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https://www.readbyqxmd.com/read/29051020/draft-genome-sequences-of-three-multidrug-resistant-cutibacterium-formerly-propionibacterium-acnes-strains-isolated-from-acne-patients-china
#1
Nanxue Zhang, Zhong Lu, Ying Ma
OBJECTIVES: Cutibacterium acnes (formerly Propionibacterium acnes), an anaerobic Gram-positive bacterium, is a skin commensal and considered to be associated with acne. Here we report draft genome sequences of three multidrug-resistant C. acnes strains (CA17, CA39, and CA51), isolated from skin lesions of acne patients from China. METHODS: The whole genome of the three multidrug-resistant C. acnes strains were sequenced using an Illumina HiSeq 2500 platform. De novo assembly and annotation were performed with SPAdes-3...
October 16, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29049343/a-sequential-monte-carlo-approach-to-gene-expression-deconvolution
#2
Oyetunji E Ogundijo, Xiaodong Wang
High-throughput gene expression data are often obtained from pure or complex (heterogeneous) biological samples. In the latter case, data obtained are a mixture of different cell types and the heterogeneity imposes some difficulties in the analysis of such data. In order to make conclusions on gene expresssion data obtained from heterogeneous samples, methods such as microdissection and flow cytometry have been employed to physically separate the constituting cell types. However, these manual approaches are time consuming when measuring the responses of multiple cell types simultaneously...
2017: PloS One
https://www.readbyqxmd.com/read/29048578/genome-assembly-and-transcriptome-resource-for-river-buffalo-bubalus-bubalis-2n-50
#3
John L Williams, Daniela Iamartino, Kim D Pruitt, Tad Sonstegard, Timothy P L Smith, Wai Yee Low, Tommaso Biagini, Lorenzo Bomba, Stefano Capomaccio, Bianca Castiglioni, Angelo Coletta, Federica Corrado, Fabrizio Ferré, Leopoldo Iannuzzi, Cynthia Lawley, Nicolò Macciotta, Matthew McClure, Giordano Mancini, Donato Matassino, Raffaele Mazza, Marco Milanesi, Bianca Moioli, Nicola Morandi, Luigi Ramunno, Vincenzo Peretti, Fabio Pilla, Paola Ramelli, Steven Schroeder, Francesco Strozzi, Francoise Thibaud-Nissen, Luigi Zicarelli, Paolo Ajmone-Marsan, Alessio Valentini, Giovanni Chillemi, Aleksey Zimin
Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well annotated, reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are two species of domestic water buffalo, the river (2n = 50) and the swamp (2n = 48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29048540/long-read-sequencing-of-the-coffee-bean-transcriptome-reveals-the-diversity-of-full-length-transcripts
#4
Bing Cheng, Agnelo Furtado, Robert J Henry
Background: Polyploidization contributes to the complexity of gene expression resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of tetraploid Arabica coffee ( Coffea arabica ) bean. Long-read sequencing (LRS) by Pacbio Isoform sequencing (Iso-seq) was used to obtain full-length transcripts without the difficulty and uncertainty of assembly required for reads from short read technologies. The tetraploid transcriptome was annotated and compared with data from the sub-genome progenitors...
August 30, 2017: GigaScience
https://www.readbyqxmd.com/read/29040498/genome-stability-of-bovine-in-vivo-conceived-cleavage-stage-embryos-is-higher-compared-to-invitro-produced-embryos
#5
Olga Tšuiko, Maaike Catteeuw, Masoud Zamani Esteki, Aspasia Destouni, Osvaldo Bogado Pascottini, Urban Besenfelder, Vitezslav Havlicek, Katrien Smits, Ants Kurg, Andres Salumets, Thomas D'Hooghe, Thierry Voet, Ann Van Soom, Joris Robert Vermeesch
STUDY QUESTION: Is the rate and nature of chromosome instability (CIN) similar between bovine in vivo-derived and in vitro-cultured cleavage-stage embryos? SUMMARY ANSWER: There is a major difference regarding chromosome stability of in vivo-derived and in vitro-cultured embryos, as CIN is significantly lower in in vivo-derived cleavage-stage embryos compared to in vitro-cultured embryos. WHAT IS KNOWN ALREADY: CIN is common during in vitro embryogenesis and is associated with early embryonic loss in humans, but the stability of in vivo-conceived cleavage-stage embryos remains largely unknown...
September 23, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29036629/nanotechnology-a-promising-new-paradigm-for-the-control-of-pain
#6
Krishnan V Chakravarthy, Frank J Boehm, Paul J Christo
Objective: The objective of this article is to critically review both preclinical and clinical studies that focus on the use of nanotechnology for both acute and chronic pain management, surveying both diagnostic and therapeutic applications. The article also provides information on nanotechnology for pain practitioners, so that they may better understand how this technology works and how it may be applied to their day-to-day clinical practice. Study Design: Narrative review...
