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https://www.readbyqxmd.com/read/29166280/differentiation-of-infectious-bronchitis-virus-vaccine-strains-ma5-and-4-91-by-taqman-real-time-pcr
#1
T Stenzel, D Dziewulska, M Śmiałek, B Tykałowski, J Kowalczyk, A Koncicki
The aim of this study was to develop rapid molecular assays for differentiating vaccine strains Ma5 and 4/91 of the infectious bronchitis virus (IBV). Specific primers and probes for S1 and N genes were designed based on the nucleotide sequences of both vaccine strains. Cross-reactivity was not observed. Assay sensitivity was 2.373 × 103 copies of the Ma5 strain, and 3.852 x 103 copies of the 4/91 strain. Samples belonging to a known genotype demonstrated that the designed assays supported rapid and sensitive detection of Ma5 and 4/91 vaccine strains of IBV...
September 26, 2017: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/29166127/bat-biology-genomes-and-the-bat1k-project-to-generate-chromosome-level-genomes-for-all-living-bat-species
#2
Emma Teeling, Sonja Vernes, Liliana M Davalos, David A Ray, M Thomas P Gilbert, Eugene Myers, Bat K Consortium
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene...
November 20, 2017: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/29165790/physician-interpretation-of-genomic-test-results-and-treatment-selection
#3
Lauren L Brusco, Chetna Wathoo, Kenna R Mills Shaw, Vijaykumar R Holla, Ann M Bailey, Amber M Johnson, Yekaterina B Khotskaya, Beate C Litzenburger, Nora S Sanchez, Jia Zeng, Elmer V Bernstam, Cathy Eng, Bryan K Kee, Rodabe N Amaria, Mark J Routbort, Gordon B Mills, John Mendelsohn, Funda Meric-Bernstam
BACKGROUND: Genomic testing is increasingly performed in oncology, but concerns remain regarding the clinician's ability to interpret results. In the current study, the authors sought to determine the agreement between physicians and genomic annotators from the Precision Oncology Decision Support (PODS) team at The University of Texas MD Anderson Cancer Center in Houston regarding actionability and the clinical use of test results. METHODS: On a prospective protocol, patients underwent clinical genomic testing for hotspot mutations in 46 or 50 genes...
November 22, 2017: Cancer
https://www.readbyqxmd.com/read/29165368/human-protoparvoviruses
#4
REVIEW
Elina Väisänen, Yu Fu, Klaus Hedman, Maria Söderlund-Venermo
Next-generation sequencing and metagenomics have revolutionized the discovery of novel viruses. In recent years, three novel protoparvoviruses have been discovered in fecal samples of humans: bufavirus (BuV) in 2012, tusavirus (TuV) in 2014, and cutavirus (CuV) in 2016. BuV has since been studied the most, disclosing three genotypes that also represent serotypes. Besides one nasal sample, BuV DNA has been found exclusively in diarrheal feces, but not in non-diarrheal feces, suggesting a causal relationship...
November 22, 2017: Viruses
https://www.readbyqxmd.com/read/29165300/foxi2-a-possible-gene-contributing-to-ectodermal-dysplasia
#5
Mazen Kurban, Savo Bou Zeineddine, Lamiaa Hamie, Remi Safi, Ossama Abbas, Abdul Ghani Kibbi, Fadi Bitar, Georges Nemer
Cardio-facio-cutaneous syndrome (CFC), Noonan syndrome (NS), and Costello syndrome are a group of diseases that belong to the RASopathies. The syndromes share clinical features making diagnosis a challenge. To investigate the phenotype and genotype of a 10-year-old Iraqi girl with overlapping features of CFC, NS, and Costello syndromes, with additional features of ectodermal dysplasia. DNA was examined by exome sequencing and protein expression by immunohistochemistry. Exome sequencing identified a mutation in the SOS1 gene and a de novo deletion in the FOXI2 gene which was neither present in the international databases, nor in 400 chromosomes from the same population...
