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https://www.readbyqxmd.com/read/28330888/defining-a-core-genome-multilocus-sequence-typing-scheme-for-the-global-epidemiology-of-vibrio-parahaemolyticus
#1
Narjol Gonzalez-Escalona, Keith A Jolley, Elizabeth Reed, Jaime Martinez-Urtaza
Vibrio parahaemolyticus is an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database for V. parahaemolyticus was created in 2008 and a large number of clones have been identified causing severe outbreaks worldwide (ST3), recurrent outbreaks in certain regions (e.g., ST36) or spreading to other regions where they are non-endemic (e.g...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330244/elucidation-of-impact-of-heavy-metal-pollution-on-soil-bacterial-growth-and-extracellular-polymeric-substances-flexibility
#2
Muniswamy David, Paidi Murali Krishna, Jeybalan Sangeetha
Metal bioaccessibility is an alarming issue in croplands of mining sites due to overloading of toxic metals. Hence, the present study is aimed to determine the overloading of toxic metal in croplands across the Tawag village, Hutti, Raichur, India. Correspondingly, to identify the soil bacterial growth, physiological oxidative stress enzyme activity and surface macromolecular functional group evolution were analysed in and around the toxic metal contaminated sites through FT-IR and FT-Raman spectrometry. The evaluated results attribute that the study area is heavily polluted with the toxic metals such as arsenic, cadmium, chromium, lead and zinc...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330204/endophytic-fungal-isolate-mediated-biosynthesis-of-silver-nanoparticles-and-their-free-radical-scavenging-activity-and-anti-microbial-studies
#3
Vasudeva Reddy Netala, Venkata Subbaiah Kotakadi, Pushpalatha Bobbu, Susmila Aparna Gaddam, Vijaya Tartte
The present study reports that the biosynthesis of AgNPs using an endophytic fungus isolated from the ethnomedicinal plant Centella asiatica. The endophytic fungus was identified as Aspergillus versicolor ENT7 based on 18S rRNA gene sequencing (NCBI Accession number KF493864). The AgNPs synthesized were characterized by UV-visible spectroscopy, Fourier transform infra-red spectroscopy (FTIR), transmission electron microscopy (TEM), X-ray diffraction (XRD), particle size analyzer, and zeta potential measurements...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330192/differential-display-reverse-transcription-pcr-ddrt-pcr-a-new-technology-for-molecular-detection-and-studying-one-of-the-antagonistic-factors-of-bacillus-endophyticus-strain-sa-against-staphylococcus-aureus-mrsa
#4
Mahmoud F Moustafa, Tarek H Taha, M Helal, Sulaiman A Alrumman
Differential Display (DDRT-PCR) is a powerful technique for analyzing differences in gene expression. In-vivo expression technologies and differential display RT-PCR are providing new approaches to further examine a microbe's response to experimental conditions which more closely resemble natural microbial associations and habitats. In this study, Bacillus endophyticus strain SA isolated from the inner tissue of the stem of the cultivated plant (Salvadora persica, Asir, Kingdom of Saudi Arabia) produces an antagonistic factor...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330127/diversity-of-toxic-and-phytopathogenic-fusarium-species-occurring-on-cereals-grown-in-karnataka-state-india
#5
H Nagaraja, G Chennappa, K Poorna Chandra Rao, G Mahadev Prasad, M Y Sreenivasa
A total of 198 cereal samples (53 maize, 54 sorghum, 37 paddy and 54 wheat) were collected from 11 districts of Karnataka to understand the percent infection (PI), relative density (RD) and their frequency (Fr) caused by Fusarium spp. All samples were screened by agar plating method using MGA 2.5 agar media and incubated at 25 ± 2 °C for 3-5 days. The study revealed the association of 10 different Fusarium species known trichothecene producers such as Fusarium acuminatum, F. avenaceum, F. crookwellense, F...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28324789/evaluation-of-the-abbott-realtime-hcv-genotype-ii-plus-ruo-plus-assay-with-reference-to-core-and-ns5b-sequencing
#6
Melanie A Mallory, Danijela Lucic, Mark T W Ebbert, Gavin A Cloherty, Dan Toolsie, David R Hillyard
BACKGROUND: HCV genotyping remains a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen. Current commercial genotyping assays may have difficulty identifying 1a, 1b and genotype 6. OBJECTIVE: To evaluate the concordance for identifying 1a, 1b, and genotype 6 between two methods: the PLUS assay and core/NS5B sequencing. STUDY DESIGN: This study included 236 plasma and serum samples previously genotyped by core/NS5B sequencing...
