked-to-chromosomal-aberrations-and-adverse-tumor-biology-in-prostate-cancer
#18
Frank Jacobsen, Billurvan Taskin, Nathaniel Melling, Charlotte Sauer, Corinna Wittmer, Claudia Hube-Magg, Martina Kluth, Ronald Simon, Dirk Pehrke, Burkhard Beyer, Thomas Steuber, Imke Thederan, Guido Sauter, Thorsten Schlomm, Waldemar Wilczak, Katharina Möller, Sören A Weidemann, Susanne Burdak-Rothkamm
BACKGROUND: Animal model experiments have suggested a role of the DNA repair protein ERCC1 (Excision Repair Cross-Complementation Group 1) in prostate cancer progression. METHODS: To better understand the impact of ERCC1 protein expression in human prostate cancer, a preexisting tissue microarray (TMA) containing more than 12,000 prostate cancer specimens was analyzed by immunohistochemistry and data were compared with tumor phenotype, PSA recurrence and several of the most common genomic alterations (TMPRSS2:ERG fusions: deletions of PTEN, 6q, 5q, 3p)...
July 26, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28746220/copy-number-variations-of-neurotrophic-tyrosine-receptor-kinase-3-ntrk3-may-predict-prognosis-of-ovarian-cancer
#19
Li Ge, Ning Li, Mei Liu, Ning-Zhi Xu, Ming-Rong Wang, Ling-Ying Wu
Platinum resistance is a critical barrier for clinicians to improve the survival of ovarian cancer. Our study evaluated the correlation between copy number variations (CNVs) of neurotrophic tyrosine receptor kinase 3 (NTRK3) and the prognosis of ovarian cancer, which might predict platinum resistance in ovarian cancer patients.Array comparative genomic hybridization (CGH) was used to test gene backgrounds between platinum-sensitive and platinum-resistant relapsed populations and CNVs of NTRK3 were indicated by cluster analysis...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28746207/integrating-nested-pcr-with-high-throughput-sequencing-to-characterize-mutations-of-hbv-genome-in-low-viral-load-samples
#20
Xianjun Wang, Lihui Xu, Yueming Chen, Anbing Liu, Liqian Wang, Peisong Xu, Yunhui Liu, Lei Li, Fei Meng
Due to the low viral load of hepatitis B virus (HBV) in plasma samples, conventional techniques have limitations to the detection of antiviral resistance mutations. To solve the problem, we developed a fast, highly sensitive, and accurate method to sequence the HBV whole-genome sequencing in plasma samples which had various viral loads from very low to high.Twenty-one plasma samples were collected from patients who were carriers of HBV from the Hangzhou First People's Hospital. Two pairs of conserved, overlapping, nested primers were used to amplify and sequence the whole HBV genome in 8 plasma samples with different viral loads...
July 2017: Medicine (Baltimore)
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