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https://www.readbyqxmd.com/read/28738474/-hiv-1-drug-resistance-transmission-threshold-survey-in-dehong-prefecture-of-yunnan-province-2015
#1
M Chen, J B Wang, H Xing, Y L Ma, J Yang, H C Chen, S T Yao, H B Luo, X Duan, Y K Wang, S Duan, M H Jia
Objective: To study the HIV-1 drug resistance transmission level in HIV infected persons receiving no antiviral therapy in Dehong prefecture of Yunnan province in 2015. Methods: A total of 72 plasma samples were collected from recently reported HIV-infected persons aged 16-25 years in Dehong from January to July 2015 for drug resistance gene detection. Results: Forty eight samples were successfully sequenced and analyzed. Among them, 31.2% (15/48) were from Chinese, and 68.8% (33/48) were from Burmese. Based on pol sequences, HIV genotypes included URF (52...
July 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28738459/-gene-gene-interaction-on-central-obesity-in-school-aged-children-in-china
#2
L W Fu, M X Zhang, L J Wu, L W Gao, J Mi
Objective: To investigate possible effect of 6 obesity-associated SNPs in contribution to central obesity and examine whether there is an interaction in the 6 SNPs in the cause of central obesity in school-aged children in China. Methods: A total of 3 502 school-aged children who were included in Beijing Child and Adolescent Metabolic Syndrome (BCAMS) Study were selected, and based on the age and sex specific waist circumference (WC) standards in the BCAMS study, 1 196 central obese cases and 2 306 controls were identified...
July 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28737288/linkage-disequilibrium-among-commonly-genotyped-snp-variants-detected-from-bull-sequence
#3
W M Snelling, L A Kuehn, B N Keel, R M Thallman, G L Bennett
Genomic prediction utilizing causal variants could increase selection accuracy above that achieved with SNPs genotyped by currently available arrays used for genomic selection. A number of variants detected from sequencing influential sires are likely to be causal, but noticeable improvements in prediction accuracy using imputed sequence variant genotypes have not been reported. Improvement in accuracy of predicted breeding values may be limited by the accuracy of imputed sequence variants. Using genotypes of SNPs on a high-density array and non-synonymous SNPs detected in sequence from influential sires of a multibreed population, results of this examination suggest that linkage disequilibrium between non-synonymous and array SNPs may be insufficient for accurate imputation from the array to sequence...
July 24, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28737247/a-single-base-deletion-in-the-slc45a2-gene-in-a-bullmastiff-with-oculocutaneous-albinism
#4
M Caduff, A Bauer, V Jagannathan, T Leeb
Oculocutaneous albinism type 4 (OCA4) in humans and similar phenotypes in many animal species are caused by variants in the SLC45A2 gene, encoding a putative sugar transporter. In dog, two independent SLC45A2 variants are known that cause oculocutaneous albinism in Doberman Pinschers and several small dog breeds respectively. For the present study, we investigated a Bullmastiff with oculocutaneous albinism. The affected dog was highly inbred and resulted from the mating of a sire to its own grandmother. We obtained whole genome sequence data from the affected dog and searched specifically for variants in candidate genes known to cause albinism...
July 24, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28737063/genetic-diversity-and-antimicrobial-resistance-profile-of-enterococcus-faecalis-isolated-from-broilers-with-vertebral-osteomyelitis-in-southeast-brazil
#5
Juliana Fortes Vilarinho Braga, Carlos Augusto Gomes Leal, Camila Costa Silva, André Almeida Fernandes, Nelson Rodrigo da Silva Martins, Roselene Ecco
Vertebral osteomyelitis (VO) is a worldwide emerging disease that affects broilers. Recently, the isolation of Enterococcus faecalis in cases of the disease has been described. This study aimed at determining the genetic diversity and antimicrobial resistance profile of 12 Enterococcus faecalis strains isolated from broilers with VO. Strains were isolated from nine flocks from six farms in a high-density poultry production area in Southeast Brazil and were evaluated using multilocus sequence typing (MLST) and phylogenetic analysis...
