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Fan Xiaojun, Yang Chun, Liu Jianhong, Zhang Chang, Li Yao
The Asian gypsy moth (Lymantria dispar) is a serious pest of forest and shade trees in many Asian and some European countries. However, there have been few studies of L. dispar genetic information and comprehensive genetic analyses of this species are needed in order to understand its genetic and metabolic sensitivities, such as the molting mechanism during larval development. In this study, high-throughput sequencing technology was used to sequence the transcriptome of the Asian subspecies of the gyspy moth, after which a comprehensive analysis of chitin metabolism was undertaken...
October 20, 2016: Genetics and Molecular Biology
Mohammad Mahfuz Ali Khan Shawan, Md Ashraful Hasan, Md Mozammel Hossain, Md Mahmudul Hasan, Afroza Parvin, Salina Akter, Kazi Rasel Uddin, Subrata Banik, Mahbubul Morshed, Md Nazibur Rahman, S M Badier Rahman
Nucleotide (DNA) sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531) is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database...
December 2016: Data in Brief
Damarius S Fleming, Laura C Miller
Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi) that generated 1,927,547 unique tag sequences...
December 2016: Genomics Data
Robert Ringseis, Wilhelm Windisch, Klaus Eder
In the present study, transcript profiling was carried out in liver biopsies from high-yielding dairy cows at week 5 of lactation in order to identify genes and pathways regulated by feeding rumen-protected conjugated linoleic acid (CLA) during the transition period. Analysis of a bovine whole genome microarray revealed a total number of 130 annotated differentially expressed genes (DEGs) in the liver between cows of the CLA group and the control group (filter: P < 0.05 and fold change (FC) ≥ 1.3 or ≤- 1...
December 2016: Genomics Data
Norah Lynn-Anne Mund, Wycliffe Omurwa Masanta, Anne-Marie Goldschmidt, Raimond Lugert, Uwe Groß, Andreas E Zautner
Campylobacter jejuni's flagellar locomotion is controlled by eleven chemoreceptors. Assessment of the distribution of the relevant chemoreceptor genes in the C. jejuni genomes deposited in the National Center for Biotechnology Information (NCBI) database led to the identification of two previously unknown tlp genes and a tlp5 pseudogene. These two chemoreceptor genes share the same locus in the C. jejuni genome with tlp4 and tlp11, but the gene region encoding the periplasmic ligand binding domain differs significantly from other chemoreceptor genes...
September 29, 2016: European Journal of Microbiology & Immunology
Abhishek Srivastava, Katherine D McMahon, Ramunas Stepanauskas, Hans-Peter Grossart
The National Center for Biotechnology Information [] database enlists more than 15,500 bacterial species. But this also includes a plethora of uncultured bacterial representations. Owing to their metabolism, they directly influence biogeochemical cycles, which underscores the the important status of bacteria on our planet. To study the function of a gene from an uncultured bacterium, we have undertaken a de novo gene synthesis approach. Actinobacteria of the acI-B subcluster are important but yet uncultured members of the bacterioplankton in temperate lakes of the northern hemisphere such as oligotrophic Lake Stechlin (NE Germany)...
December 2015: International Microbiology: the Official Journal of the Spanish Society for Microbiology
Robim M Rodrigues, Olivier Govaere, Tania Roskams, Tamara Vanhaecke, Vera Rogiers, Joery De Kock
This data set is composed of transcriptomics analyses of (i) liver samples from patients suffering from acetaminophen-induced acute liver failure (ALF) and (ii) hepatic cell systems exposed to acetaminophen and their respective controls. The in vitro systems include widely employed cell lines i.e. HepaRG and HepG2 cells as well as a novel stem cell-derived model i.e. human skin-precursors-derived hepatocyte-like cells (hSKP-HPC). Data from primary human hepatocytes was also added to the data set "Open TG-GATEs: a large-scale toxicogenomics database" (Igarashi et al...