November 22, 2017: European Journal of Dermatology: EJD
https://www.readbyqxmd.com/read/29165144/isolation-and-identification-of-acanthamoeba-strains-from-soil-and-tap-water-in-yanji-china
#6
Yinghua Xuan, Yanqin Shen, Yuxi Ge, Gen Yan, Shanzi Zheng
BACKGROUND: Members of the genus Acanthamoeba are widely distributed throughout the world, and some of them are considered pathogenic, as they are capable of causing corneal and central nervous system diseases. In this study, we isolated Acanthamoeba strains from soil and tap water in Yanji, China. METHODS: We identified four strains of Acanthamoeba (CJY/S1, CJY/S2, CJY/S3, and CJY/W1) using mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) analysis...
June 30, 2017: Environmental Health and Preventive Medicine
https://www.readbyqxmd.com/read/29164140/phenotypic-and-genotypic-features-of-a-salmonella-heidelberg-strain-isolated-in-broilers-in-brazil-and-their-possible-association-to-antibiotics-and-short-chain-organic-acids-resistance-and-susceptibility
#7
Elizabeth Santin, Ricardo Mitsuo Hayashi, Jessica Caroline Wammes, Ricardo Gonzalez-Esquerra, Marcelo Falsarella Carazzolle, Caio César de Melo Freire, Paulo Sérgio Monzani, Anderson Ferreira da Cunha
Salmonella enterica serovar Heidelberg is a human pathogen also found in broilers. A strain (UFPR1) has been associated with field reports of resistance to short-chain organic acids (SCOA) in broilers in the South of Brazil, but was susceptible to a Bacillus subtilis-based probiotic added in feed in a related study. This work aimed to (i) report clinical symptoms caused by SH UFPR1 in broilers, (ii) study its susceptibility to some antibiotics in vitro, and (iii) SCOA in vivo; and (iv) relate these phenotypic observations with its genome characteristics...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29163817/characteristics-and-genetic-diversity-of-multi-drug-resistant-extended-spectrum-beta-lactamase-esbl-producing-escherichia-coli-isolated-from-bovine-mastitis
#8
Tariq Ali, Sadeeq Ur Rahman, Limei Zhang, Muhammad Shahid, Dandan Han, Jian Gao, Shiyao Zhang, Pamela L Ruegg, Umer Saddique, Bo Han
A characterization of the drug resistance profiles, identification of PCR-based replicon typing, and multilocus sequence typing (MLST) and analysis of 46 ESBL-producing Escherichia coli from cows with mastitis are described. All multidrug-resistant isolates of various phylogenetic groups (A = 31, B1= 3, B2 = 2, D = 10) were ESBL-producers of genotypes CTX-M-15 (29), CTX-M-55 (4), CTX-M-14 (4), CTX-M-3 (1), CTX-M-1 (1), TEM (22) and SHV (8) that were found on conjugative plasmids of diverse incompatibility groups (primarily IncF)...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29163652/phylogenic-analysis-of-serotype-asia1-foot-and-mouth-disease-virus-from-sulaimani-iraq-using-vp1-protein-heterogeneity-with-vaccine-strain-as1-shamir-89
#9
M O Baba Sheikh, P M A Rashid, A S Marouf, Z H Raheem, S C Janga
Foot-and-mouth disease virus (FMDV) serotypes O, A and Asia1 are responsible for a significant number of disease outbreaks in Iraq. The current study can be considered as the first molecular characterization of serotype Asia1 in Iraq. The present investigation reports the detection of serotype FMDV Asia1 from local farms in Sulaimani districts in 2012 and 2014 outbreaks. Phylogenetic analysis of the complete VP1 gene has shown that FMDV Asia1 field isolates were under genetic novel variant Sindh-08 (group VII) including PAK/iso/11 and TUR/13 strains...
