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https://www.readbyqxmd.com/read/29775592/dietary-and-microbial-oxazoles-induce-intestinal-inflammation-by-modulating-aryl-hydrocarbon-receptor-responses
#1
Shankar S Iyer, Thomas Gensollen, Amit Gandhi, Sungwhan F Oh, Joana F Neves, Frederic Collin, Richard Lavin, Carme Serra, Jonathan Glickman, Punyanganie S A de Silva, R Balfour Sartor, Gurdyal Besra, Russell Hauser, Anthony Maxwell, Amadeu Llebaria, Richard S Blumberg
Genome-wide association studies have identified risk loci associated with the development of inflammatory bowel disease, while epidemiological studies have emphasized that pathogenesis likely involves host interactions with environmental elements whose source and structure need to be defined. Here, we identify a class of compounds derived from dietary, microbial, and industrial sources that are characterized by the presence of a five-membered oxazole ring and induce CD1d-dependent intestinal inflammation. We observe that minimal oxazole structures modulate natural killer T cell-dependent inflammation by regulating lipid antigen presentation by CD1d on intestinal epithelial cells (IECs)...
May 17, 2018: Cell
https://www.readbyqxmd.com/read/29774869/genetic-epidemiology-and-risk-factors-for-brain-tumors
#2
Xuejun Li, Hang Cao, Yanhong Liu
This report summarized current knowledge and findings relevant to environmental and genetic risk factors in brain tumors, with a particular focus on glioma. To date, the established risk factors for brain tumors are family history and ionizing radiation exposure; whereas there is an inverse association between tumors and other factors such as history of allergies, atopic conditions, chickenpox, and varicella zoster virus infection. To identify inherited genetic variants impacting susceptibility of brain tumors, large scale familial linkage-scan pedigree analysis, population-based candidate genes, and genome-wide association study were performed...
April 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29774858/genomic-epidemiology-of-global-carbapenemase-producing-enterobacter-spp-2008-2014
#3
Gisele Peirano, Yasufumi Matsumura, Mark D Adams, Patricia Bradford, Mary Motyl, Liang Chen, Barry N Kreiswirth, Johann D D Pitout
We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-β-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam...
June 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29774847/genomic-sequencing-of-bordetella-pertussis-for-epidemiology-and-global-surveillance-of-whooping-cough
#4
Valérie Bouchez, Julien Guglielmini, Mélody Dazas, Annie Landier, Julie Toubiana, Sophie Guillot, Alexis Criscuolo, Sylvain Brisse
Bordetella pertussis causes whooping cough, a highly contagious respiratory disease that is reemerging in many world regions. The spread of antigen-deficient strains may threaten acellular vaccine efficacy. Dynamics of strain transmission are poorly defined because of shortcomings in current strain genotyping methods. Our objective was to develop a whole-genome genotyping strategy with sufficient resolution for local epidemiologic questions and sufficient reproducibility to enable international comparisons of clinical isolates...
June 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29774212/alkaline-peptone-water-based-enrichment-method-for-mcr-3-from-acute-diarrheic-outpatient-gut-samples
#5
Qiaoling Sun, Yanyan Hu, Hongwei Zhou, Lingbin Shu, Hanyu Wang, Zixian Huang, Rong Zhang
A third plasmid-mediated colistin resistance gene, mcr-3 , is increasingly being reported in Enterobacteriaceae and Aeromonas spp. from animals and humans. To investigate the molecular epidemiology of mcr in the gut flora of Chinese outpatients, 152 stool specimens were randomly collected from outpatients in our hospital from May to June, 2017. Stool specimens enriched in alkaline peptone water or Luria-Bertani (LB) broth were screened for mcr-1, mcr-2 , and mcr-3 using polymerase chain reaction (PCR)-based assays...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29772771/a-novel-hepadnavirus-identified-in-an-immunocompromised-domestic-cat-in-australia
#6
Mahdis Aghazadeh, Mang Shi, Vanessa R Barrs, Alicia J McLuckie, Scott A Lindsay, Barbara Jameson, Bronte Hampson, Edward C Holmes, Julia A Beatty
High-throughput transcriptome sequencing allows for the unbiased detection of viruses in host tissues. The application of this technique to immunosuppressed animals facilitates the detection of viruses that might otherwise be excluded or contained in immunocompetent individuals. To identify potential viral pathogens infecting domestic cats we performed high-throughput transcriptome sequencing of tissues from cats infected with feline immunodeficiency virus (FIV). A novel member of the Hepadnaviridae , tentatively named domestic cat hepadnavirus, was discovered in a lymphoma sample and its complete 3187 bp genome characterized...