June 2016: Data in Brief
Junting Pan, Weidong Wang, Dongqin Li, Zaifa Shu, Xiaoli Ye, Pinpin Chang, Yuhua Wang
BACKGROUND: Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress...
October 18, 2016: BMC Genomics
Junqing Wang, Yunyun Zhou, Xiaochun Fei, Xunhua Chen, Zhenggang Zhu
The Wnt/β-catenin signaling pathway dominates numerous cellular processes including cell proliferation, differentiation, and epithelial-mesenchymal transition, which play a crucial role in human cancer malignancies. Regulator of G-protein signaling 3 (RGS3) is a pivotal molecule involved in the Wnt/β-catenin signaling pathway, which is worthy of intensive research as a potential target in cancer treatment. In this study, we found that RGS3 is significantly upregulated in gastric cancer (GC) tumor samples compared with normal samples from the analysis of two independent GC mRNA microarray datasets in the NCBI public database...
October 14, 2016: Anti-cancer Drugs
Bharat Bhushan, S K Tomar, Arun Chauhan
An appropriate selection of Lactobacillus strain (probiotic/starter/functional) on the basis of its techno-functional characteristics is required before developing a novel fermented functional food. We compared vitamin B12 (B12, cobalamin) producing Lactobacillus plantarum isolates, BHM10 and BCF20, for functional (vitamin over-production, genomic insight to B12 structural genes, and probiotic attributes) and technological [milks (skim and soy) fermentation and B12 bio-fortification] characteristics. Addition of B12 precursors (5-amonolevulinate and dimethylbenzimidazole) to cobalamin-free fermentation medium increased vitamin production in BHM10, BCF20, and DSM20016 (a positive standard) by 3...
October 17, 2016: Applied Microbiology and Biotechnology
Yin-Ku Liang, Liu-Jiao Bian
Kringle 5, the fifth fragment of plasminogen, is known to be important for inhibiting the proliferation and migration of vascular endothelial cell (VEC), while not having any effects on normal endothelial cells. Therefore, it may be a potential tumor therapy candidate. However, the ligand of the Kringle 5 in VEC has not yet been identified. In this study, the possible ligand of Kringle 5 in vitro was screened and validated using Ph.D.-7 phage display peptide library with molecular docking, along with surface plasma resonance (SPR)...
2016: PloS One
Ana L Neves, Tiago Henriques-Coelho, Adelino Leite-Moreira, José C Areias
OBJECTIVE: The aim of this article is to evaluate the clinical utility of brain natriuretic peptide in pediatric patients, examining the diagnostic value, management, and prognostic relevance, by critical assessment of the literature. DATA SOURCES: In December 2015, a literature search was performed (PubMed access to MEDLINE citations; and included these Medical Subject Headings and text terms for the key words: "brain natriuretic peptide," "amino-terminal pro-brain natriuretic peptide," "children," "neonate/s," "newborn/s," "infant/s," and "echocardiography...
September 30, 2016: Pediatric Critical Care Medicine
Julie C Fitzgerald, Scott L Weiss, Niranjan Kissoon
OBJECTIVE: To review important articles in the field of pediatric shock and pediatric septic shock published subsequent to the Fifth Edition of the Rogers' Textbook of Pediatric Intensive Care. DATA SOURCES: The U.S. National Library of Medicine PubMed ( was searched for combination of the term "pediatric" and the following terms: "sepsis, septic shock, shock, antibiotics, extracorporeal membrane oxygenation, and steroid." The abstract lists generated by these searches were screened for potential inclusion...
