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https://www.readbyqxmd.com/read/28438015/genome-characteristics-of-lactobacillus-fermentum-strain-jdfm216-for-application-as-probiotic-bacteria
#1
Sung Yong Jang, Jaeyoung Heo, Mi Ri Park, Min-Ho Song, Jong Nam Kim, Sung Ho Jo, Do-Youn Jeong, Hak Kyo Lee, Younghoon Kim, Sangnam Oh
Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces, possesses an enhancement of longevity and immune response on Caenorhabditis elegans host. To explore the molecular characteristics of strain JDFM216, we performed a whole-genome sequencing using PacBio system. The single circular DNA chromosome of 2,076,427 bp was completely assembled and 2,623 encoding sequences were predicted. Phylogenetically featured five genes possibly related to longevity and immune response of host were identified in L...
April 25, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28437703/antiviral-treatment-strategies-based-on-gene-silencing-and-genome-editing
#2
REVIEW
Roger Badia, Ester Ballana, José A Esté, Eva Riveira-Muñoz
The ability of some viruses to establish latently infected chronic reservoirs that escape to immune control becomes a major roadblock that impedes the cure of these infections. Therefore, new alternatives are needed to pursuit the eradication of viral persistent infections. Gene silencing technologies are in constant evolution and provide an outstanding sequence specificity that allows targeting any coding sequence of interest. Here we provide an overview of the development of gene silencing technologies ranging from initially RNA interference to the recently developed CRISPR/Cas9 and their potential as new antiviral strategies focusing on the eradication of HIV...
April 21, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28437675/whole-blood-sequencing-reveals-circulating-microrna-associations-with-high-risk-traits-in-non-st-segment-elevation-acute-coronary-syndrome
#3
Alice Wang, Lydia Coulter Kwee, Elizabeth Grass, Megan L Neely, Simon G Gregory, Keith A A Fox, Paul W Armstrong, Harvey D White, E Magnus Ohman, Matthew T Roe, Svati H Shah, Mark Y Chan
BACKGROUND AND AIMS: Although circulating microRNA (miRNAs) have emerged as biomarkers predicting mortality in acute coronary syndrome (ACS), more data are needed to understand these mechanisms. Mapping miRNAs to high-risk traits may identify miRNAs involved in pathways conferring risk for poor outcome in ACS. We aim to investigate the relationship between circulating miRNAs and high-risk traits in non-ST-segment elevation acute coronary syndrome (NSTE-ACS). METHODS: Whole-genome miRNA sequencing was performed on RNA extracted from whole blood of 199 patients with NSTE-ACS...
March 30, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28437475/the-school-malaise-trap-program-coupling-educational-outreach-with-scientific-discovery
#4
Dirk Steinke, Vanessa Breton, Emily Berzitis, Paul D N Hebert
The School Malaise Trap Program (SMTP) provides a technologically sophisticated and scientifically relevant educational experience that exposes students to the diversity of life, enhancing their understanding of biodiversity while promoting environmental stewardship. Since 2013, the SMTP has allowed 15,000 students at 350 primary and secondary schools to explore insect diversity in Canadian schoolyards. Students at each school collected hundreds of insects for an analysis of DNA sequence variation that enabled their rapid identification to a species...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28437468/role-of-cleavage-at-the-core-e1-junction-of-hepatitis-c-virus-polyprotein-in-viral-morphogenesis
#5
Véronique Pène, Matthieu Lemasson, Francis Harper, Gérard Pierron, Arielle R Rosenberg
In hepatitis C virus (HCV) polyprotein sequence, core protein terminates with E1 envelope signal peptide. Cleavage by signal peptidase (SP) separates E1 from the complete form of core protein, anchored in the endoplasmic reticulum (ER) membrane by the signal peptide. Subsequent cleavage of the signal peptide by signal-peptide peptidase (SPP) releases the mature form of core protein, which preferentially relocates to lipid droplets. Both of these cleavages are required for the HCV infectious cycle, supporting the idea that HCV assembly begins at the surface of lipid droplets, yet SPP-catalyzed cleavage is dispensable for initiation of budding in the ER...