July 24, 2017: Avian Pathology: Journal of the W.V.P.A
https://www.readbyqxmd.com/read/28736914/internal-diversification-of-non-sub-saharan-haplogroups-in-sahelian-populations-and-the-spread-of-pastoralism-beyond-the-sahara
#6
Iva Kulichová, Verónica Fernandes, Alioune Deme, Jana Nováčková, Vlastimil Stenzl, Andrea Novelletto, Luísa Pereira, Viktor Černý
BACKGROUND: Today, African pastoralists are found mainly in the Sahel/Savannah belt spanning 6,000 km from west to east, flanked by the Sahara to the north and tropical rainforests to the south. The most significant group among them are the Fulani who not only keep cattle breeds of possible West Eurasian ancestry, but form themselves a gene pool containing some paternally and maternally-transmitted West Eurasian haplogroups. MATERIALS AND METHODS: We generated complete sequences for 33 mitogenomes belonging to haplogroups H1 and U5 (23 and 10, respectively), and genotyped 16 STRs in 65 Y chromosomes belonging to haplogroup R1b-V88...
July 24, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28736873/standardised-molecular-diagnostic-tool-for-the-identification-of-cryptic-species-within-the-bemisia-tabaci-complex
#7
S Elfekih, W T Tay, K Gordon, L Court, P De Barro
BACKGROUND: The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterisation of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade i.e. 'MED', 'MEAM1', 'MEAM2' and IO'. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection, however no standardised B...
July 23, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28736753/combination-of-rt-pcr-and-proteomics-for-the-identification-of-crimean-congo-hemorrhagic-fever-virus-in-ticks
#8
Isabel G Fernández de Mera, Ilias Chaligiannis, Angélica Hernández-Jarguín, Margarita Villar, Lourdes Mateos-Hernández, Anna Papa, Smaragda Sotiraki, Francisco Ruiz-Fons, Alejandro Cabezas-Cruz, Christian Gortázar, José de la Fuente
Crimean-Congo hemorrhagic fever (CCHF) is an emerging tick-borne zoonotic disease caused by the CCHF virus (CCHFV). In this study, an experimental approach combining RT-PCR and proteomics was used for the identification and characterization of CCHFV in 106 ticks from 7 species that were collected from small ruminants in Greece. The methodological approach included an initial screening for CCHFV by RT-PCR followed by proteomics analysis of positive and control negative tick samples. This novel approach allowed the identification of CCHFV-positive ticks and provided additional information to corroborate the RT-PCR findings using a different approach...
July 2017: Heliyon
https://www.readbyqxmd.com/read/28736702/cultivar-specific-transcriptome-prediction-and-annotation-in-ficus-carica-l
#9
Liceth Solorzano Zambrano, Gabriele Usai, Alberto Vangelisti, Flavia Mascagni, Tommaso Giordani, Rodolfo Bernardi, Andrea Cavallini, Riccardo Gucci, Giovanni Caruso, Claudio D'Onofrio, Mike Frank Quartacci, Piero Picciarelli, Barbara Conti, Andrea Lucchi, Lucia Natali
The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28736571/evaluation-of-quality-assessment-protocols-for-high-throughput-genome-resequencing-data
#10
REVIEW
Matteo Chiara, Giulio Pavesi
Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human "variome," through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28736259/molecular-epidemiology-and-antimicrobial-susceptibility-of-clostridium-difficile-isolated-from-the-chinese-people-s-liberation-army-general-hospital-in-china
#11
Rui Wang, Hui Xia Chen, Lin Jian Song, Yue Yun Shen, Yan Ping Luo
Clostridium difficile is a gram-positive, spore-forming obligate anaerobe responsible for antibiotic-associated diarrhea. Its virulence is associated with the production of endotoxins A and B and endospores, which can cause symptoms, such as diarrhea, toxic megacolon and pseudomembranous colitis. Given the increasing elderly population and the well-recognized problem of over-prescribing of broad spectrum antibiotics, it is critical to understand molecular epidemiology and antimicrobial susceptibility in China...
