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https://www.readbyqxmd.com/read/28431355/genome-wide-identification-and-analysis-of-the-populus-trichocarpa-tify-gene-family
#1
Yue Wang, Feng Pan, Danmei Chen, Wenyuan Chu, Huanlong Liu, Yan Xiang
The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome...
April 13, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28431273/chromosomal-instability-in-gastric-cancer-biology
#2
REVIEW
Saffiyeh Saboor Maleki, Christoph Röcken
Gastric cancer (GC) is the fifth most common cancer in the world and accounts for 7% of the total cancer incidence. The prognosis of GC is dismal in Western countries due to late diagnosis: approximately 70% of the patients die within 5 years following initial diagnosis. Recently, integrative genomic analyses led to the proposal of a molecular classification of GC into four subtypes, i.e.,microsatellite-instable, Epstein-Barr virus-positive, chromosomal-instable (CIN), and genomically stable GCs. Molecular classification of GC advances our knowledge of the biology of GC and may have implications for diagnostics and patient treatment...
April 18, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28431213/genome-mining-unearths-a-hybrid-nonribosomal-peptide-synthetase-like-pteridine-synthase-biosynthetic-gene-cluster
#3
Hyun Bong Park, Corey E Perez, Karl W Barber, Jesse Rinehart, Jason M Crawford
Nonribosomal peptides represent a large class of metabolites with pharmaceutical relevance. Pteridines, such as pterins, folates, and flavins, are heterocyclic metabolites that often serve as redox-active cofactors. The biosynthetic machineries for construction of these distinct classes of small molecules operate independently in the cell. Here, we discovered an unprecedented nonribosomal peptide synthetase-like-pteridine synthase hybrid biosynthetic gene cluster in Photorhabdus luminescens using genome synteny analysis...
March 15, 2017: ELife
https://www.readbyqxmd.com/read/28431148/truncated-orf1-proteins-can-suppress-line-1-retrotransposition-in-trans
#4
Mark Sokolowski, May Chynces, Dawn deHaro, Claiborne M Christian, Victoria P Belancio
Long interspersed element 1 (L1) is an autonomous non-LTR retroelement that is active in mammalian genomes. Although retrotranspositionally incompetent and functional L1 loci are present in the same genomes, it remains unknown whether non-functional L1s have any trans effect on mobilization of active elements. Using bioinformatic analysis, we identified over a thousand of human L1 loci containing at least one stop codon in their ORF1 sequence. RNAseq analysis confirmed that many of these loci are expressed...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28431039/genomic-data-for-78-chickens-from-14-populations
#5
Diyan Li, Tiandong Che, Binlong Chen, Shilin Tian, Xuming Zhou, Guolong Zhang, Miao Li, Uma Gaur, Yan Li, Majing Luo, Long Zhang, Zhongxian Xu, Xiaoling Zhao, Huadong Yin, Yan Wang, Long Jin, Qianzi Tang, Huailiang Xu, Mingyao Yang, Rongjia Zhou, Ruiqiang Li, Qing Zhu, Mingzhou Li
Background: Since the domestication of the red jungle fowls ( Gallus gallus ) (dating back to ∼10,000 B.P.) in Asia, domestic chickens ( Gallus gallus domesticus ) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production and skin color. Population genomic variations through diversifying selection have not been fully investigated...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28431016/somatic-transposition-and-meiotically-driven-elimination-of-an-active-helitron-family-in-pleurotus-ostreatus
#6
Alessandra Borgognone, Raúl Castanera, Elaia Muguerza, Antonio G Pisabarro, Lucía Ramírez
Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28431015/large-scale-collection-of-full-length-cdna-and-transcriptome-analysis-in-hevea-brasiliensis
#7
Yuko Makita, Kiaw Kiaw Ng, G Veera Singham, Mika Kawashima, Hideki Hirakawa, Shusei Sato, Ahmad Sofiman Othman, Minami Matsui
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430989/gene-fractionation-and-function-in-the-ancient-subgenomes-of-maize
#8
Simon Renny-Byfield, Eli Rodgers-Melnick, Jeffrey Ross-Ibarra
The maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts...