2017: PloS One
https://www.readbyqxmd.com/read/28437450/esprit-forest-parallel-clustering-of-massive-amplicon-sequence-data-in-subquadratic-time
#6
Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun
The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analy- sis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28437448/expression-profiling-of-chrysanthemum-crassum-under-salinity-stress-and-the-initiation-of-morphological-changes
#7
Zhiyong Guan, Yitong Feng, Aiping Song, Xiaomeng Shi, Yachao Mao, Sumei Chen, Jiafu Jiang, Lian Ding, Fadi Chen
Chrysanthemum crassum is a decaploid species of Chrysanthemum with high stress tolerance that allows survival under salinity stress while maintaining a relatively ideal growth rate. We previously recorded morphological changes after salt treatment, such as the expansion of leaf cells. To explore the underlying salinity tolerance mechanisms, we used an Illumina platform and obtained three sequencing libraries from samples collected after 0 h, 12 h and 24 h of salt treatment. Following de novo assembly, 154,944 transcripts were generated, and 97,833 (63...
2017: PloS One
https://www.readbyqxmd.com/read/28437427/bacterial-diversity-of-bacteriomes-and-organs-of-reproductive-digestive-and-excretory-systems-in-two-cicada-species-hemiptera-cicadidae
#8
Zhou Zheng, Dandan Wang, Hong He, Cong Wei
Cicadas form intimate symbioses with bacteria to obtain nutrients that are scarce in the xylem fluid they feed on. The obligate symbionts in cicadas are purportedly confined to specialized bacteriomes, but knowledge of bacterial communities associated with cicadas is limited. Bacterial communities in the bacteriomes and organs of reproductive, digestive and excretory systems of two cicada species (Platypleura kaempferi and Meimuna mongolica) were investigated using different methods, and the bacterial diversity and distribution patterns of dominant bacteria in different tissues were compared...
2017: PloS One
https://www.readbyqxmd.com/read/28436983/stable-polycomb-dependent-transgenerational-inheritance-of-chromatin-states-in-drosophila
#9
Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, Quentin Szabo, Anne Xuéreb, Christophe Klopp, Alexei Aravin, Renato Paro, Frédéric Bantignies, Giacomo Cavalli
Transgenerational epigenetic inheritance (TEI) describes the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known about the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, as defined by differential levels of Polycomb-dependent trimethylation of histone H3 Lys27 (forming H3K27me3)...
April 24, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28436748/disruption-of-tetr-type-regulator-aden-by-mobile-genetic-element-confers-elevated-virulence-in-acinetobacter-baumannii
#10
Rajagopalan Saranathan, Sudhakar Pagal, Ajit R Sawant, Archana Tomar, M Madhangi, Suresh Sah, Annapurna Satti, K P Arunkumar, K Prashanth
Acinetobacter baumannii is an important human pathogen and considered as a major threat due to its extreme drug resistance. In this study, the genome of a hyper-virulent MDR strain PKAB07 of A. baumannii isolated from an Indian patient was sequenced and analysed to understand its mechanisms of virulence, resistance and evolution. Comparative genomics analysis of PKAB07 revealed virulence and resistance related genes scattered throughout the genome, instead of being organized as an island, indicating the highly mosaic nature of the genome...