March 9, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28322330/distribution-of-bathyarchaeota-communities-across-different-terrestrial-settings-and-their-potential-ecological-functions
#7
Xing Xiang, Ruicheng Wang, Hongmei Wang, Linfeng Gong, Baiying Man, Ying Xu
High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S rRNA clone libraries of peat from the Dajiuhu Peatland, coupling with bioinformatics analysis of 16S rRNA data available to date in NCBI database...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28321468/hyperglycaemic-memory-affects-the-neurovascular-unit-of-the-retina-in-a-diabetic-mouse-model
#8
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/28316214/-expression-of-tyrosine-and-threonine-protein-kinase-in-carcinogenic-process-of-colorectal-cancer-and-its-relationship-with-prognosis
#9
X L Zhang, W X Han, Y M Ma, H W Y Baohan, X H Zhao, H Y Wang
Objective: To investigate the expression of TTK (tyrosine and threonine protein kinase) in the process of colorectal cancer (CRC) development and its relationship to prognosis in CRC patients. Methods: Colitis-associated colon cancer model was induced by azoxymethane (AOM) and dextran sulfate sodium (DSS) in C57BL/6 mice. Mice at four different stages of colon cancer development were obtained, named AD1 (inflammation of the recovery), AD2 (mild dysplasia), AD3 (adenoma) and AD4 (adenocarcinoma), as well as negative control (no treatment)...
March 23, 2017: Zhonghua Zhong Liu za Zhi [Chinese Journal of Oncology]
https://www.readbyqxmd.com/read/28302154/the-israeli-national-genetic-database-a-10-year-experience
#10
Joël Zlotogora, George P Patrinos
BACKGROUND: The Israeli National and Ethnic Mutation database ( http://server.goldenhelix.org/israeli ) was launched in September 2006 on the ETHNOS software to include clinically relevant genomic variants reported among Jewish and Arab Israeli patients. In 2016, the database was reviewed and corrected according to ClinVar ( https://www.ncbi.nlm.nih.gov/clinvar ) and ExAC ( http://exac.broadinstitute.org ) database entries. The present article summarizes some key aspects from the development and continuous update of the database over a 10-year period, which could serve as a paradigm of successful database curation for other similar resources...
March 16, 2017: Human Genomics
https://www.readbyqxmd.com/read/28298902/global-distribution-and-evolutionary-history-of-enterovirus-d68-with-emphasis-on-the-2014-outbreak-in-ontario-canada
#11
Alireza Eshaghi, Venkata R Duvvuri, Sandra Isabel, Philip Banh, Aimin Li, Adriana Peci, Samir N Patel, Jonathan B Gubbay
Despite its first appearance in 1962, human enterovirus D68 (EV-D68) has been recognized as an emerging respiratory pathogen in the last decade when it caused outbreaks and clusters in several countries including Japan, the Philippines, and the Netherlands. The most recent and largest outbreak of EV-D68 associated with severe respiratory illness took place in North America between August 2014 and January 2015. Between September 1 and October 31 2014, EV-D68 infection was laboratory confirmed among 153/907 (16...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28294702/safety-and-efficacy-of-a-glucagon-like-peptide-1-receptor-agonist-added-to-basal-insulin-therapy-versus-basal-insulin-with-or-without-a-rapid-acting-insulin-in-patients-with-type-2-diabetes-results-of-a-meta-analysis
#12
Carol H Wysham, Jay Lin, Louis Kuritzky
OBJECTIVE: To consolidate the evidence from randomized controlled trials evaluating the use of glucagon-like peptide-1 receptor agonists (GLP-1 RAs) as add-on to basal insulin therapy in type 2 diabetes (T2D) patients. RESEARCH DESIGN AND METHODS: We searched the EMBASE® and NCBI PubMed (Medline) databases and relevant congress abstracts for randomized controlled trials evaluating the efficacy and safety of GLP-1 RAs as add-on to basal insulin compared with basal insulin with or without rapid-acting insulin (RAI) through 23 May 2016...
March 15, 2017: Postgraduate Medicine
https://www.readbyqxmd.com/read/28293298/rapid-development-of-entity-based-data-models-for-bioinformatics-with-persistence-object-oriented-design-and-structured-interfaces
#13
Elishai Ezra Tsur
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed...
2017: BioData Mining
https://www.readbyqxmd.com/read/28293079/pediatric-gastrointestinal-bleeding-perspectives-from-the-italian-society-of-pediatric-gastroenterology
#14
REVIEW
Claudio Romano, Salvatore Oliva, Stefano Martellossi, Erasmo Miele, Serena Arrigo, Maria Giovanna Graziani, Sabrina Cardile, Federica Gaiani, Gian Luigi de'Angelis, Filippo Torroni
There are many causes of gastrointestinal bleeding (GIB) in children, and this condition is not rare, having a reported incidence of 6.4%. Causes vary with age, but show considerable overlap; moreover, while many of the causes in the pediatric population are similar to those in adults, some lesions are unique to children. The diagnostic approach for pediatric GIB includes definition of the etiology, localization of the bleeding site and determination of the severity of bleeding; timely and accurate diagnosis is necessary to reduce morbidity and mortality...
