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Genomics Data

Sooyeon Lim, Dong-Ho Chang, Byoung-Chan Kim
Bacillus solimangrovi GH 2-4(T) was isolated from mangrove soil and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession MJEH00000000.
December 2016: Genomics Data
Nicolas Feau, Greg Taylor, Angela L Dale, Braham Dhillon, Guillaume J Bilodeau, Inanç Birol, Steven J M Jones, Richard C Hamelin
The Phytophthora genus comprises of some of the most destructive plant pathogens and attack a wide range of hosts including economically valuable tree species, both angiosperm and gymnosperm. Many known species of Phytophthora are invasive and have been introduced through nursery and agricultural trade. As part of a larger project aimed at utilizing genomic data for forest disease diagnostics, pathogen detection and monitoring (The TAIGA project: Tree Aggressors Identification using Genomic Approaches; http://taigaforesthealth...
December 2016: Genomics Data
Petra Kraus, Thomas Lufkin
The adult bovine (Bos taurus) intervertebral disc is primarily comprised of two major tissue types: The outer annulus fibrosus (AF) and the central nucleus pulposus (NP). We isolated several primary cell lineages of passage (P) 0 cells from the AF tissue omitting typically used enzymatic tissue digestion protocols. The cells grow past p10 without signs of senescence in DMEM + 10% FCS on 0.1% gelatin coated/uncoated surfaces of standard cell culture plates and survive freeze-thawing. Preliminary analysis of the AF derived cells for expression of the two structural genes Col1a1 and Col2a1 was performed by PISH recapitulating the expression observed in vivo...
December 2016: Genomics Data
Vincent Doublet, Robert J Paxton, Cynthia M McDonnell, Emeric Dubois, Sabine Nidelet, Robin F A Moritz, Cédric Alaux, Yves Le Conte
Regulation of gene expression in the brain plays an important role in behavioral plasticity and decision making in response to external stimuli. However, both can be severely affected by environmental factors, such as parasites and pathogens. In honey bees, the emergence and re-emergence of pathogens and potential for pathogen co-infection and interaction have been suggested as major components that significantly impaired social behavior and survival. To understand how the honey bee is affected and responds to interacting pathogens, we co-infected workers with two prevalent pathogens of different nature, the positive single strand RNA virus Black queen cell virus (BQCV), and the Microsporidia Nosema ceranae, and explored gene expression changes in brains upon single infections and co-infections...
December 2016: Genomics Data
Farhad Shahsavar, Shaghayegh Mapar, Seyyed Amir Yasin Ahmadi
Multiple sclerosis (MS) is a disease in which we can recognize destruction of the myelin that is around nerve cells of brain and spinal cord called as oligodendrocytes. Both genetic and environmental factors play roles in MS. One of these genes is the killer-cell immunoglobulin-like receptor (KIR) which expressed on surface of natural killer cells (NKs). These genes have loci (not locus) in human genome, so they inherit as haplotypes. The results of previous studies show that different genes of KIR may affect both susceptibility and resistance to such autoimmune disorders that their pathogenesis in MS is still unclear...
December 2016: Genomics Data
Ilaria Piccini, Marcos Araúzo-Bravo, Guiscard Seebohm, Boris Greber
Cardiac induction of human embryonic stem cells (hESCs) is a process bearing increasing medical relevance, yet it is poorly understood from a developmental biology perspective. Anticipated technological progress in deriving stably expandable cardiac precursor cells or in advancing cardiac subtype specification protocols will likely require deeper insights into this fascinating system. Recent improvements in controlling hESC differentiation now enable a near-homogeneous induction of the cardiac lineage. This is based on an optimized initial stimulation of mesoderm-inducing signaling pathways such as Activin and/or FGF, BMP, and WNT, followed by WNT inhibition as a secondary requirement...
December 2016: Genomics Data
Sooyeon Lim, Dong-Ho Chang, Byoung-Chan Kim
Dermabacter vaginalis AD1-86(T) was isolated from the vaginal fluid of a Korean woman. Whole genome sequencing analysis was conducted using a PacBio RS II platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession NZ_CP012117.