2017: Iranian journal of veterinary research
https://www.readbyqxmd.com/read/29163587/global-dna-methylation-patterns-can-play-a-role-in-defining-terroir-in-grapevine-vitis-vinifera-cv-shiraz
#10
Huahan Xie, Moumouni Konate, Na Sai, Kiflu G Tesfamicael, Timothy Cavagnaro, Matthew Gilliham, James Breen, Andrew Metcalfe, John R Stephen, Roberta De Bei, Cassandra Collins, Carlos M R Lopez
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163438/culture-strategies-for-isolation-of-fastidious-leptospira-serovar-hardjo-and-molecular-differentiation-of-genotypes-hardjobovis-and-hardjoprajitno
#11
Roberta T Chideroli, Daniela D Gonçalves, Suelen A Suphoronski, Alice F Alfieri, Amauri A Alfieri, Admilton G de Oliveira, Julio C de Freitas, Ulisses de Padua Pereira
The Leptospira serovar Hedjo belongs to the serogroup sejroe and this serovar is the most prevalent in bovine herds worldwide. The sejroe serogroup is the most frequently detected by serology in Brazilian cattle herds suggesting that it is due serovar Hardjo. In the molecular classification, this serovar has two genotypes: Hardjobovis and Hardjoprajitno. This serovar is as considered as fastidious pathogens, and their isolation is one of the bottlenecks in leptospirosis laboratories. In addition, its molecular characterization using genomic approaches is oftentimes not simple and time-consuming...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163422/a-novel-inca-c1-group-conjugative-plasmid-encoding-vim-1-metallo-beta-lactamase-mediates-the-acquisition-of-carbapenem-resistance-in-st104-klebsiella-pneumoniae-isolates-from-neonates-in-the-intensive-care-unit-of-v-monaldi-hospital-in-naples
#12
Eliana P Esposito, Stefano Gaiarsa, Mariateresa Del Franco, Valeria Crivaro, Mariano Bernardo, Susanna Cuccurullo, Francesca Pennino, Maria Triassi, Piero Marone, Davide Sassera, Raffaele Zarrilli
The emergence of carbapenemase producing Enterobacteriaceae has raised major public health concern. The aim of this study was to investigate the molecular epidemiology and the mechanism of carbapenem resistance acquisition of multidrug-resistant Klebsiella pneumoniae isolates from 20 neonates in the neonatal intensive care unit (NICU) of the V. Monaldi Hospital in Naples, Italy, from April 2015 to March 2016. Genotype analysis by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) identified PFGE type A and subtypes A1 and A2 in 17, 2, and 1 isolates, respectively, and assigned all isolates to sequence type (ST) 104...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163399/minion-nanopore-sequencing-enables-correlation-between-resistome-phenotype-and-genotype-of-coliform-bacteria-in-municipal-sewage
#13
Yu Xia, An-Dong Li, Yu Deng, Xiao-Tao Jiang, Li-Guan Li, Tong Zhang
Wastewater treatment plants (WWTPs) functioned as the intersection between the human society and nature environment, are receiving increasingly more attention on risk assessment of the acquisition of environmental antibiotic resistance genes (ARGs) by pathogenetic populations during treatment. However, because of the general lack of robust resistome profiling methods, genotype, and resistance phenotype is still poorly correlated in human pathogens of sewage samples. Here we applied MinION sequencing to quantify the resistance genes of multiple antibiotic resistant (MAR) coliform bacteria, a common indicator for human enteric pathogens in sewage samples...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163392/clonal-expansion-of-biofilm-forming-salmonella-typhimurium-st34-with-multidrug-resistance-phenotype-in-the-southern-coastal-region-of-china
#14
Wanli Li, Yinghui Li, Yao Liu, Xiaolu Shi, Min Jiang, Yiman Lin, Yaqun Qiu, Qian Zhang, Qiongcheng Chen, Li Zhou, Qun Sun, Qinghua Hu
To disclose the antibiotics susceptibility and wide adaptability of commonly occurring genotypes of Salmonella Typhimurium, the antibiotic resistance and biofilm formation of different multi-locus sequence typing (MLST) types of a collection of 240 S. Typhimurium isolates (33 food and 207 clinical ones) during 2010-2014 in Shenzhen were analyzed. Among these strains, 167 was ST34 (69.58%), and 57 was ST19 (23.75%), respectively. A total of 159 (95.21%) ST34 strains displayed the multidrug resistant phenotype (≥ three classes of antibiotic), whereas only 23 (40...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163336/two-novel-mutations-associated-with-ataxia-telangiectasia-identified-using-an-ion-ampliseq-inherited-disease-panel
#15
Maria V Kuznetsova, Dmitry Yu Trofimov, Ekaterina S Shubina, Taisiya O Kochetkova, Natalia A Karetnikova, Ilya Yu Barkov, Vladimir A Bakharev, Oleg A Gusev, Gennady T Sukhikh
