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https://www.readbyqxmd.com/read/28527409/molecular-characterization-of-pigeon-torque-teno-virus-pttv-in-jiangsu-province
#1
Zhicheng Zhang, Wei Dai, Dingzhen Dai
The torque teno virus (TTV) is a recently discovered DNA virus that has been detected in many different hosts, including humans, livestock and poultry. To date, there is no report of pigeon TTV (PTTV) from anywhere in the world. To investigate the distribution of PTTV in pigeons from the eastern Chinese province of Jiangsu and characterize their genomes, we employed PCR to detect PTTV in 144 samples collected from 6 pigeon plants in Jiangsu province, amplify complete genomes from representative samples and analyze genetic characteristics using bioinformatics...
May 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28527335/dissection-of-cis-regulatory-element-architecture-of-the-rice-oleosin-gene-promoters-to-assess-abscisic-acid-responsiveness-in-suspension-cultured-rice-cells
#2
Sol Kim, Soo-Bin Lee, Chae-Seong Han, Mi-Na Lim, Sung-Eun Lee, In Sun Yoon, Yong-Sic Hwang
Oleosins are the most abundant proteins in the monolipid layer surrounding neutral storage lipids that form oil bodies in plants. Several lines of evidence indicate that they are physiologically important for the maintenance of oil body structure and for mobilization of the lipids stored inside. Rice has six oleosin genes in its genome, the expression of all of which was found to be responsive to abscisic acid (ABA) in our examination of mature embryo and aleurone tissues. The 5'-flanking region of OsOle5 was initially characterized for its responsiveness to ABA through a transient expression assay system using the protoplasts from suspension-cultured rice cells...
May 1, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28527269/-first-evidence-of-lymphocytic-choriomeningitis-virus-arenavirus-infection-in-mus-musculus-rodents-captured-in-the-urban-area-of-the-municipality-of-sincelejo-sucre-colombia
#3
Anais Castellar, Marco Guevara, Juan D Rodas, Andrés F Londoño, Esteban Arroyave, Francisco J Díaz, Silvana Levis, Pedro J Blanco
INTRODUCTION: The lymphocytic choriomeningitis virus is an Old World arenavirus that infects Mus musculus, and can cause congenital hydrocephalus, chorioretinitis and multisystemic failure in transplant human recipients. Although the disease has not been clinically diagnosed in Colombia yet, there have been reports of infection with the Pichindé virus in rodents from Cauca and Valle del Cauca departments, and with the Guanarito virus in rodents from Córdoba department. OBJECTIVE: To identify the lymphocytic choriomeningitis virus from Mus musculus captured in the municipality of Sincelejo...
April 1, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/28527107/an-immune-related-six-lncrna-signature-to-improve-prognosis-prediction-of-glioblastoma-multiforme
#4
Meng Zhou, Zhaoyue Zhang, Hengqiang Zhao, Siqi Bao, Liang Cheng, Jie Sun
Recent studies have demonstrated the utility and superiority of long non-coding RNAs (lncRNAs) as novel biomarkers for cancer diagnosis, prognosis, and therapy. In the present study, the prognostic value of lncRNAs in glioblastoma multiforme was systematically investigated by performing a genome-wide analysis of lncRNA expression profiles in 419 glioblastoma patients from The Cancer Genome Atlas (TCGA) project. Using survival analysis and Cox regression model, we identified a set of six lncRNAs (AC005013.5, UBE2R2-AS1, ENTPD1-AS1, RP11-89C21...
May 19, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28527099/molecular-diversity-among-viroids-infecting-chrysanthemum-in-india
#5
C R Adkar-Purushothama, G Chennappa, K Poornachandra Rao, M Y Sreenivasa, P K Maheshwar, M N Nagendra Prasad, T Sano
Association of Chrysanthemum stunt viroid (CSVd) and Chrysanthemum chlorotic mottle viroid (CChMVd) with the Chrysanthemum plants exhibiting severe stunting, distinct yellow leaf mottling, and chlorosis was detected in the main chrysanthemum-growing regions of India. Sequence analysis of 90 cDNA clones obtained for CSVd and CChMVd, representing the chrysanthemum-growing regions of India, revealed the high degree of sequence variation throughout the genome under natural conditions. Additionally, all the analyzed CChMVd clones revealed the presence of UUUC in the tetraloop, a signature of symptomatic variants in susceptible cultivars...
