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https://www.readbyqxmd.com/read/27914105/genetic-variants-in-the-integrin-signaling-pathway-genes-predict-cutaneous-melanoma-survival
#1
Hongyu Li, Yanru Wang, Hongliang Liu, Qiong Shi, Yinghui Xu, Wenting Wu, Dakai Zhu, Christopher I Amos, Shenying Fang, Jeffrey E Lee, Jiali Han, Qingyi Wei
To identify genetic variants involved in prognosis of cutaneous melanoma (CM), we investigated associations of single nucleotide polymorphisms (SNPs) of genes in the integrin signaling pathway with CM survival by re-analyzing a published genome-wide association study (GWAS) from The University of Texas M.D. Anderson Cancer Center (MDACC), and then validated significant SNPs in another GWAS from Harvard University. In the MDACC study, 1,148 SNPs were significantly associated with CM-specific survival (CMSS) (P ≤ 0...
December 3, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27914071/differential-radial-capillary-action-of-ligand-assay-dracala-for-high-throughput-detection-of-protein-metabolite-interactions-in-bacteria
#2
Mona W Orr, Vincent T Lee
Bacteria rely on numerous nucleotide second messengers for signal transduction such as cyclic AMP, cyclic-di-GMP, and cyclic-di-AMP. Although a number of receptors responsible for known regulated phenotypes have been established, the completeness of protein receptors in any given organism remains elusive. We have developed a method called differential radial capillary action of ligand assay (DRaCALA) that allows for an unbiased, systematic high-throughput screen for the detection of ligand binding proteins encoded by a genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913980/complete-nucleotide-sequences-and-construction-of-full-length-infectious-cdna-clones-of-cucumber-green-mottle-mosaic-virus-cgmmv-in-a-versatile-newly-developed-binary-vector-including-both-35s-and-t7-promoters
#3
Chan-Hwan Park, Hye-Kyoung Ju, Jae-Yeong Han, Jong-Seo Park, Ik-Hyun Kim, Eun-Young Seo, Jung-Kyu Kim, John Hammond, Hyoun-Sub Lim
Seed-transmitted viruses have caused significant damage to watermelon crops in Korea in recent years, with cucumber green mottle mosaic virus (CGMMV) infection widespread as a result of infected seed lots. To determine the likely origin of CGMMV infection, we collected CGMMV isolates from watermelon and melon fields and generated full-length infectious cDNA clones. The full-length cDNAs were cloned into newly constructed binary vector pJY, which includes both the 35S and T7 promoters for versatile usage (agroinfiltration and in vitro RNA transcription) and a modified hepatitis delta virus ribozyme sequence to precisely cleave RNA transcripts at the 3' end of the tobamovirus genome...
December 2, 2016: Virus Genes
https://www.readbyqxmd.com/read/27913844/global-dna-methylation-profiling-of-manganese-exposed-human-neuroblastoma-sh-sy5y-cells-reveals-epigenetic-alterations-in-parkinson-s-disease-associated-genes
#4
Prashant Tarale, Saravanadevi Sivanesan, Atul P Daiwile, Reinhard Stöger, Amit Bafana, Pravin K Naoghare, Devendra Parmar, Tapan Chakrabarti, Krishnamurthi Kannan
Manganese (Mn) is an essential trace element required for optimal functioning of cellular biochemical pathways in the central nervous system. Elevated exposure to Mn through environmental and occupational exposure can cause neurotoxic effects resulting in manganism, a condition with clinical symptoms identical to idiopathic Parkinson's disease. Epigenetics is now recognized as a biological mechanism involved in the etiology of various diseases. Here, we investigated the role of DNA methylation alterations induced by chronic Mn (100 µM) exposure in human neuroblastoma (SH-SY5Y) cells in relevance to Parkinson's disease...
December 2, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27913833/tight-repulsion-linkage-between-sr36-and-sr39-was-revealed-by-genetic-cytogenetic-and-molecular-analyses
#5
Bosco Chemayek, Urmil K Bansal, Naeela Qureshi, Peng Zhang, William W Wagoire, Harbans S Bariana
The shortening of Aegilops speltoides segment did not facilitate recombination between stem rust resistance genes Sr36 and Sr39 . Robustness of marker rwgs28 for marker-assisted selection of Sr39 was demonstrated. Stem rust resistance genes Sr39 and Sr36 were transferred from Aegilops speltoides and Triticum timopheevii, respectively, to chromosome 2B of wheat. Genetic stocks RL6082 and RWG1 carrying Sr39 on a large and a shortened Ae. speltoides segments, respectively, and the Sr36-carrying Australian wheat cultivar Cook were used in this study...