April 24, 2017: Virulence
https://www.readbyqxmd.com/read/28436598/the-expression-of-helicobacter-pylori-tfs-plasticity-zone-cluster-is-regulated-by-ph-and-adherence-and-its-composition-is-associated-with-differential-gastric-il-8-secretion
#11
Bruno Silva, Alexandra Nunes, Filipa F Vale, Raquel Rocha, João Paulo Gomes, Ricardo Dias, Mónica Oleastro
BACKGROUND: Helicobacter pylori virulence is associated with different clinical outcomes. The existence of an intact dupA gene from tfs4b cluster has been suggested as a predictor for duodenal ulcer development. However, the role of tfs plasticity zone clusters in the development of ulcers remains unclear. We studied several H. pylori strains to characterize the gene arrangement of tfs3 and tfs4 clusters and their impact in the inflammatory response by infected gastric cells. METHODS: The genome of 14 H...
April 24, 2017: Helicobacter
https://www.readbyqxmd.com/read/28436493/an-attenuated-mycobacterium-tuberculosis-clinical-strain-with-a-defect-in-esx-1-secretion-induces-minimal-host-immune-responses-and-pathology
#12
Helena Strand Clemmensen, Niels Peter Hell Knudsen, Erik Michael Rasmussen, Jessica Winkler, Ida Rosenkrands, Ahmad Ahmad, Troels Lillebaek, David R Sherman, Peter Lawætz Andersen, Claus Aagaard
Although Mycobacterium tuberculosis (M.tb) DK9897 is an attenuated strain, it was isolated from a patient with extrapulmonary tuberculosis and vaccination with a subunit vaccine (H56) induced poor protection against it. Both attenuation and lack of protection are because M.tb DK9897 cannot secrete the EsxA virulence factor nor induce a host response against it. Genome sequencing identified a frameshift mutation in the eccCa1 gene. Since the encoded EccCa1 protein provides energy for ESX-1 secretion, it suggested a defect in the ESX-1 type VII secretion system...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28436466/genome-wide-profiling-of-heritable-and-de-novo-str-variations
#13
Thomas Willems, Dina Zielinski, Jie Yuan, Assaf Gordon, Melissa Gymrek, Yaniv Erlich
Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, it has proven problematic to genotype STRs from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations. HipSTR is freely available at https://hipstr-tool...
April 24, 2017: Nature Methods
https://www.readbyqxmd.com/read/28436151/whole-genome-sequence-association-and-ancestry-informed-polygenic-profile-of-eeg-alpha-in-a-native-american-population
#14
Qian Peng, Nicholas J Schork, Kirk C Wilhelmsen, Cindy L Ehlers
EEG alpha activity is the dominant oscillation in most adult humans, is highly heritable, and has been associated with a number of cognitive functions. Two EEG phenotypes, low- and high-voltage alpha (LVA & HVA), have been demonstrated to have high heritabilities. They have different prevalence depending on a population's ancestral origins. In the present study we assessed the influence of ancestry admixture on EEG alpha power, and conducted a whole genome sequencing association analysis and an ancestry-informed polygenic study on those phenotypes in a Native American (NA) population that has a high prevalence of LVA...
April 24, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28436089/a-novel-dense-granule-protein-gra41-regulates-timing-of-egress-and-calcium-sensitivity-in-toxoplasma-gondii
#15
Kaice A LaFavers, Karla M Márquez-Nogueras, Isabelle Coppens, Silvia N J Moreno, Gustavo Arrizabalaga
Toxoplasma gondii is an obligate intracellular apicomplexan parasite with high seroprevalence in humans. Repeated lytic cycles of invasion, replication and egress drive both the propagation and the virulence of this parasite. Key steps in this cycle, including invasion and egress, depend on tightly regulated calcium fluxes and, while many of the calcium-dependent effectors have been identified, the factors that detect and regulate the calcium fluxes are mostly unknown. To address this knowledge gap, we used a forward genetic approach to isolate mutants resistant to extracellular exposure to the calcium ionophore A23187...