May 19, 2017: Virus Genes
https://www.readbyqxmd.com/read/28526936/fingerprint-of-long-non-coding-rna-regulated-by-cyclic-mechanical-stretch-in-human-aortic-smooth-muscle-cells-implications-for-hypertension
#6
Laura-Eve Mantella, Krishna K Singh, Paul Sandhu, Crystal Kantores, Azza Ramadan, Nadiya Khyzha, Adrian Quan, Mohammed Al-Omran, Jason E Fish, Robert P Jankov, Subodh Verma
Emerging evidence suggests that long non-coding RNAs (lncRNAs) represent a cellular hub coordinating various cellular processes that are critical in health and disease. Mechanical stress triggers changes in vascular smooth muscle cells (VSMCs) that in turn contribute to pathophysiological changes within the vasculature. We sought to evaluate the role that lncRNAs play in mechanical stretch-induced alterations of human aortic smooth muscle cells (HASMCs). RNA (lncRNA and mRNA) samples isolated from HASMCs that had been subjected to 10 or 20% elongation (1 Hz) for 24 h were profiled with the Arraystar Human LncRNA Microarray V3...
May 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28526913/mapping-qtls-controlling-kernel-dimensions-in-a-wheat-inter-varietal-ril-mapping-population
#7
Ruiru Cheng, Zhongxin Kong, Liwei Zhang, Quan Xie, Haiyan Jia, Dong Yu, Yulong Huang, Zhengqiang Ma
Seven kernel dimension QTLs were identified in wheat, and kernel thickness was found to be the most important dimension for grain weight improvement. Kernel morphology and weight of wheat (Triticum aestivum L.) affect both yield and quality; however, the genetic basis of these traits and their interactions has not been fully understood. In this study, to investigate the genetic factors affecting kernel morphology and the association of kernel morphology traits with kernel weight, kernel length (KL), width (KW) and thickness (KT) were evaluated, together with hundred-grain weight (HGW), in a recombinant inbred line population derived from Nanda2419 × Wangshuibai, with data from five trials (two different locations over 3 years)...
May 19, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28526858/expression-and-activity-of-the-bioh-esterase-of-biotin-synthesis-is-independent-of-genome-context
#8
Xinyun Cao, Lei Zhu, Zhe Hu, John E Cronan
BioH is an α/β-hydrolase required for synthesis of the pimelate moiety of biotin in diverse bacteria. The bioH gene is found in different genomic contexts. In some cases (e.g., Escherichia coli) the gene is not located within a biotin synthetic operon and its transcription is not coregulated with the other biotin synthesis genes. In other genomes such as Pseudomonas aeruginosa the bioH gene is within a biotin synthesis operon and its transcription is coregulated with the other biotin operon genes. The esterases of pimelate moiety synthesis show remarkable genomic plasticity in that in some biotin operons bioH is replaced by other α/ß hydrolases of diverse sequence...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526842/revealing-genome-scale-transcriptional-regulatory-landscape-of-ompr-highlights-its-expanded-regulatory-roles-under-osmotic-stress-in-escherichia-coli-k-12-mg1655
#9
Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Jina Yang, Byung-Kwan Cho, Bernhard O Palsson
A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the osmotic stress response in bacteria. Here, we reveal a genome-scale OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level in an OmpR knock-out strain. Specifically, we find that: 1) OmpR regulates mostly membrane-located gene products involved in diverse fundamental biological processes, such as narU (encoding nitrate/nitrite transporter), ompX (encoding outer membrane protein X), and nuoN (encoding NADH:ubiquinone oxidoreductase); 2) by investigating co-regulation of entire sets of genes regulated by other stress-response TFs, stresses are surprisingly independently regulated among each other; and, 3) a detailed investigation of the physiological roles of the newly discovered OmpR regulon genes reveals that activation of narU represents a novel strategy to significantly improve osmotic stress tolerance of E...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526793/genomic-analysis-of-calderihabitans-maritimus-kkc1-a-thermophilic-hydrogenogenic-carboxydotrophic-bacterium-isolated-from-marine-sediment
#10
Kimiho Omae, Yasuko Yoneda, Yuto Fukuyama, Takashi Yoshida, Yoshihiko Sako