April 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#9
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28430657/microrna-signatures-predict-prognosis-of-patients-with-glioblastoma-multiforme-through-the-cancer-genome-atlas
#10
Ying Yuan, Hua Zhang, Xuexia Liu, Zhongming Lu, Guojun Li, Meixia Lu, Xiaofeng Tao
MicroRNAs (miRNAs) play major roles in various biological processes and have been implicated in the pathogenesis and malignant progression of glioblastoma multiforme (GBM). The aim of this study was to assess the predictive values of miRNAs for overall survival (OS) of patients with GBM. MiRNA expression profiles and clinical information of 563 GBM patients were obtained from the Cancer Genome Atlas. The most significantly altered miRNAs were identified and miRNA expression profiles were performed, through principal component analysis, the least absolute shrinkage and selection operator method...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430625/mir-766-induces-p53-accumulation-and-g2-m-arrest-by-directly-targeting-mdm4
#11
Qingqing Wang, Luke A Selth, David F Callen
p53, a transcription factor that participates in multiple cellular functions, is considered the most important tumor suppressor. Previous evidence suggests that post-transcriptional deregulation of p53 by microRNAs contributes to tumorigenesis, tumor progression and therapeutic resistance. In the present study, we found that the microRNA miR-766 was aberrantly expressed in breast cancer, and that over-expression of miR-766 caused accumulation of wild-type p53 protein in multiple cancer cell lines. Supporting its role in the p53 signalling pathway, miR-766 decreased cell proliferation and colony formation in several cancer cell lines, and cell cycle analyses revealed that miR-766 causes G2 arrest...
February 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430373/a-five-mirna-expression-signature-predicts-survival-in-hepatocellular-carcinoma
#12
Gang Liu, Hui Wang, Jin-Dong Fu, Jing-Ying Liu, Ai-Guo Yan, Yan-Yan Guan
The aim of this study was to identify a microRNA (miRNA) expression signature for predicting HCC (hepatocellular carcinoma) survival. A total of 322 HCC patients in The Cancer Genome Atlas (TCGA) database were randomly divided into training and testing set. miRNAs, associated with survival time in the training set, were identified by using univariate Cox regression analysis. The risk score was formulated based on the expression levels of these miRNAs. Then the miRNA signature was validated in testing set through Kaplan-Meier analysis and log-rank test...
April 21, 2017: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/28430174/whole-exome-analysis-reveals-novel-somatic-genomic-alterations-associated-with-cell-of-origin-in-diffuse-large-b-cell-lymphoma
#13
B A Manso, K Wenzl, Y W Asmann, M J Maurer, M Manske, Z-Z Yang, S L Slager, G S Nowakowski, S M Ansell, T E Witzig, A L Feldman, L Rimsza, B Link, J R Cerhan, A J Novak
No abstract text is available yet for this article.
April 21, 2017: Blood Cancer Journal
https://www.readbyqxmd.com/read/28430172/ezh2-alterations-in-follicular-lymphoma-biological-and-clinical-correlations
#14
S Huet, L Xerri, B Tesson, S Mareschal, S Taix, L Mescam-Mancini, E Sohier, M Carrère, J Lazarovici, O Casasnovas, L Tonon, S Boyault, S Hayette, C Haioun, B Fabiani, A Viari, F Jardin, G Salles
The histone methyltransferase EZH2 has an essential role in the development of follicular lymphoma (FL). Recurrent gain-of-function mutations in EZH2 have been described in 25% of FL patients and induce aberrant methylation of histone H3 lysine 27 (H3K27). We evaluated the role of EZH2 genomic gains in FL biology. Using RNA sequencing, Sanger sequencing and SNP-arrays, the mutation status, copy-number and gene-expression profiles of EZH2 were assessed in a cohort of 159 FL patients from the PRIMA trial. Immunohistochemical (IHC) EZH2 expression (n=55) and H3K27 methylation (n=63) profiles were also evaluated...
April 21, 2017: Blood Cancer Journal
https://www.readbyqxmd.com/read/28430103/genomic-characterization-of-recrudescent-plasmodium-malariae-after-treatment-with-artemether-lumefantrine
#15
Gavin G Rutledge, Ian Marr, G Khai Lin Huang, Sarah Auburn, Jutta Marfurt, Mandy Sanders, Nicholas J White, Matthew Berriman, Chris I Newbold, Nicholas M Anstey, Thomas D Otto, Ric N Price
Plasmodium malariae is the only human malaria parasite species with a 72-hour intraerythrocytic cycle and the ability to persist in the host for life. We present a case of a P. malariae infection with clinical recrudescence after directly observed administration of artemether/lumefantrine. By using whole-genome sequencing, we show that the initial infection was polyclonal and the recrudescent isolate was a single clone present at low density in the initial infection. Haplotypic analysis of the clones in the initial infection revealed that they were all closely related and were presumably recombinant progeny originating from the same infective mosquito bite...