Ataxia-telangiectasia (A-T), or Louis-Bar syndrome, is a rare neurodegenerative disorder associated with immunodeficiency. For families with at least one affected child, timely A-T genotyping during any subsequent pregnancy allows the parents to make an informed decision about whether to continue to term when the fetus is affected. Mutations in the ATM gene, which is 150 kb long, give rise to A-T; more than 600 pathogenic variants in ATM have been characterized since 1990 and new mutations continue to be discovered annually...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/29163129/biomarkers-of-presbycusis-and-tinnitus-in-a-portuguese-older-population
#16
Haúla F Haider, Marisa Flook, Mariana Aparicio, Diogo Ribeiro, Marilia Antunes, Agnieszka J Szczepek, Derek J Hoare, Graça Fialho, João C Paço, Helena Caria
Introduction: Presbycusis or age-related hearing loss (ARHL) is a ubiquitous health problem. It is estimated that it will affect up to 1.5 billion people by 2025. In addition, tinnitus occurs in a large majority of cases with presbycusis. Glutamate metabotropic receptor 7 (GRM7) and N-acetyltransferase 2 (NAT2) are some of the genetic markers for presbycusis. Objectives: To explore patterns of hearing loss and the role of GRM7 and NAT2 as possible markers of presbycusis and tinnitus in a Portuguese population sample...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/29162615/precision-oncology-between-vaguely-right-and-precisely-wrong
#17
REVIEW
Amy Brock, Sui Huang
Precision Oncology seeks to identify and target the mutation that drives a tumor. Despite its straightforward rationale, concerns about its effectiveness are mounting. What is the biological explanation for the "imprecision?" First, Precision Oncology relies on indiscriminate sequencing of genomes in biopsies that barely represent the heterogeneous mix of tumor cells. Second, findings that defy the orthodoxy of oncogenic "driver mutations" are now accumulating: the ubiquitous presence of oncogenic mutations in silent premalignancies or the dynamic switching without mutations between various cell phenotypes that promote progression...
November 21, 2017: Cancer Research
https://www.readbyqxmd.com/read/29162551/using-a-new-rad-sequencing-approach-to-study-the-evolution-of-micromeria-in-the-canary-islands
#18
Manuel Curto, Christina Schachtler, Pamela Puppo, Harald Meimberg
As found in other oceanic islands, the Canary Islands include a large number of single island endemic species, some of which form clades that are broadly distributed within the archipelago. The genus Micromeria (Lamiaceae), for instance, includes groups of morphologically similar but ecologically diverse species on each island, representing a great model to investigate niche shifts and adaptation within the Canary Archipelago. Previous attempts to reconstruct phylogenetic relationships within the genus did not lead to robust phylogenies, presumably due to introgression and/or incomplete lineage sorting...
November 18, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29162515/whole-exome-sequencing-in-a-japanese-family-with-highly-aggregated-diabetes-identifies-a-candidate-susceptibility-mutation-in-adamtsl3
#19
Byambatseren Jambaljav, Daisuke Tanaka, Kazuaki Nagashima, Shin-Ichi Harashima, Norio Harada, Takanari Harada, Yuta Fujiwara, Yu Wang, Yanyan Liu, Yasuharu Tabara, Fumihiko Matsuda, Akio Koizumi, Nobuya Inagaki
AIMS: The aim of this study was to clarify the genetic background of a family with multiple cases of diabetes accompanied by absolute insulin deficiency using whole-exome sequencing (WES). METHODS: In a Japanese family, WES was performed in four affected members with absolute insulin deficiency and two unaffected members. We focused on variants that were predicted to be disease-causing by bioinformatics and were shared by all of the four affected members but were not present in the two unaffected members...
November 18, 2017: Diabetes Research and Clinical Practice
https://www.readbyqxmd.com/read/29162348/human-aniridia-limbal-epithelial-cells-lack-expression-of-keratins-k3-and-k12
#20
Lorenz Latta, Arne Viestenz, Tanja Stachon, Sarah Colanesi, Nóra Szentmáry, Berthold Seitz, Barbara Käsmann-Kellner
Patients with aniridia often develop aniridia-related keratopathy (ARK), due to limbal stem cell insufficiency. This study aimed to determine the proliferative capacity and differentiation status of limbal epithelial cells (LECs) in patients with ARK. We also investigated the influences of PAX6 genotype on PAX6-transcript and protein level. Here two patients with aniridia underwent keratoplasty were examined. During the surgery, small limbal biopsies and pannus tissue were excised and processed for cell culture...
November 18, 2017: Experimental Eye Research
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