May 17, 2018: Viruses
https://www.readbyqxmd.com/read/29772398/molecular-epidemiology-and-characterization-of-picobirnaviruses-in-small-ruminant-populations-in-india
#7
Yashpal Singh Malik, Shubhankar Sircar, Kuldeep Dhama, Rashmi Singh, Souvik Ghosh, Krisztián Bányai, Anastasia N Vlasova, Touil Nadia, Raj Kumar Singh
Picobirnavirus (PBV) is recognized as a putative cause of diarrhea and respiratory illnesses. Although PBV has been reported in several mammalian (including humans) and avian host species, data pertaining to its presence in small ruminants are limited. We report, here, PBV infection in small ruminants (ovine and caprine), in India. From January 2015 to December 2017, 400 samples were tested for the presence of PBV, using an RT-PCR assay specific for the genome segment-2. The overall rate of PBV infection was 35...
May 14, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29770590/genomic-and-antigenic-characterization-of-porcine-epidemic-diarrhoea-virus-strains-isolated-from-south-korea-2017
#8
Sunhee Lee, Changhee Lee
Porcine epidemic diarrhoea virus (PEDV) is a globally emerging and re-emerging enteric coronavirus in pigs causing serious economic threats to the world swine industry. Since the re-emergence of massive PEDV outbreaks in South Korea in 2013-2014, domestic pig farms have continued to experience PED epidemics or endemics. This study represents the molecular characterization of PEDV isolates identified in diarrhoeic animals collected across the country in 2017. Initial sequencing analysis of the full-length S genes revealed that 70% of the 2017 isolates (7/10) belong to the G2b subgroup, while the remaining isolates were classified as G1b...
May 16, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29769160/cross-border-outbreak-of-extensively-drug-resistant-tuberculosis-linked-to-a-university-in-romania
#9
O Popovici, Ph Monk, D Chemtob, D Chiotan, P J Freidlin, R Groenheit, M Haanperä, D Homorodean, M Mansjö, E Robinson, E Rorman, G Smith, H Soini, M J Van Der Werf
Extensively drug-resistant (XDR) tuberculosis (TB) poses a threat to public health due to its complicated, expensive and often unsuccessful treatment. A cluster of three XDR TB cases was detected among foreign medical students of a Romanian university. The contact investigations included tuberculin skin testing or interferon gamma release assay, chest X-ray, sputum smear microscopy, culture, drug susceptibility testing, genotyping and whole-genome sequencing (WGS), and were addressed to students, personnel of the university, family members or other close contacts of the cases...
May 2018: Epidemiology and Infection
https://www.readbyqxmd.com/read/29765675/-leishmania-naiffi-and-leishmania-guyanensis-reference-genomes-highlight-genome-structure-and-gene-evolution-in-the-viannia-subgenus
#10
Simone Coughlan, Ali Shirley Taylor, Eoghan Feane, Mandy Sanders, Gabriele Schonian, James A Cotton, Tim Downing
The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America, where the Viannia subgenus predominates, so far only L. ( Viannia ) braziliensis and L. ( V. ) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. ( V. ) naiffi and L. ( V. ) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29764422/hmmibd-software-to-infer-pairwise-identity-by-descent-between-haploid-genotypes
#11
Stephen F Schaffner, Aimee R Taylor, Wesley Wong, Dyann F Wirth, Daniel E Neafsey
BACKGROUND: A number of recent malaria studies have used identity by descent (IBD) to study epidemiological processes relevant to malaria control. In this paper, a software package, hmmIBD, is introduced for estimating pairwise IBD between haploid genomes, such as those of the malaria parasite, sampled from one or two populations. Source code is freely available. METHODS: The performance of hmmIBD was verified using simulated data and benchmarked against an existing method for detecting IBD within populations...
May 15, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29763627/evaluation-of-minion-nanopore-sequencing-for-rapid-enterovirus-genotyping
#12
Emily Rames, Joanne Macdonald
Enteroviruses (EV) are associated with a range of serious infections, including aseptic meningitis, hand foot and mouth disease, myocarditis, acute flaccid paralysis and encephalitis. Improved methods for assessing EV genotypic diversity could assist molecular epidemiology studies, clinical diagnosis and environmental surveillance. We report new methods for EV genome amplification, and subsequent genotyping using the miniaturised MinION sequencing device. Importantly, this next-generation sequencer enabled correct strain-level assignment of identity for the EV-A71 isolate assessed, where strains with up to 99...
May 12, 2018: Virus Research
https://www.readbyqxmd.com/read/29763449/a-novel-specific-duplex-real-time-rt-pcr-method-for-absolute-quantitation-of-grapevine-pinot-gris-virus-in-plant-material-and-single-mites
#13
Félix Morán, Antonio Olmos, Leonidas Lotos, Lukáš Predajňa, Nikolaos Katis, Miroslav Glasa, Varvara Maliogka, Ana B Ruiz-García
Grapevine Pinot gris virus (GPGV) is a widely distributed grapevine pathogen that has been associated to the grapevine leaf mottling and deformation disease. With the aim of better understanding the disease epidemiology and providing efficient control strategies a specific and quantitative duplex TaqMan real-time RT-PCR assay has been developed. This method has allowed reliable quantitation of the GPGV titer ranging from 30 up to 3 x 108 transcript copies, with a detection limit of 70 viral copies in plant material...