April 24, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28435889/multidrug-resistance-salmonella-genomic-island-1-in-a-morganella-morganii-subsp-morganii-human-clinical-isolate-from-france
#16
Eliette Schultz, Olivier Barraud, Jean-Yves Madec, Marisa Haenni, Axel Cloeckaert, Marie-Cécile Ploy, Benoît Doublet
Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that harbors a great diversity of antimicrobial resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. A serious threat to public health was revealed in the recent description in P. mirabilis of a SGI1-derivative multidrug resistance island named PGI1 (Proteus genomic island 1) carrying extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase resistance genes, blaVEB-6 and blaNDM-1, respectively...
March 2017: MSphere
https://www.readbyqxmd.com/read/28435885/phylogenomic-reconstruction-of-the-oomycete-phylogeny-derived-from-37-genomes
#17
Charley G P McCarthy, David A Fitzpatrick
The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus...
March 2017: MSphere
https://www.readbyqxmd.com/read/28435450/exome-sequencing-of-oral-squamous-cell-carcinoma-reveals-molecular-subgroups-and-novel-therapeutic-opportunities
#18
Shih-Chi Su, Chiao-Wen Lin, Yu-Fan Liu, Wen-Lang Fan, Mu-Kuan Chen, Chun-Ping Yu, Wei-En Yang, Chun-Wen Su, Chun-Yi Chuang, Wen-Hsiung Li, Wen-Hung Chung, Shun-Fa Yang
Oral squamous cell carcinoma (OSCC), an epithelial malignancy affecting a variety of subsites in the oral cavity, is prevalent in Asia. The survival rate of OSCC patients has not improved over the past decades due to its heterogeneous etiology, genetic aberrations, and treatment outcomes. Improvement in therapeutic strategies and tailored treatment options is an unmet need. To unveil the mutational spectrum, whole-exome sequencing of 120 OSCC from male individuals in Taiwan was conducted. Analyzing the contributions of the five mutational signatures extracted from the dataset of somatic variations identified four groups of tumors that were significantly associated with demographic and clinical features...
2017: Theranostics
https://www.readbyqxmd.com/read/28435299/genetic-interrelations-in-the-actinomycin-biosynthetic-gene-clusters-of-streptomyces-antibioticus-imru-3720-and-streptomyces-chrysomallus-atcc11523-producers-of-actinomycin-x-and-actinomycin-c
#19
Ivana Crnovčić, Christian Rückert, Siamak Semsary, Manuel Lang, Jörn Kalinowski, Ullrich Keller
Sequencing the actinomycin (acm) biosynthetic gene cluster of Streptomyces antibioticus IMRU 3720, which produces actinomycin X (Acm X), revealed 20 genes organized into a highly similar framework as in the bi-armed acm C biosynthetic gene cluster of Streptomyces chrysomallus but without an attached additional extra arm of orthologues as in the latter. Curiously, the extra arm of the S. chrysomallus gene cluster turned out to perfectly match the single arm of the S. antibioticus gene cluster in the same order of orthologues including the the presence of two pseudogenes, scacmM and scacmN, encoding a cytochrome P450 and its ferredoxin, respectively...
2017: Advances and Applications in Bioinformatics and Chemistry: AABC
https://www.readbyqxmd.com/read/28435197/development-of-nested-polymerase-chain-reaction-based-diagnosis-of-duck-enteritis-virus-and-detection-of-dna-polymerase-gene-from-non-descriptive-duck-breeds-of-west-bengal-india
#20
Partha Sarathi Mandal, Sunit Kumar Mukhopadhayay, Saktipada Pradhan, Samiran Mondal, Chandrakanta Jana, Nimai Chandra Patra, Rabindra Nath Hansda
AIM: The study was undertaken to detect the clinical signs, postmortem lesions of embryonated duck plague (DP) infected eggs, and histopathological changes of chorioallantoic membrane (CAM) in non-descriptive ducks of West Bengal with special reference to standardize nested polymerase chain reaction (PCR). MATERIALS AND METHODS: After postmortem of suspected carcasses, samples were collected for virus isolation and identification through specific pathogen free (Khaki Campbell) embryonated duck eggs...
March 2017: Veterinary World
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