Calderihabitans maritimus KKC1 is a thermophilic hydrogenogenic carboxydotroph isolated from a submerged marine caldera. Here, we describe the de novo sequencing and feature analysis of the C. maritimus KKC1 genome. Genome-based phylogenetic analysis confirmed that C. maritimus KKC1 was most closely related to the genus Moorella, which includes well-studied acetogenic members. Comparative genomic analysis revealed that, like Moorella, C. maritimus KKC1 retained both the CO2-reducing Wood-Ljungdahl pathway and energy-converting hydrogenase-based module activated by reduced ferredoxin, but lacked the HydABC and NfnAB electron bifurcating enzymes and pyruvate:ferredoxin oxidoreductase required for ferredoxin reduction during acetogenic growth...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28526791/pseudomonas-chlororaphis-produces-two-distinct-r-tailocins-that-contribute-to-bacterial-competition-in-biofilms-and-on-roots
#11
Robert J Dorosky, Jun Myoung Yu, Leland S Pierson, Elizabeth A Pierson
R-type tailocins are high molecular weight bacteriocins that resemble bacteriophage tails and are encoded within the genomes of many Pseudomonas species. In this study, analysis of the P. chlororaphis 30-84 R-tailocin gene cluster revealed that it encodes the structural components to produce two R-tailocins of different ancestral origin. Two distinct R-tailocin populations differing in length were observed in UV induced lysates of P. chlororaphis 30-84 via transmission electron microscopy. Mutants defective in the production of one or both R-tailocins demonstrated that the killing spectrum of each tailocin is limited to Pseudomonas species...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28526731/validated-bayesian-differentiation-of-causative-and-passenger-mutations
#12
Frederick R Cross, Michal Breker, Kristi Lieberman
In many contexts, the problem arises of determining which of many candidate mutations is the most likely to be causative for some phenotype. It is desirable to have a way to evaluate this probability that relies as little as possible on previous knowledge, to avoid bias against discovering new genes or functions. We are isolating mutants with blocked cell cycle progression in Chlamydomonas, and determining mutant genome sequences. Due to the intensity of UV mutagenesis required for efficient mutant collection, the mutants contain multiple mutations altering coding sequence...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526730/a-targeted-capture-linkage-map-anchors-the-genome-of-the-schistosomiasis-vector-snail-biomphalaria-glabrata
#13
Jacob A Tennessen, Stephanie R Bollmann, Michael S Blouin
The aquatic planorbid snail Biomphalaria glabrate is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here we used targeted capture markers to map over 10,000 B. glabrate scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups. We added additional scaffolds to these linkage groups based on linkage disequilibrium analysis of targeted capture and whole-genome sequences of 96 unrelated snails...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526729/phased-genotyping-by-sequencing-enhances-analysis-of-genetic-diversity-and-reveals-divergent-copy-number-variants-in-maize
#14
Heather Manching, Subhajit Sengupta, Keith R Hopper, Shawn W Polson, Yuan Ji, Randall J Wisser
High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires a number of issues encountered with GBS be considered, including the sequencing of non-overlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526608/microrna-analysis-of-taenia-crassiceps-cysticerci-under-praziquantel-treatment-and-genome-wide-identification-of-taenia-solium-mirnas
#15
Matías Gastón Pérez, Natalia Macchiaroli, Gabriel Lichtenstein, Gabriela Conti, Sebastián Asurmendi, Diego Humberto Milone, Georgina Stegmayer, Laura Kamenetzky, Marcela Cucher, Mara Cecilia Rosenzvit
MicroRNAs (miRNAs) are small non-coding RNAs that have emerged as important regulators of gene expression and perform critical functions in development and disease. In spite of the increased interest in miRNAs from helminth parasites, no information is available on miRNAs from Taenia solium, the causative agent of cysticercosis, a neglected disease affecting millions of people worldwide. Here we performed a comprehensive analysis of miRNAs from Taenia crassiceps, a laboratory model for T. solium studies, and identified miRNAs in the T...