August 15, 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28430102/variable-virulence-phenotype-of-xenorhabdus-bovienii-%C3%AE-proteobacteria-enterobacteriaceae-in-the-absence-of-their-vector-hosts
#16
John G McMullen, Rebecca McQuade, Jean-Claude Ogier, Sylvie Pagès, Sophie Gaudriault, S Patricia Stock
Xenorhabdus bovienii bacteria have a dual lifestyle: they are mutualistic symbionts to many species of Steinernema nematodes and are pathogens to a wide array of insects. Previous studies have shown that virulence of X.bovienii-Steinernema spp. pairs decreases when the nematodes associate with non-cognate bacterial strains. However, the virulence of the X. bovienii strains alone has not been fully investigated. In this study, we characterized the virulence of nine X. bovienii strains in Galleria mellonella and Spodoptera littoralis and performed a comparative genomic analysis to correlate observed phenotypes with strain genotypes...
April 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28430100/discovery-of-african-bat-polyomaviruses-and-infrequent-recombination-in-the-large-t-antigen-in-the-polyomaviridae
#17
Michael Carr, Gabriel Gonzalez, Michihito Sasaki, Kimihito Ito, Akihiro Ishii, Bernard M Hang'ombe, Aaron S Mweene, Yasuko Orba, Hirofumi Sawa
Bat species represent natural reservoirs for a number of high-consequence human pathogens. The present study investigated the diversity of polyomaviruses (PyVs) in Zambian insectivorous and fruit bat species. We describe the complete genomes from four newly proposed African bat PyV species employing the recently recommended criteria provided by the Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses. A comprehensive phylogenetic and recombination analysis was performed to determine genetic relationships and the distribution of recombination events in PyV from mammalian and avian species...
April 22, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28429828/genomic-clustering-of-adaptive-loci-during-parallel-evolution-of-an-australian-wildflower
#18
Federico Roda, Greg M Walter, Rick Nipper, Daniel Ortiz-Barrientos
The buildup of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the co-segregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process but evidence is still scarce. Here we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of the Australian wildflower Senecio lautus...
April 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28429797/sirtuins-in-the-phylum-basidiomycota-a-role-in-virulence-in-cryptococcus-neoformans
#19
Samantha D M Arras, Jessica L Chitty, Maha S I Wizrah, Paige E Erpf, Benjamin L Schulz, Milos Tanurdzic, James A Fraser
Virulence of Cryptococcus neoformans is regulated by a range of transcription factors, and is also influenced by the acquisition of adaptive mutations during infection. Beyond the temporal regulation of virulence factor production by transcription factors and these permanent microevolutionary changes, heritable epigenetic modifications such as histone deacetylation may also play a role during infection. Here we describe the first comprehensive analysis of the sirtuin class of NAD+ dependent histone deacetylases in the phylum Basidiomycota, identifying five sirtuins encoded in the C...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429758/intracellular-lipid-binding-protein-family-diversity-from-oyster-crassostrea-gigas-genomic-and-structural-features-of-invertebrate-lipid-transporters
#20
Guilherme de Toledo-Silva, Guilherme Razzera, Flavia Lucena Zacchi, Nestor Cubas Wendt, Jacó Joaquim Mattos, Afonso Celso Dias Bainy
Intracellular lipid binding proteins (iLBPs) play a role in the transport and cellular uptake of fatty acids and gene expression regulation. The aim of this work was to characterize the iLBP gene family of the Pacific oyster Crassostrea gigas, one of the most cultivated marine bivalves in the world, using bioinformatics and molecular biology approaches. A total of 26 different iLBPs transcripts were identified in the Pacific oyster genome, including alternative splicing and gene duplication events. The oyster iLBP gene family seems to be more expanded than in other invertebrates...
April 21, 2017: Scientific Reports
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