June 27, 2017: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
https://www.readbyqxmd.com/read/29036546/crocoblast-running-blast-efficiently-in-the-age-of-next-generation-sequencing
#7
Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva, Jaroslav Koca
Summary: CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036529/itsonedb-a-comprehensive-collection-of-eukaryotic-ribosomal-rna-internal-transcribed-spacer-1-its1-sequences
#8
Monica Santamaria, Bruno Fosso, Flavio Licciulli, Bachir Balech, Ilaria Larini, Giorgio Grillo, Giorgio De Caro, Sabino Liuni, Graziano Pesole
A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036513/scangeo-parallel-mining-of-high-throughput-gene-expression-data
#9
Katja Koeppen, Bruce A Stanton, Thomas H Hampton
Summary: Current options to mine publicly available gene expression data deposited in NCBI's gene expression omnibus (GEO), such as the GEO web portal and related applications, are optimized to reanalyze a single study, or search for a single gene, and therefore require manual intervention to reanalyze multiple studies for user-specified gene sets. ScanGEO is a simple, user-friendly Shiny web application designed to identify differentially expressed genes across all GEO studies matching user-specified criteria, for a flexible set of genes, visualize results and provide summary statistics and other reports using a single command...
July 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29035139/novel-17-bp-deletion-in-kdm1b-gene-is-significantly-associated-with-testis-weight-in-male-piglet
#10
Yang Cui, Tao Hu, Rui Chen, Shuai Yu, Wuzi Dong, Xiaoyan Lv, Chuanying Pan
Lysine-specific demethylase 1B (KDM1B) which plays a crucial role in regulating methylation status at lysine 4 of histone 3 is important for male fertility. The aim of this study was to explore the KDM1B mRNA expression profiles and to identify novel genetic variants of the pig KDM1B gene, as well as to determine the association between these variants and testis measurement traits in male piglets. The KDM1B mRNA expression profiles indicated that this gene widely expressed in all tested organs. In addition, a novel 17-bp deletion (NC_010449...
October 16, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/29032156/suppressor-of-cytokine-signaling-2-12-regulates-antimicrobial-peptides-and-ecdysteroid-signaling-pathways-in-bombyx-mori-dazao
#11
Muhammad Nadeem Abbas, Bao-Jian Zhu, Saima Kausar, Li-Shang Dai, Yu-Xuan Sun, Ji Wu Tian, Chao-Liang Liu
Suppressors of cytokine signaling (SOCS) are a potent negative regulator of diverse cytokine-related responses to maintain various physiological processes in animals. Here, we obtained the SOCS2-12 gene sequence of Bombyx mori (Dazao) (BmSOCS2-12) from the National Center for Biotechnology Information (NCBI) to study its expression profile in different tissues, as well as in the immune tissues following larval exposure to pathogens. Further, we investigated the role of BmSOCS2-12 in producing antimicrobial peptides (AMPs) and as a regulator of ecdysteroid signaling transduction...
October 12, 2017: Journal of Insect Physiology
https://www.readbyqxmd.com/read/29030042/genetic-variability-and-transcontinental-sharing-of-giardia-duodenalis-infrapopulations-determined-by-glutamate-dehydrogenase-gene
#12
Adel Spotin, Majid Karamat, Mahmoud Mahami-Oskouei, Abbas Shahbazi, Ehsan Ahmadpour, Tahereh Mikaeili Galeh, Shirzad Fallahi
Microevolutionary data of Giardia duodenalis sub-assemblages is a prerequisite for determining the invasion zoonotic patterns of the parasite. To infer transmission patterns that could not be differentiated by the phenotypic features, a population genetic investigation is crucial for the elucidation of the genetic structure of G. duodenalis among the continents. Forty G. duodenalis positive fecal samples were collected from different foci of Northwest Iran. The specimens were subjected to Trichrome staining and sucrose gradient flotation...
October 13, 2017: Acta Tropica
https://www.readbyqxmd.com/read/29029598/a-method-for-named-entity-normalization-in-biomedical-articles-application-to-diseases-and-plants
#13
Hyejin Cho, Wonjun Choi, Hyunju Lee
BACKGROUND: In biomedical articles, a named entity recognition (NER) technique that identifies entity names from texts is an important element for extracting biological knowledge from articles. After NER is applied to articles, the next step is to normalize the identified names into standard concepts (i.e., disease names are mapped to the National Library of Medicine's Medical Subject Headings disease terms). In biomedical articles, many entity normalization methods rely on domain-specific dictionaries for resolving synonyms and abbreviations...
