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https://www.readbyqxmd.com/read/28330166/a-molecular-phylogenetic-framework-for-bacillus-subtilis-using-genome-sequences-and-its-application-to-bacillus-subtilis-subspecies-stecoris-strain-d7xpn1-an-isolate-from-a-commercial-food-waste-degrading-bioreactor
#1
Joseph Adelskov, Bharat K C Patel
A thermophilic, heterotrophic and facultatively anaerobic bacterium designated strain D7XPN1 was isolated from Baku BakuKing™, a commercial food-waste degrading bioreactor (composter). The strain grew optimally at 45 °C (growth range between 24 and 50 °C) and pH 7 (growth pH range between pH 5 and 9) in Luria Broth supplemented with 0.3 % glucose. Strain D7XPN1 tolerated up to 7 % NaCl and showed amylolytic and xylanolytic activities. 16S rRNA gene analysis placed strain D7XPN1 in the cluster represented by Bacillus subtilis and the genome analysis of the 4...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327996/genome-sequencing-of-the-sweetpotato-whitefly-bemsia-tabaci-med-q
#2
Wen Xie, Chunhai Chen, Zezhong Yang, Litao Guo, Xin Yang, Dan Wang, Ming Chen, Jinqun Huang, Yanan Wen, Yang Zeng, Yating Liu, Jixing Xia, Lixia Tian, Hongying Cui, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xianchun Li, Xinqiu Tan, Murad Ghanim, Baoli Qiu, Huipeng Pan, Dong Chu, Helene Delatte, M N Maruthi, Feng Ge, Xueping Zhou, Xiaowei Wang, Fanghao Wan, Yuzhou Du, Chen Luo, Fengming Yan, Evan L Preisser, Xiaoguo Jiao, Brad S Coates, Jinyang Zhao, Qiang Gao, Jinquan Xia, Ye Yin, Yong Liu, Judith K Brown, Xuguo Joe Zhou, Youjun Zhang
Background: The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. Findings: A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries...
March 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28327967/genome-sequence-of-pacific-abalone-haliotis-discus-hannai-the-first-draft-genome-in-family-haliotidae
#3
Bo-Hye Nam, Woori Kwak, Young-Ok Kim, Dong-Gyun Kim, Hee Jeong Kong, Woo-Jin Kim, Jeong-Ha Kang, Jung Youn Park, Cheul Min An, Ji-Young Moon, Choul Ji Park, Jae Woong Yu, Joon Yoon, Minseok Seo, Kwondo Kim, Duk Kyung Kim, SaetByeol Lee, Samsun Sung, Chul Lee, Younhee Shin, Myunghee Jung, Byeong-Chul Kang, Shin Ga-Hee, Sojeong Ka, Kelsey Caetano-Anolles, Seoae Cho, Heebal Kim
Background: Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [1]. Abalone is an economically important fishery and aquaculture animal which is considered a highly-prized seafood delicacy...
March 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28327954/genome-sequencing-of-the-winged-midge-parochlus-steinenii-from-the-antarctic-peninsula
#4
Sanghee Kim, Mijin Oh, Woongsic Jung, Joonho Park, Han-Gu Choi, Seung Chul Shin
Background: In the Antarctic, only two species of Chironomidae occur naturally-the wingless midge, Belgica antarctica , and the winged midge, Parochlus steinenii . B. antarctica is an extremophile with unusual adaptations. The larvae of B. antarctica are desiccation- and freeze-tolerant and the adults are wingless. Recently, the compact genome of B. antarctica was reported and it is the first Antarctic eukaryote to be sequenced. Although P. steinenii occurs naturally in the Antarctic with B...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327943/whole-genome-sequencing-of-chinese-clearhead-icefish-protosalanx-hyalocranius
#5
Kai Liu, Dongpo Xu, Jia Li, Chao Bian, Jinrong Duan, Yanfeng Zhou, Minying Zhang, Xinxin You, Yang You, Jieming Chen, Hui Yu, Gangchun Xu, Di-An Fang, Jun Qiang, Shulun Jiang, Jie He, Junmin Xu, Qiong Shi, Zhiyong Zhang, Pao Xu
Background: Chinese clearhead icefish, Protosalanx hyalocranius , is a representative icefish species with economic importance and special appearance. Due to its great economic values in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327911/the-genome-sequence-of-the-wisent-bison-bonasus
#6
Kun Wang, Lizhong Wang, Johannes A Lenstra, Jianbo Jian, Yongzhi Yang, Quanjun Hu, Deyong Lai, Qiang Qiu, Tao Ma, Zheng Du, Richard Abbott, Jianquan Liu
Background: The wisent, also known as the European bison, was rescued from extinction approximately 80 years ago through the conservation of 12 individuals. Here, we present the draft genome sequence of a male wisent individual descended from this founding stock. Findings: A total of 366 billion base pairs (Gb) of raw reads from whole-genome sequencing of this wisent were generated using the Illumina HiSeq2000 platform. The final genome assembly (2.58 Gb) is composed of 29,074 scaffolds with an N50 of 4...