July 20, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28736138/how-viral-genetic-variants-and-genotypes-influence-disease-and-treatment-outcome-of-chronic-hepatitis-b-time-for-an-individualized-approach
#12
REVIEW
Neil Rajoriya, Christophe Combet, Fabien Zoulim, Harry L A Janssen
Chronic hepatitis B virus (HBV) infection remains a global problem. Several HBV (sub)genotypes exist with different biology and geographical preponderances. While the future aim of HBV treatment remains virus eradication, current strategies of treatment aim to suppress the virus and prevent the progression of liver disease. Current strategies also involve identification of patients for treatment - those at risk of progressive liver disease. Identification of HBV genotype, HBV mutants and other predictive factors allow for tailored treatments, and also risk-surveillance pathways such as for hepatocellular cancer screening...
July 20, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28736074/a-novel-genetic-variant-of-streptococcus-pneumoniae-serotype-11a-discovered-in-fiji
#13
Sam Manna, Belinda Ortika, Eileen M Dunne, Kathryn E Holt, Mike Kama, Fiona M Russell, Jason Hinds, Catherine Satzke
OBJECTIVES: As part of annual cross-sectional Streptococcus pneumoniae carriage surveys in Fiji (2012-2015), we detected pneumococci in over 100 nasopharyngeal swabs that serotyped as '11F-like' by microarray. We examined the genetic basis of this divergence in the 11F-like capsular polysaccharide (cps) locus, compared to the reference 11F cps sequence. The impact of this diversity on capsule phenotype, as well as serotyping results using genetic and serological methods, was determined...
July 20, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28735882/antibiotic-resistance-and-population-structure-of-cystic-fibrosis-pseudomonas-aeruginosa-isolates-from-a-spanish-multi-centre-study
#14
Carla López-Causapé, Juan de Dios-Caballero, Marta Cobo, Amparo Escribano, Óscar Asensio, Antonio Oliver, Rosa Del Campo, Rafael Cantón
The first Spanish multi-centre study on the microbiology of cystic fibrosis (CF) was conducted from 2013 to 2014. The study involved 24 CF units from 17 hospitals, and recruited 341 patients. The aim of this study was to characterise Pseudomonas aeruginosa isolates, 79 of which were recovered from 75 (22%) patients. The study determined the population structure, antibiotic susceptibility profile and genetic background of the strains. Fifty-five percent of the isolates were multi-drug-resistant, and 16% were extensively-drug-resistant...
July 20, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28735798/the-etiology-of-essential-tremor-genes-versus-environment
#15
Franziska Hopfner, Rick C Helmich
INTRODUCTION: Essential tremor (ET) is characterized by bilateral upper limb action tremor. Here we review the pathophysiology (cerebral mechanisms) and etiology (genetic and environmental risk factors) of ET. METHODS: We reviewed the literature (until June 2017) by searching PubMed for relevant papers. RESULTS: The pathophysiology of ET involves oscillatory activity in the cortico-olivo-cerebello-thalamic circuit, evidenced by electrophysiological and metabolic imaging...