December 2, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27913729/qsea-modelling-of-genome-wide-dna-methylation-from-sequencing-enrichment-experiments
#6
Matthias Lienhard, Sabrina Grasse, Jana Rolff, Steffen Frese, Uwe Schirmer, Michael Becker, Stefan Börno, Bernd Timmermann, Lukas Chavez, Holger Sültmann, Gunda Leschber, Iduna Fichtner, Michal R Schweiger, Ralf Herwig
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913688/left-ventricle-transcriptomic-analysis-reveals-connective-tissue-accumulation-associates-with-initial-age-dependent-decline-in-v%C3%AC-o2peak-from-its-lifetime-apex
#7
Gregory N Ruegsegger, Ryan G Toedebusch, Joshua F Braselton, Thomas E Childs, Frank W Booth
Peak oxygen consumption (V̇O2peak) strongly predicts morbidity and mortality better than other established risk factors, yet mechanisms associated with its age-associated decline are unknown. Our lab has shown that V̇O2peak first begins to decrease at the same age of 19-20 weeks old in both sedentary and wheel-running, female Wistar rats (Toedebusch et al., Physiol Genomics. 48:101-15, 2016). Here, we employed a total systemic approach using unsupervised interrogation of mRNA with RNA-sequencing. The purpose of our study was to analyze transcriptomic profiles from both sedentary (SED) and wheel-running (RUN) conditions as a strategy to identify pathways in the left ventricle that may contribute to the initial reductions in V̇O2peak occurring between 19 and 27 weeks of age...
December 2, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/27913634/comparative-analysis-highlights-variable-genome-content-of-wheat-rusts-and-divergence-of-the-mating-loci
#8
Christina A Cuomo, Guus Bakkeren, Hala Badr Khalil, Vinay Panwar, David Joly, Rob Linning, Sharadha Sakthikumar, Xiao Song, Xian Adiconis, Lin Fan, Jonathan M Goldberg, Joshua Z Levin, Sarah Young, Qiandong Zeng, Yehoshua Anikster, Myron Bruce, Meinan Wang, Chuntao Yin, Brent McCallum, Les J Szabo, Scot Hulbert, Xiaming Chen, John P Fellers
Three members of the Puccinia genus, P. triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi and basidiomycetes, and to identify genes of significance for infection...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27913617/evaluating-sequence-based-genomic-prediction-with-an-efficient-new-simulator
#9
Miguel Pérez-Enciso, Natalia Forneris, Gustavo de Los Campos, Andrés Legarra
The vast amount of sequence data to analyze complex traits is posing new challenges in terms of analysis and interpretation of the results. Although simulation is a fundamental tool to investigate the reliability of genomic analyses and to optimize experimental design, existing software cannot simulate complete genomes realistically. To remedy this, we have developed a new strategy (Sequence Based Virtual Breeding, SBVB) that consists of using real sequence data and simulating new offspring genomes and phenotypes in a very efficient and flexible manner...
December 2, 2016: Genetics
https://www.readbyqxmd.com/read/27913434/a-study-of-tp53-rna-splicing-illustrates-pitfalls-of-rna-seq-methodology
#10
Sunali Mehta, Peter Tsai, Annette Lasham, Hamish Campbell, Roger Reddel, Antony Braithwaite, Cristin Print
TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to infer isoform abundance. In this study, we used deep RNA-seq, droplet digital PCR (ddPCR), and real-time quantitative reverse transcriptase PCR (RT-qPCR) from nine human cell lines and RNA-seq data available for tumors in The Cancer Genome Atlas to analyze TP53 splice variant expression...
October 20, 2016: Cancer Research
https://www.readbyqxmd.com/read/27913420/multiple-evolutionary-trajectories-have-led-to-the-emergence-of-races-in-fusarium-oxysporum-f-sp-lycopersici
#11
Biju V Chellappan, Like Fokkens, Petra M Houterman, Martijn Rep, Ben J C Cornelissen
: Race 1 isolates of Fusarium oxysporum f. sp. lycopersici (Fol) are characterized by the presence of AVR1 in their genome. The product of this gene, Avr1, triggers resistance in tomato cultivars carrying resistance gene I In Fol race 2 and race 3 isolates, AVR1 is absent and hence they are virulent on tomato cultivars carrying I In this study, we analyze an approximately 100 kb genomic fragment containing the AVR1 locus of race 1 isolate Fol004, and compare it to the sequenced genome of Fol race 2 isolate 4287 (Fol4287)...
December 2, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27913415/a-highly-expressed-high-molecular-weight-s-layer-complex-of-pelosinus-strain-ufo1-binds-uranium
#12
Michael P Thorgersen, W Andrew Lancaster, Lara Rajeev, Xiaoxuan Ge, Brian J Vaccaro, Farris L Poole, Adam P Arkin, Aindrila Mukhopadhyay, Michael W W Adams
: Cells suspensions of Pelosinus sp. strain UFO1 were previously shown, using spectroscopic analysis, to sequester uranium as U(IV) complexed with carboxyl and phosphoryl ligands on protein(s). The goal of this project was to characterize the proteins involved in uranium binding. Virtually all of the uranium in UFO1 cells was associated with a heterodimeric protein, which was termed the uranium-binding complex (UBC). UBC was composed of two S-layer domain proteins encoded by UFO1_4202 and UFO1_4203...