March 10, 2017: GigaScience
https://www.readbyqxmd.com/read/28327897/towards-a-global-cancer-knowledge-network-dissecting-the-current-international-cancer-genomic-sequencing-landscape
#7
D J Vis, J Lewin, R G Liao, M Mao, F Andre, R L Ward, F Calvo, B T Teh, A A Camargo, B M Knoppers, C Sawyers, L F A Wessels, M Lawler, L L Siu, E Voest
Background: While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. Methods: A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally...
February 3, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327092/metax-a-flexible-and-comprehensive-software-for-processing-metabolomics-data
#8
Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
BACKGROUND: Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated from mass spectrometry requires intensive computational processing for annotation of mass spectra and identification of metabolites. Computational analysis tools that are fully integrated with multiple functions and are easily operated by users who lack extensive knowledge in programing are needed in this research field...
March 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28326685/hugonella-massiliensis-gen-nov-sp-nov-genome-sequence-and-description-of-a-new-strictly-anaerobic-bacterium-isolated-from-the-human-gut
#9
Ziena Elsawi, Amadou Hamidou Togo, Mamadou Beye, Grégory Dubourg, Claudia Andrieu, Nicholas Armsrtong, Magali Richez, Fabrizio di Pinto, Fadi Bittar, Noémie Labas, Pierre-Edouard Fournier, Didier Raoult, Saber Khelaifia
The human gut is composed of a large diversity of microorganisms, which have been poorly described. Here, using culturomics, a new concept based on the variation in culture conditions and MALDI-TOF MS identification, we proceed to explore the microbial diversity of the complex ecosystem of the human gut. Using this approach, we isolated strain AT8(T) (=CSUR P2118 =  DSM 101782) from stool specimens collected from a 51-year-old obese French woman. Strain AT8(T) is a strictly anaerobic, nonmotile, nonspore-forming gram-positive coccus that do not exhibit catalase and oxidase activities...
March 21, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28325812/thecellmap-org-a-web-accessible-database-for-visualizing-and-mining-the-global-yeast-genetic-interaction-network
#10
Matej Usaj, Yizhao Tan, Wen Wang, Benjamin VanderSluis, Albert Zou, Chad L Myers, Michael Costanzo, Brenda Andrews, Charles Boone
Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae In particular, TheCellMap.org allows users to easily access, visualize, explore and functionally annotate genetic interactions, or to extract and reorganize sub-networks, using data-driven network layouts in an intuitive and interactive manner...
March 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28325279/gene-is-time-efficient-and-accurate-analysis-of-viral-integration-events-in-large-scale-gene-therapy-data
#11
Saira Afzal, Stefan Wilkening, Christof von Kalle, Manfred Schmidt, Raffaele Fronza
Integration site profiling and clonality analysis of viral vector distribution in gene therapy is a key factor to monitor the fate of gene-corrected cells, assess the risk of malignant transformation, and establish vector biosafety. We developed the Genome Integration Site Analysis Pipeline (GENE-IS) for highly time-efficient and accurate detection of next-generation sequencing (NGS)-based viral vector integration sites (ISs) in gene therapy data. It is the first available tool with dual analysis mode that allows IS analysis both in data generated by PCR-based methods, such as linear amplification method PCR (LAM-PCR), and by rapidly evolving targeted sequencing (e...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28323836/single-nucleotide-variants-and-indels-identified-from-whole-genome-re-sequencing-of-guzerat-gyr-girolando-and-holstein-cattle-breeds
#12
Nedenia Bonvino Stafuzza, Adhemar Zerlotini, Francisco Pereira Lobo, Michel Eduardo Beleza Yamagishi, Tatiane Cristina Seleguim Chud, Alexandre Rodrigues Caetano, Danísio Prado Munari, Dorian J Garrick, Marco Antonio Machado, Marta Fonseca Martins, Maria Raquel Carvalho, John Bruce Cole, Marcos Vinicius Gualberto Barbosa da Silva
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel...