October 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29028923/detecting-presence-of-mutational-signatures-in-cancer-with-confidence
#14
Xiaoqing Huang, Damian Wojtowicz, Teresa M Przytycka
Motivation: Cancers arise as the result of somatically acquired changes in the DNA of cancer cells. However, in addition to the mutations that confer a growth advantage, cancer genomes accumulate a large number of somatic mutations resulting from normal DNA damage and repair processes as well as carcinogenic exposures or cancer related aberrations of DNA maintenance machinery. These mutagenic processes often produce characteristic mutational patterns called mutational signatures. The decomposition of a cancer genome's mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29024264/deutetrabenazine-for-tardive-dyskinesia-a-systematic-review-of-the-efficacy-and-safety-profile-for-this-newly-approved-novel-medication-what-is-the-number-needed-to-treat-number-needed-to-harm-and-likelihood-to-be-helped-or-harmed
#15
REVIEW
Leslie Citrome
OBJECTIVE: Deutetrabenazine is a deuterated formulation of tetrabenazine. The aim of this systematic review is to describe the efficacy, tolerability and safety of deutetrabenazine for the treatment of tardive dyskinesia (TD). DATA SOURCES: The pivotal registration trials were accessed by querying http://www.ncbi.nlm.nih.gov/pubmed/ and http://www.clinicaltrials.gov, for the search terms 'deutetrabenazine' OR 'SD-809', and by also querying the EMBASE (Elsevier) commercial database for clinical poster abstracts, and by asking the manufacturer for copies of posters presented at congresses...
October 12, 2017: International Journal of Clinical Practice
https://www.readbyqxmd.com/read/29023534/bewith-a-between-within-method-to-discover-relationships-between-cancer-modules-via-integrated-analysis-of-mutual-exclusivity-co-occurrence-and-functional-interactions
#16
Phuong Dao, Yoo-Ah Kim, Damian Wojtowicz, Sanna Madan, Roded Sharan, Teresa M Przytycka
The analysis of the mutational landscape of cancer, including mutual exclusivity and co-occurrence of mutations, has been instrumental in studying the disease. We hypothesized that exploring the interplay between co-occurrence, mutual exclusivity, and functional interactions between genes will further improve our understanding of the disease and help to uncover new relations between cancer driving genes and pathways. To this end, we designed a general framework, BeWith, for identifying modules with different combinations of mutation and interaction patterns...
October 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29023515/a-novel-bacteriocin-from-enterococcus-faecalis-478-exhibits-a-potent-activity-against-vancomycin-resistant-enterococci
#17
Uraporn Phumisantiphong, Kanokrat Siripanichgon, Onrapak Reamtong, Pornphan Diraphat
The emergence of multidrug-resistant enterococci (MDRE) and particularly vancomycin-resistant enterococci (VRE) is considered a serious health problem worldwide, causing the need for new antimicrobials. The aim of this study was to discover and characterize bacteriocin against clinical isolates of MDRE and VRE. Over 10,000 bacterial isolates from water, environment and clinical samples were screened. E. faecalis strain 478 isolated from human feces produced the highest antibacterial activity against several MDRE and VRE strains...
2017: PloS One
https://www.readbyqxmd.com/read/29023475/de-novo-transcriptome-sequencing-of-isaria-cateniannulata-and-comparative-analysis-of-gene-expression-in-response-to-heat-and-cold-stresses
#18
Dingfeng Wang, Liangde Li, Guangyuan Wu, Liette Vasseur, Guang Yang, Pengrong Huang
Isaria cateniannulata is a very important and virulent entomopathogenic fungus that infects many insect pest species. Although I. cateniannulata is commonly exposed to extreme environmental temperature conditions, little is known about its molecular response mechanism to temperature stress. Here, we sequenced and de novo assembled the transcriptome of I. cateniannulata in response to high and low temperature stresses using Illumina RNA-Seq technology. Our assembly encompassed 17,514 unigenes (mean length = 1,197 bp), in which 11,445 unigenes (65...
2017: PloS One
https://www.readbyqxmd.com/read/29018627/independent-evolution-of-tetraloop-in-enterovirus-oril-replicative-element-and-its-putative-binding-partners-in-virus-protein-3c
#19
Maria A Prostova, Andrei A Deviatkin, Irina O Tcelykh, Alexander N Lukashev, Anatoly P Gmyl
BACKGROUND: Enteroviruses are small non-enveloped viruses with a (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features a low-fidelity process, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature...
2017: PeerJ
https://www.readbyqxmd.com/read/29017889/complete-genome-sequence-of-acinetobacter-baumannii-a1296-st1469-with-a-small-plasmid-harboring-the-tet39-tetracycline-resistance-gene
#20
Xiaoting Hua, Chao Pan, Li Zhu, Zhicheng Liu, Qingye Xu, Hengliang Wang, Yunsong Yu
OBJECTIVES: Acinetobacter baumannii is considered an important nosocomial pathogen worldwide due to its increasing antibiotic resistance. This study aimed to determine the complete genome sequence of A. baumannii strain A1296 and comparative analysis among A. baumannii. METHODS: The complete genome sequence of A. baumannii A1296 was sequenced on two SMRT cells using P6C4 chemistry on a Pacific Biosciences Single Molecule, Real-Time RS II instrument. The A1296 genome sequence was annotated via NCBI, and its MLST and resistance genes were analyzed...
October 7, 2017: Journal of Global Antimicrobial Resistance
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