February 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28289604/metagenome-analysis-of-the-root-endophytic-microbial-community-of-indian-rice-o-sativa-l
#15
Subhadipa Sengupta, Sayak Ganguli, Pankaj K Singh
This study reports the root endophytic microbial community profile in rice (Oryza sativa L.), the largest food crop of Asia, using 16S rRNA gene amplicon sequencing. Metagenome of OS01 and OS04 consisted of 11,17,900 sequences with 300 Mbp size and average 55.6% G + C content. Data of this study are available at NCBI Bioproject (PRJNA360379). The taxonomic analysis of 843 OTU's showed that the sequences belonged to four major phyla revealing dominance of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28286183/ordering-the-mob-insights-into-replicon-and-mob-typing-schemes-from-analysis-of-a-curated-dataset-of-publicly-available-plasmids
#16
Alex Orlek, Hang Phan, Anna E Sheppard, Michel Doumith, Matthew Ellington, Tim Peto, Derrick Crook, A Sarah Walker, Neil Woodford, Muna F Anjum, Nicole Stoesser
Plasmid typing can provide insights into the epidemiology and transmission of plasmid-mediated antibiotic resistance. The principal plasmid typing schemes are replicon typing and MOB typing, which utilize variation in replication loci and relaxase proteins respectively. Previous studies investigating the proportion of plasmids assigned to a type by these schemes ('typeability') have yielded conflicting results; moreover, thousands of plasmid sequences have been added to NCBI in recent years, without consistent annotation to indicate which sequences represent complete plasmids...
March 9, 2017: Plasmid
https://www.readbyqxmd.com/read/28286139/de-novo-transcriptome-sequencing-and-analysis-of-the-juvenile-and-adult-stages-of-fasciola-gigantica
#17
Xiao-Xuan Zhang, Wei Cong, Hany M Elsheikha, Guo-Hua Liu, Jian-Gang Ma, Wei-Yi Huang, Quan Zhao, Xing-Quan Zhu
Fasciola gigantica is regarded as the major liver fluke causing fasciolosis in livestock in tropical countries. Despite the significant economic and public health impacts of F. gigantica there are few studies on the pathogenesis of this parasite and our understanding is further limited by the lack of genome and transcriptome information. In this study, de novo Illumina RNA sequencing (RNA-seq) was performed to obtain a comprehensive transcriptome profile of the juvenile (42days post infection) and adult stages of F...
March 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28286046/rudimentary-expression-of-ryamide-in-drosophila-melanogaster-relative-to-other-drosophila-species-points-to-a-functional-decline-of-this-neuropeptide-gene
#18
Jan A Veenstra, Hela Khammassi
RYamides are arthropod neuropeptides with unknown function. In 2011 two RYamides were isolated from D. melanogaster as the ligands for the G-protein coupled receptor CG5811. The D. melanogaster gene encoding these neuropeptides is highly unusual, as there are four RYamide encoding exons in the current genome assembly, but an exon encoding a signal peptide is absent. Comparing the D. melanogaster gene structure with those from other species, including D. virilis, suggests that the gene is degenerating. RNAseq data from 1634 short sequence read archives at NCBI containing more than 34 billion spots yielded numerous individual spots that correspond to the RYamide encoding exons, of which a large number include the intron-exon boundary at the start of this exon...
March 7, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28283005/-comparison-of-maldi-tof-and-16s-rrna-methods-in-identification-of-viridans-group-streptococci
#19
Serap Süzük Yıldız, Banu Kaşkatepe, Salih Altınok, Mustafa Çetin, Alper Karagöz, Sümeyra Savaş
Accurate identification of viridans group streptococci (VGS) frequently encountered as a causative agent of infective endocarditis is always a challenge for the clinical microbiology laboratory. Clinical microbiology laboratories generally use semi automatic/full automatic systems, molecular methods and also conventional methods for the identification of these bacteria. There are recent published studies that have used MALDI-TOF (Matrix Assisted Laser Ionization Mass Spectrometry-Time of Flight) systems in the identification of VGS...
January 2017: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/28282845/extrinsic-feedback-and-upper-limb-motor-skill-learning-in-typically-developing-children-and-children-with-cerebral-palsy-review
#20
Maxime T Robert, Krithika Sambasivan, Mindy F Levin
BACKGROUND: Improvment of upper limb motor skills occurs through motor learning that can be enhanced by providing extrinsic feedback. Different types and frequencies of feedback are discussed but specific guidelines for use of feedback for motor learning in typically-developing (TD) children and children with Cerebral Palsy (CP) are not available. OBJECTIVE: Identify the most effective modalities and frequencies of feedback for improving upper limb motor skills in TD children and children with CP...
2017: Restorative Neurology and Neuroscience
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