December 2, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27913161/novel-brain-expressed-rna-identified-at-the-mir137-schizophrenia-associated-locus
#13
Olympia Gianfrancesco, Alix Warburton, David A Collier, Vivien J Bubb, John P Quinn
Genome-wide association studies (GWAS) have identified a locus on chromosome 1p21.3 to be highly associated with schizophrenia. A microRNA, MIR137, within this locus has been proposed as the gene causally associated with schizophrenia, due to its known role as a regulator of neuronal development and function. However, the involvement of other genes within this region, including DPYD (dihydropyrimidine dehydrogenase), is also plausible. In this communication, we describe a previously uncharacterised, brain-expressed RNA, EU358092, within the schizophrenia-associated region at 1p21...
November 29, 2016: Schizophrenia Research
https://www.readbyqxmd.com/read/27913093/genome-of-the-carbapenemase-producing-clinical-isolate-elizabethkingia-miricola-em_chuv-and-comparative-genomics-with-elizabethkingia-meningoseptica-and-elizabethkingia-anophelis-evidence-for-intrinsic-multidrug-resistance-trait-of-emerging-pathogens
#14
Onya Opota, Seydina M Diene, Claire Bertelli, Guy Prod'hom, Philippe Eckert, Gilbert Greub
Elizabethkingia miricola is a Gram-negative non-fermenting rod emerging as a life-threatening human pathogen. The multidrug-resistant (MDR) carbapenemase-producing clinical isolate E. miricola EM_CHUV was recovered in the setting of severe nosocomial pneumonia. In this study, the genome of E. miricola EM_CHUV was sequenced and a functional analysis was performed, including a comparative genomic study with Elizabethkingia meningoseptica and Elizabethkingia anophelis. The resistome of EM_CHUV revealed the presence of a high number of resistance genes, including the presence of the blaGOB-13 and blaB-9 carbapenemase-encoding genes...
November 15, 2016: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/27913074/draft-genome-and-description-of-orrella-dioscoreae-gen-nov-sp-nov-a-new-species-of-alcaligenaceae-isolated-from-leaf-acumens-of-dioscorea-sansibarensis
#15
Aurelien Carlier, Margo Cnockaert, Linda Fehr, Peter Vandamme, Leo Eberl
Dioscorea sansibarensis is a monocot species of inedible yam native of tropical Africa and Madagascar. Leaves of D. sansibarensis feature prominent acumen glands that are densely colonized by bacteria. We describe here the isolation and characterization of bacteria from leaf glands of D. sansibarensis specimens obtained from various botanical gardens. Phylogenetic and phenotypic characterizations indicate that the isolates belong to a novel genus and species of the Alcaligenaceae family for which we propose the name Orrella dioscoreae gen...
November 24, 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27912968/validation-of-a-thin-layer-chromatography-densitometry-method-for-the-characterization-of-invertase-activity
#16
Justine Ferey, David Da Silva, Sophie Bravo-Veyrat, Pierre Lafite, Richard Daniellou, Benoît Maunit
This paper presents a kinetic study of invertase, a specific fructofuranosidase cloned from the Leishmania major genome. The kinetic parameters of the β-d-fructofuranosidase from Leishmania major (BfrA) were determined using Thin-Layer Chromatography (TLC) and UV-densitometry (TLC@UV) specifically developed for the separation and detection of three carbohydrates namely sucrose, glucose and fructose. Separation was performed on TLC silica gel 60 F254 plates impregnated with sodium bisulphate and citrate and heated prior to development...
November 25, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27912769/three-novel-bacteriophages-isolated-from-the-east-african-rift-valley-soda-lakes
#17
Leonardo Joaquim van Zyl, Shonisani Nemavhulani, James Cass, Donald Arthur Cowan, Marla Trindade
BACKGROUND: Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. METHODS: Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays...
December 3, 2016: Virology Journal
https://www.readbyqxmd.com/read/27912743/str-realigner-a-realignment-method-for-short-tandem-repeat-regions
#18
Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori, Masao Nagasaki
BACKGROUND: In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27912729/genomic-insights-from-whole-genome-sequencing-of-four-clonal-outbreak-campylobacter-jejuni-assessed-within-the-global-c-jejuni-population
#19
Clifford G Clark, Chrystal Berry, Matthew Walker, Aaron Petkau, Dillon O R Barker, Cai Guan, Aleisha Reimer, Eduardo N Taboada
BACKGROUND: Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27912315/genetics-of-infectious-and-inflammatory-diseases-overlapping-discoveries-from-association-and-exome-sequencing-studies
#20
David Langlais, Nassima Fodil, Philippe Gros
Genome technologies have defined a complex genetic architecture in major infectious, inflammatory, and autoimmune disorders. High density marker arrays and Immunochips have powered genome-wide association studies (GWAS) that have mapped nearly 450 genetic risk loci in 22 major inflammatory diseases, including a core of common genes that play a central role in pathological inflammation. Whole-exome and whole-genome sequencing have identified more than 265 genes in which mutations cause primary immunodeficiencies and rare forms of severe inflammatory bowel disease...
December 1, 2016: Annual Review of Immunology
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