2017: PloS One
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#13
Sílvia Vilarinho, Zeynep Erson-Omay, Kisha Mitchell-Richards, Charles Cha, Carol Nelson-Williams, Akdes Serin Harmancı, Katsuhito Yasuno, Murat Günel, Tamar H Taddei
Hepatocellular adenoma (HCA) is a rare benign liver tumor, predominantly seen in young women. Its major complications are malignant transformation, spontaneous hemorrhage, and rupture. We describe a case of a young female with no underlying liver disease who presented with acute abdominal pain and was found to have a 17 cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14 cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28322934/comparative-immunogenomics-of-molluscs
#14
Jonathan H Schultz, Coen M Adema
Comparative immunology, studying both vertebrates and invertebrates, provided the earliest descriptions of phagocytosis as a general immune mechanism. However, the large scale of animal diversity challenges all-inclusive investigations and the field of immunology has developed by mostly emphasizing study of a few vertebrate species. In addressing the lack of comprehensive understanding of animal immunity, especially that of invertebrates, comparative immunology helps toward management of invertebrates that are food sources, agricultural pests, pathogens, or transmit diseases, and helps interpret the evolution of animal immunity...
March 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28322933/the-chemokinome-superfamily-ii-the-64-cc-chemokines-in-channel-catfish-and-their-involvement-in-disease-and-hypoxia-responses
#15
Qiang Fu, Yujia Yang, Chao Li, Qifan Zeng, Tao Zhou, Ning Li, Yang Liu, Yun Li, Xiaozhu Wang, Shikai Liu, Daoji Li, Zhanjiang Liu
Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in regulating cell migration and activation. Based on the arrangement of the first four cysteine residues, they are classified into CC, CXC, C and CX3C subfamilies. In this study, a complete set of 64 CC chemokine ligand (CCL) genes was systematically identified, annotated, and characterized from the channel catfish genome. Extensive phylogenetic and comparative genomic analyses supported their annotations, allowing establishment of their orthologies, revealing fish-specific CC chemokines and the expansion of CC chemokines in the teleost genomes through lineage-specific tandem duplications...
March 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28321969/the-pangenome-of-the-genus-clostridium
#16
Zulema Udaondo, Estrella Duque, Juan Luis Ramos
We present the pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species, some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair...
March 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28321518/identification-and-characterization-of-durum-wheat-micrornas-in-leaf-and-root-tissues
#17
Veronica Fileccia, Edoardo Bertolini, Paolo Ruisi, Dario Giambalvo, Alfonso Salvatore Frenda, Gina Cannarozzi, Zerihun Tadele, Cristina Crosatti, Federico Martinelli
MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs...
March 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28321468/hyperglycaemic-memory-affects-the-neurovascular-unit-of-the-retina-in-a-diabetic-mouse-model
#18
Patrick Friedrichs, Andrea Schlotterer, Carsten Sticht, Matthias Kolibabka, Paulus Wohlfart, Axel Dietrich, Thomas Linn, Grietje Molema, Hans-Peter Hammes
AIMS/HYPOTHESIS: The aim of this study was to evaluate damage to the neurovascular unit in a mouse model of hyperglycaemic memory. METHODS: A streptozotocin-induced mouse model of diabetes (C57BL/6J background) received insulin-releasing pellets and pancreatic islet-cell transplantation. Damage to the neurovascular unit was studied by quantitative retinal morphometry for microvascular changes and microarray analysis, with subsequent functional annotation clustering, for changes of the retinal genome...
March 20, 2017: Diabetologia
https://www.readbyqxmd.com/read/28321234/a-review-of-bioinformatics-tools-for-bio-prospecting-from-metagenomic-sequence-data
#19
REVIEW
Despoina D Roumpeka, R John Wallace, Frank Escalettes, Ian Fotheringham, Mick Watson
The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28320757/additional-candidate-genes-for-human-atherosclerotic-disease-identified-through-annotation-based-on-chromatin-organization
#20
Saskia Haitjema, Claartje A Meddens, Sander W van der Laan, Daniel Kofink, Magdalena Harakalova, Vinicius Tragante, Hassan Foroughi Asl, Jessica van Setten, Maarten M Brandt, Joshua C Bis, Christopher O'Donnell, Caroline Cheng, Imo E Hoefer, Johannes Waltenberger, Erik Biessen, J Wouter Jukema, Pieter A F M Doevendans, Edward E S Nieuwenhuis, Jeanette Erdmann, Johan L M Björkegren, Gerard Pasterkamp, Folkert W Asselbergs, Hester M den Ruijter, Michal Mokry
BACKGROUND: As genome-wide association efforts, such as CARDIoGRAM and METASTROKE, are ongoing to reveal susceptibility loci for their underlying disease-atherosclerotic disease-identification of candidate genes explaining the associations of these loci has proven the main challenge. Many disease susceptibility loci colocalize with DNA regulatory elements, which influence gene expression through chromatin interactions. Therefore, the target genes of these regulatory elements can be considered candidate genes...
April 2017: Circulation. Cardiovascular Genetics
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