2018: PloS One
https://www.readbyqxmd.com/read/29760616/high-frequency-of-primary-hereditary-ichthyoses-in-the-north-east-region-of-cairo-egypt
#14
Nermine El-Sayed, Neveen S Seifeldin, Christine K T Gobrial
Introduction: Inherited ichthyoses are caused by mutations in various genes important for keratinocyte differentiation and epidermal barrier function. Although ichthyoses are rare disorders, they require costly long-term medical management, and thus there is a need for efficient preventive and therapeutic strategies. Aim: We performed a retrospective study to determine the frequency, types, clinical presentation and associated genomic errors of primary hereditary ichthyoses in Egyptian patients and their relatives consulting the Genetics Clinic, Pediatric Hospital, Ain Shams University...
April 2018: Postȩpy Dermatologii i Alergologii
https://www.readbyqxmd.com/read/29758083/correction-epidemiological-links-between-tuberculosis-cases-identified-twice-as-efficiently-by-whole-genome-sequencing-than-conventional-molecular-typing-a-population-based-study
#15
Rana Jajou, Albert de Neeling, Rianne van Hunen, Gerard de Vries, Henrieke Schimmel, Arnout Mulder, Richard Anthony, Wim van der Hoek, Dick van Soolingen
[This corrects the article DOI: 10.1371/journal.pone.0195413.].
2018: PloS One
https://www.readbyqxmd.com/read/29758076/high-throughput-generation-and-characterization-of-replication-competent-clade-c-transmitter-founder-simian-human-immunodeficiency-viruses
#16
Debashis Dutta, Samuel Johnson, Alisha Dalal, Martin J Deymier, Eric Hunter, Siddappa N Byrareddy
Traditional restriction endonuclease-based cloning has been routinely used to generate replication-competent simian-human immunodeficiency viruses (SHIV) and simian tropic HIV (stHIV). This approach requires the existence of suitable restriction sites or the introduction of nucleotide changes to create them. Here, using an In-Fusion cloning technique that involves homologous recombination, we generated SHIVs and stHIVs based on epidemiologically linked clade C transmitted/founder HIV molecular clones from Zambia...
2018: PloS One
https://www.readbyqxmd.com/read/29757994/bioinformatics-meets-virology-the-european-virus-bioinformatics-center-s-second-annual-meeting
#17
Bashar Ibrahim, Ksenia Arkhipova, Arno C Andeweg, Susana Posada-Céspedes, François Enault, Arthur Gruber, Eugene V Koonin, Anne Kupczok, Philippe Lemey, Alice C McHardy, Dino P McMahon, Brett E Pickett, David L Robertson, Richard H Scheuermann, Alexandra Zhernakova, Mark P Zwart, Alexander Schönhuth, Bas E Dutilh, Manja Marz
The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions...
May 14, 2018: Viruses
https://www.readbyqxmd.com/read/29757395/genotyping-and-whole-genome-sequencing-to-identify-tuberculosis-transmission-to-pediatric-patients-in-british-columbia-canada-2005-2014
#18
Jennifer L Guthrie, Andy Delli Pizzi, David Roth, Clare Kong, Danielle Jorgensen, Mabel Rodrigues, Patrick Tang, Victoria J Cook, James Johnston, Jennifer L Gardy
Background: Tuberculosis (TB) in children is often an indicator of recent transmission. Genotyping and whole genome sequencing (WGS) can enhance pediatric TB investigations by confirming or refuting transmission events. Methods: Mycobacterium tuberculosis isolates from all pediatric patients <18 years with culture-confirmed TB in British Columbia (BC) from 2005-2014 (n=49) were genotyped by MIRU-VNTR and compared to adult isolates. Genotypically clustered cases underwent WGS...
May 11, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29755603/bacterial-crispr-regions-general-features-and-their-potential-for-epidemiological-molecular-typing-studies
#19
REVIEW
Zahra Karimi, Ali Ahmadi, Ali Najafi, Reza Ranjbar
Introduction: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods: These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements...
2018: Open Microbiology Journal
https://www.readbyqxmd.com/read/29753823/analysis-of-differentially-changed-gene-expression-in-ea-hy926-human-endothelial-cell-after-exposure-of-fine-particulate-matter-on-the-basis-of-microarray-profile
#20
Yan Wang, Lilin Xiong, Tianshu Wu, Ting Zhang, Lu Kong, Yuying Xue, Meng Tang
Epidemiological studies have illustrated that PM2.5 is closely related to cardiovascular disease (CVD), but underlying toxicological mechanisms are not yet clear. The main purpose of this study is to disclose the potential biological mechanisms responsible for PM2.5-dependent adverse cardiovascular outcomes through the appliance of genome-wide transcription microarray. From results, compared with the control group, there are 97 genes significantly altered in 2.5 μg/cm2 PM2.5 treated group and 440 differentially expressed genes in 10 μg/cm2 group...
May 10, 2018: Ecotoxicology and Environmental Safety
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