December 2016: Genomics Data
Farzaneh Moghadam, M B Couger, Breeanna Russ, Randi Ramsey, Radwa A Hanafy, Connie Budd, Donald P French, Wouter D Hoff, Noha Youssef
The genus Pantoea is a predominant member of host-associated microbiome. We here report on the genomic analysis of Pantoea eucrina strain Russ that was isolated from a trashcan at Oklahoma State University, Stillwater, OK. The draft genome of Pantoea eucrina strain Russ consists of 3,939,877 bp of DNA with 3704 protein-coding genes and 134 RNA genes. This is the first report of a genome sequence of a member of Pantoea eucrina. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of all amino acids as well as glucose, fructose, mannose, xylose, arabinose and galactose, suggesting the organism is a versatile heterotroph...
December 2016: Genomics Data
Anton P Avramov, M B Couger, Emily L Hartley, Craig Land, Rachel Wellendorf, Radwa A Hanafy, Connie Budd, Donald P French, Wouter D Hoff, Noha Youssef
Microbacterium oleivorans is a predominant member of hydrocarbon-contaminated environments. We here report on the genomic analysis of M. oleivorans strain Wellendorf that was isolated from an indoor door handle. The partial genome of M. oleivorans strain Wellendorf consists of 2,916,870 bp of DNA with 2831 protein-coding genes and 49 RNA genes. The organism appears to be a versatile mesophilic heterotroph potentially capable of hydrolysis a suite of carbohydrates and amino acids. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of glucose, fructose, rhamnose, galactose, xylose, arabinose, alanine, aspartate, asparagine, glutamate, serine, glycine, threonine and cysteine...
December 2016: Genomics Data
Sumantra Chatterjee, Petra Kraus, V Sivakamasundari, Sook Peng Yap, Vibhor Kumar, Shyam Prabhakar, Thomas Lufkin
This work pertains to GEO submission GSE36672, in vivo and in vitro genome wide binding (ChIP-Seq) of Bapx1/Nkx3.2 and Sox9 proteins. We have previously shown that data from a genome wide binding assay combined with transcriptional profiling is an insightful means to divulge the mechanisms directing cell type specification and the generation of tissues and subsequent organs [1]. Our earlier work identified the role of the DNA-binding homeodomain containing protein Bapx1/Nkx3.2 in midgestation murine embryos...
December 2016: Genomics Data
Nobuhiro Wada, Satoru Yamanaka, Junko Shibato, Randeep Rakwal, Satoshi Hirako, Yuzuru Iizuka, Hyounju Kim, Akiyo Matsumoto, Ai Kimura, Fumiko Takenoya, Genta Yasunaga, Seiji Shioda
This study investigates effects of dipeptide balenine, as a major component of whale meat extract (hereafter, WME), supplementation on senescence-accelerated mouse prone 8 (SAMP8), an Alzheimer's disease (AD) model at level of learning and memory formation and brain expression profiles genome-wide in brain. Mice fed experimental balenine (+ WME) supplemented diet for 26 weeks were subjected to four behavioral tests - open field, Y-maze, new object recognition, and water-filled multiple T-maze - to examine effects on learning and memory...
December 2016: Genomics Data
Deden Derajat Matra, Toshinori Kozaki, Kazuo Ishii, Roedhy Poerwanto, Eiichi Inoue
Garcinia mangostana L. (Mangosteen), of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091...
December 2016: Genomics Data
Ambika Sahoo, Basudeba Kar, Suprava Sahoo, Asit Ray, Sanghamitra Nayak
Turmeric is an economically valued crop, because of its utility in the food, pharmaceutical industries and Ayurvedic medicine, attracts the attention in many areas of research work. In the present study, we executed resequencing through transcriptome assembly of the turmeric cultivar Suvarna (CL_Suv_10). Resequencing of Suvarna variety has generated 5 Gbases raw data with 75 bp paired-end sequence. The raw data has been submitted to SRA database of NCBI with accession number SRR4042181. Reads were assembled using Cufflinks-2...
December 2016: Genomics Data
Ashagrie Gibtan, Mingyeong Woo, Dokyung Oh, Kyounghee Park, Han-Seung Lee, Jae Hak Sohn, Dong-Woo Lee, Jung-Kue Shin, Sang-Jae Lee
The draft genome sequence of Halorubrum sp. SAH-A6, isolated from commercial rock salts of the Danakil depression, Ethiopia. The genome comprised 3,325,770 bp, with the G + C content of 68.0%. The strain has many genes which are responsible for secondary metabolites biosynthesis, transport and catabolism as compared to other Halorubrum archaea members. Abundant genes responsible for numerous transport systems, solute accumulation, and aromatic/sulfur decomposition were detected. The first genomic analysis encourages further research on comparative genomics, and biotechnological applications...