September 30, 2016: Pediatric Critical Care Medicine
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
Xiao-Feng Zhu, Dian-Peng Zhang, Sen Yang, Qing-Wen Zhang
Three yeast strains designated as S44, XF1 and XF2, respectively, were isolated from Scolytus scheryrewi Semenov of apricot tree in Shule County, Xinjiang, China, and were demonstrated to be a new member of the genus Candida by sequence comparisons of 26S rRNA gene D1/D2 domain and internal transcribed spacer (ITS) region. BLASTn alignments on NCBI showed that the similarity of 26S rRNA gene sequences of S44 (type strain) to all sequences of other Candida yeasts was very low (≦93 %). The phylogenetic tree based on the 26S rRNA gene D1/D2 domain and ITS region sequences revealed that the strain S44 is closely related to C...
October 14, 2016: Archives of Microbiology
Fan Yang, Junting Gong, Guangyun Wang, Peng Chen, Li Yang, Zhengtao Wang
Waltonitone (WA), an ursane-type pentacyclic triterpene extracted from Gentiana waltonii Burkill, was recently appeared to exert anti-tumor effect. However, the biological underpinnings underlying the role of WA in hepatocellular carcinoma (HCC) cells have not been completely elucidated. Our previous report indicated that the FXR-regulated miR-22-CCNA2 pathway contributed to the progression and development of HCC. Besides, a wide spectrum of microRNAs (miRNAs) could be up- or down-regulated upon WA treatment, including miR-22...
October 12, 2016: Oncotarget
Mary Shimoyama, Stanley J F Laulederkind, Jeff De Pons, Rajni Nigam, Jennifer R Smith, Marek Tutaj, Victoria Petri, G Thomas Hayman, Shur-Jen Wang, Omid Ghiasvand, Jyothi Thota, Melinda R Dwinell
Rattus norvegicus, the laboratory rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; has been the premier resource for genomic, genetic, phenotype and strain data for the laboratory rat. The primary role of RGD is to curate rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorporation into other major databases such as NCBI, Ensembl and UniProt...
October 1, 2016: Disease Models & Mechanisms
Mithila Ferdous, Anna M D Kooistra-Smid, Kai Zhou, John W A Rossen, Alexander W Friedrich
Escherichia coli (E.coli) O157 that do not produce Shiga toxin and do not possess flagellar antigen H7 are of diverse H serotypes. In this study, the antibiotic resistance properties, genotype of a set of virulence associated genes and the phylogenetic background of E. coli O157:non-H7 groups were compared. Whole genome sequencing was performed on fourteen O157:non-H7 isolates collected in the STEC-ID-net study. The genomes were compared with E. coli O157 genomes and a typical Enteropathogenic E. coli (tEPEC) genome downloaded from NCBI...
2016: Frontiers in Microbiology
Shalini Sharma, Prasenjit Dhar, Aneesh Thakur, Vivek Sharma, Mandeep Sharma
AIM: The present study was conducted to detect the presence of canine parvovirus (CPV) among diarrheic dogs in Himachal Pradesh and to identify the most prevalent antigenic variant of CPV based on molecular typing and sequence analysis of VP2 gene. MATERIALS AND METHODS: A total of 102 fecal samples were collected from clinical cases of diarrhea or hemorrhagic gastroenteritis from CPV vaccinated or non-vaccinated dogs. Samples were tested using CPV-specific polymerase chain reaction (PCR) targeting VP2 gene, multiplex PCR for detection of CPV-2a and CPV-2b antigenic variants, and a PCR for the detection of CPV-2c...
September 2016: Veterinary World
M Constanza Mannino, Máximo Rivarola, Alejandra C Scannapieco, Sergio González, Marisa Farber, Jorge L Cladera, Silvia B Lanzavecchia
BACKGROUND: Diachasmimorpha longicaudata (Hymenoptera: Braconidae) is a solitary parasitoid of Tephritidae (Diptera) fruit flies of economic importance currently being mass-reared in bio-factories and successfully used worldwide. A peculiar biological aspect of Hymenoptera is its haplo-diploid life cycle, where females (diploid) develop from fertilized eggs and males (haploid) from unfertilized eggs. Diploid males were described in many species and recently evidenced in D. longicaudata by mean of inbreeding studies...
October 12, 2016: BMC Genomics
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