July 17, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28735491/nanofluidic-allele-specific-digital-pcr-method-for-quantifying-idh1-and-idh2-mutation-burden-in-acute-myeloid-leukemia
#16
Daniel H Wiseman, Tim C P Somervaille
Precise quantitation of allelic burden for a pathogenic mutation has diverse clinical and research applications but can be difficult to achieve with conventional qPCR-based techniques, especially at lower mutant allele frequencies. Digital PCR overcomes many of the limitations of qPCR and can be highly quantitative even for single-nucleotide variants, with distinct advantages over next-generation sequencing approaches. Here we describe a method combining the principles of TaqMan(®)-chemistry SNP genotyping with microfluidic digital PCR to generate a highly sensitive, quantitative allele-specific digital PCR assay for the six most common IDH1 and IDH2 mutations encountered in myeloid malignancy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735391/toward-a-resilient-functional-microbiome-drought-tolerance-alleviating-microbes-for-sustainable-agriculture
#17
Venkatachalam Lakshmanan, Prasun Ray, Kelly D Craven
In recent years, the utilization of novel sequencing techniques opened a new field of research into plant microbiota and was used to explore a wide diversity of microorganisms both inside and outside of plant host tissues, i.e., the endosphere and rhizosphere, respectively. An early realization from such research was that species richness and diversity of the plant microbiome are both greater than believed even a few years ago, and soil is likely home to the most abundant and diverse microbial habitats known...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735298/foxp1-related-intellectual-disability-syndrome-a-recognisable-entity
#18
Ilse Meerschaut, Daniel Rochefort, Nicole Revençu, Justine Pètre, Christina Corsello, Guy A Rouleau, Fadi F Hamdan, Jacques L Michaud, Jenny Morton, Jessica Radley, Nicola Ragge, Sixto García-Miñaúr, Pablo Lapunzina, Maria Palomares Bralo, Maria Ángeles Mori, Stéphanie Moortgat, Valérie Benoit, Sandrine Mary, Nele Bockaert, Ann Oostra, Olivier Vanakker, Milen Velinov, Thomy Jl de Ravel, Djalila Mekahli, Jonathan Sebat, Keith K Vaux, Nataliya DiDonato, Andrea K Hanson-Kahn, Louanne Hudgins, Bruno Dallapiccola, Antonio Novelli, Luigi Tarani, Joris Andrieux, Michael J Parker, Katherine Neas, Berten Ceulemans, An-Sofie Schoonjans, Darina Prchalova, Marketa Havlovicova, Miroslava Hancarova, Magdalena Budisteanu, Annelies Dheedene, Björn Menten, Patrick A Dion, Damien Lederer, Bert Callewaert
BACKGROUND: Mutations in forkhead box protein P1 (FOXP1) cause intellectual disability (ID) and specific language impairment (SLI), with or without autistic features (MIM: 613670). Despite multiple case reports no specific phenotype emerged so far. METHODS: We correlate clinical and molecular data of 25 novel and 23 previously reported patients with FOXP1 defects. We evaluated FOXP1 activity by an in vitro luciferase model and assessed protein stability in vitro by western blotting...
July 22, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28735050/antimicrobial-resistance-profiles-and-genotypes-of-extended-spectrum-%C3%AE-lactamase-and-ampc-%C3%AE-lactamase-producing-klebsiella-pneumoniae-isolated-from-dogs-in-beijing-china
#19
Yanhan Liu, Yonghui Yang, Yanyun Chen, Zhaofei Xia
OBJECTIVES: Klebsiella pneumoniae, which exists in the intestinal and respiratory tracts of humans and animals, is an important conditional pathogen in many animals. The aim of the current study was to investigate the antimicrobial resistance profiles and genotypes of extended-spectrum β-lactamase (ESBL) - and AmpC β-lactamase-producing K. pneumoniae isolated from dogs. METHODS: A total of 285 isolates, collected from fecal and urine samples of diseased dogs in a Veterinary Teaching Hospital in Beijing, were characterized by antimicrobial susceptibility testing and screened for ESBL and AmpC β-lactamase phenotypes...
July 19, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28735048/emergence-of-different-acinetobacter-baumannii-clones-in-a-croatian-hospital-and-correlation-with-antibiotic-susceptibility
#20
Ranko Ladavac, Branka Bedenić, Mirna Vranić-Ladavac, Nada Barišić, Natalie Karčić, Karoline Pompe, Antun Ferenčić, Aleksandar Stojanović, Harald Seifert, Stjepan Katić, Paul G Higgins
OBJECTIVES: During routine diagnostic laboratory work, the clinical microbiologist observed an increase of Acinetobacter baumannii isolates with three different carbapenem susceptibility patterns: susceptible, intermediate and resistant. Isolates belonging to the same carbapenem susceptibility phenotype exhibited identical susceptibility/resistance patterns to non-β-lactam antibiotics. This prompted us to analyze the mechanisms of carbapenem-resistance and the molecular epidemiology of the isolates...
July 19, 2017: Journal of Global Antimicrobial Resistance
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