December 2016: Genomics Data
Bernard J Pope, Khalid Mahmood, Chol-Hee Jung, Daniel J Park
DNA breakage arises during a variety of biological processes, including transcription, replication and genome rearrangements. In the context of disease, extensive fragmentation of DNA has been described in cancer cells and during early stages of neurodegeneration (Stephens et al., 2011 Stephens et al. (2011) [5]; Blondet et al., 2001 Blondet et al. (2001) [1]). Stults et al. (2009) Stults et al. (2009) [6] reported that human rDNA gene clusters are hotspots for recombination and that rDNA restructuring is among the most common chromosomal alterations in adult solid tumours...
December 2016: Genomics Data
Sarah Adjei-Fremah, Kingsley Ekwemalor, Emmanuel Asiamah, Hamid Ismail, Mulumebet Worku
Probiotic supplements are beneficial for animal health and rumen function; and lipopolysaccharides (LPS) from gram negative bacteria have been associated with inflammatory diseases. In this study the transcriptional profile in whole blood collected from probiotics-treated cows was investigated in response to stimulation with lipopolysaccharides (LPS) in vitro. Microarray experiment was performed between LPS-treated and control samples using the Agilent one-color bovine v2 bovine (v2) 4x44K array slides. Global gene expression analysis identified 13,658 differentially expressed genes (fold change cutoff ≥ 2, P < 0...
December 2016: Genomics Data
Eva Dunkhase, Kerstin U Ludwig, Michael Knapp, Christine F Skibola, Jane C Figueiredo, Fay Julie Hosking, Eva Ellinghaus, Maria Teresa Landi, Hongxia Ma, Hidewaki Nakagawa, Jong-Won Kim, Jiali Han, Ping Yang, Anne C Böhmer, Manuel Mattheisen, Markus M Nöthen, Elisabeth Mangold
Previous research suggests a genetic overlap between nonsyndromic cleft lip with or without cleft palate (NSCL/P) and cancer. The aim of the present study was to identify common genetic risk loci for NSCL/P and cancer entities that have been reported to co-occur with orofacial clefting. This was achieved through the investigation of large genome-wide association study datasets. Investigations of 12 NSCL/P single nucleotide polymorphisms (SNPs) in 32 cancer datasets, and 204 cancer SNPs in two NSCL/P datasets, were performed...
December 2016: Genomics Data
Muhd Danish-Daniel, Gan Han Ming, Mohd Ezhar Mohd Noor, Yik Sung Yeong, Gires Usup
Mameliella alba strain UMTAT08 was isolated from clonal culture of paralytic shellfish toxin producing dinoflagellate, Alexandrium tamiyavanichii. Genome of the strain UMTAT08 was sequenced in order to gain insights into the dinoflagellate-bacteria interactions. The draft genome sequence of strain UMTAT08 contains 5.84Mbp with an estimated G + C content of 65%, 5717 open reading frames, 5 rRNAs and 49 tRNAs. It contains genes related to nutrients uptake, quorum sensing and environmental tolerance related genes...
December 2016: Genomics Data
Taketo Okada, Hironobu Takahashi, Yutaka Suzuki, Sumio Sugano, Masaaki Noji, Hiromichi Kenmoku, Masao Toyota, Shigehiko Kanaya, Nobuo Kawahara, Yoshinori Asakawa, Setsuko Sekita
Ephedra plants are taxonomically classified as gymnosperms, and are medicinally important as the botanical origin of crude drugs and as bioresources that contain pharmacologically active chemicals. Here we show a comparative analysis of the transcriptomes of aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing by RNA-Seq. De novo assembly of short cDNA sequence reads generated 23,358, 13,373, and 28,579 contigs longer than 200 bases from aerial stems, roots, or both aerial stems and roots, respectively...
December 2016: Genomics Data
Michael B Blackburn, Michael E Sparks, Dawn E Gundersen-Rindal
The genome of Chromobacterium subtsugae strain PRAA4-1, a betaproteobacterium producing insecticidal compounds, was sequenced and compared with the genome of C. violaceum ATCC 12472. The genome of C. subtsugae displayed a reduction in genes devoted to capsular and extracellular polysaccharide, possessed no genes encoding nitrate reductases, and exhibited many more phage-related sequences than were observed for C. violaceum. The genomes of both species possess a number of gene clusters predicted to encode biosynthetic complexes for secondary metabolites; these clusters suggest they produce overlapping, but distinct assortments of metabolites...
December 2016: Genomics Data
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