May 16, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28526573/transcriptomic-variation-of-locally-infected-skin-of-epinephelus-coioides-reveals-the-mucosal-immune-mechanism-against-cryptocaryon-irritans
#16
Yazhou Hu, Anxing Li, Yang Xu, Biao Jiang, Geling Lu, Xiaochun Luo
Fish skin is the largest immunologically active mucosal organ, providing first-line defense against external pathogens. However, the skin-associated immune mechanisms of fish are still unclear. Cryptocaryon irritans is an obligate ectoparasitic ciliated protozoan that infects almost all marine fish, and is believed to be an excellent pathogen model to study fish mucosal immunity. In this study, a de novo transcriptome assembly of Epinephelus coioides skin post C. irritans tail-infection was performed for the first time using the Illumina HiSeq™ 2500 system...
May 16, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28526295/large-scale-exploratory-genetic-analysis-of-cognitive-impairment-in-parkinson-s-disease
#17
Ignacio F Mata, Catherine O Johnson, James B Leverenz, Daniel Weintraub, John Q Trojanowski, Vivianna M Van Deerlin, Beate Ritz, Rebecca Rausch, Stewart A Factor, Cathy Wood-Siverio, Joseph F Quinn, Kathryn A Chung, Amie L Peterson-Hiller, Alberto J Espay, Fredy J Revilla, Johnna Devoto, Dora Yearout, Shu-Ching Hu, Brenna A Cholerton, Thomas J Montine, Karen L Edwards, Cyrus P Zabetian
Cognitive impairment is a common and disabling problem in Parkinson's disease (PD). Identification of genetic variants that influence the presence or severity of cognitive deficits in PD might provide a clearer understanding of the pathophysiology underlying this important nonmotor feature. We genotyped 1105 PD patients from the PD Cognitive Genetics Consortium for 249,336 variants using the NeuroX array. Participants underwent assessments of learning and memory (Hopkins Verbal Learning Test-Revised [HVLT-R]), working memory/executive function (Letter-Number Sequencing and Trail Making Test [TMT] A and B), language processing (semantic and phonemic verbal fluency), visuospatial abilities (Benton Judgment of Line Orientation [JoLO]), and global cognitive function (Montreal Cognitive Assessment)...
April 20, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28526069/xlf-mediated-nhej-activity-in-hepatocellular-carcinoma-therapy-resistance
#18
Sitian Yang, Xiao Qi Wang
BACKGROUND: DNA repair pathways are used by cancer cells to overcome many standard anticancer treatments, causing therapy resistance. Here, we investigated the role of XRCC4-like factor (XLF), a core member of the non-homologous end joining (NHEJ) repair pathway, in chemoresistance in hepatocellular carcinoma (HCC). METHODS: qRT-PCR analysis and western blotting were performed to detect expression levels of genes and proteins related to NHEJ. NHEJ repair capacity was assessed in vitro (cell-free) and in vivo by monitoring the activity of the NHEJ pathway...
May 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28525968/survivalgwas_sv-software-for-the-analysis-of-genome-wide-association-studies-of-imputed-genotypes-with-time-to-event-outcomes
#19
Hamzah Syed, Andrea L Jorgensen, Andrew P Morris
BACKGROUND: Analysis of genome-wide association studies (GWAS) with "time to event" outcomes have become increasingly popular, predominantly in the context of pharmacogenetics, where the survival endpoint could be death, disease remission or the occurrence of an adverse drug reaction. However, methodology and software that can efficiently handle the scale and complexity of genetic data from GWAS with time to event outcomes has not been extensively developed. RESULTS: SurvivalGWAS_SV is an easy to use software implemented using C# and run on Linux, Mac OS X & Windows operating systems...
May 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28525654/molecular-detection-by-analysis-of-the-16s-rrna-gene-of-fecal-coliform-bacteria-from-the-two-korean-apodemus-species-apodemus-agrarius-and-a-peninsulae
#20
M M Rahman, K B Yoon, S J Lim, M G Jeon, H J Kim, H Y Kim, J Y Cho, H M Chae, Y C Park
Wild mouse feces can disseminate zoonotic microorganisms throughout a farm, which is a great threat to human health and can lead to economic loss through contaminated agricultural produce. To assess the microbial communities, especially fecal coliform bacteria, we used two methods. First, we isolated bacterial colonies onto the common media LB (lactose broth) agar, TSA (tryptic soy agar), and MRS (de Man, Rogosa, and Sharpe) agar, and then randomly select colonies from each plate and stocked them to the mother plate for genomic DNA isolation...
May 18, 2017: Genetics and Molecular Research: GMR
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