keyword
MENU ▼
Read by QxMD icon Read
search

genotypic sequence

keyword
https://www.readbyqxmd.com/read/28103318/static-and-evolving-norovirus-genotypes-implications-for-epidemiology-and-immunity
#1
Gabriel I Parra, R Burke Squires, Consolee K Karangwa, Jordan A Johnson, Cara Lepore, Stanislav V Sosnovtsev, Kim Y Green
Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII...
January 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28103310/epidemiological-and-molecular-characterization-of-a-mexican-population-isolate-with-high-prevalence-of-limb-girdle-muscular-dystrophy-type-2a-due-to-a-novel-calpain-3-mutation
#2
Carlos A Pantoja-Melendez, Antonio Miranda-Duarte, Bladimir Roque-Ramirez, Juan C Zenteno
Limb-Girdle Muscular Dystrophy type 2 (LGMD2) is a group of autosomally recessive inherited disorders defined by weakness and wasting of the shoulder and pelvic girdle muscles. In the past, several population isolates with high incidence of LGMD2 arising from founder mutation effects have been identified. The aim of this work is to describe the results of clinical, epidemiologic, and molecular studies performed in a Mexican village segregating numerous cases of LGMD2. A population census was conducted in the village to identify all LGMD affected patients...
2017: PloS One
https://www.readbyqxmd.com/read/28103259/characterization-and-genetic-variation-of-vibrio-cholerae-isolated-from-clinical-and-environmental-sources-in-thailand
#3
Achiraya Siriphap, Pimlapas Leekitcharoenphon, Rolf S Kaas, Chonchanok Theethakaew, Frank M Aarestrup, Orasa Sutheinkul, Rene S Hendriksen
Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/28102197/a-novel-dominant-gjb2-dfna3-mutation-in-a-chinese-family
#4
Hongyang Wang, Kaiwen Wu, Lan Yu, Linyi Xie, Wenping Xiong, Dayong Wang, Jing Guan, Qiuju Wang
To decipher the phenotype and genotype of a Chinese family with autosomal dominant non-syndromic hearing loss (ADNSHL) and a novel dominant missense mutation in the GJB2 gene (DFNA3), mutation screening of GJB2 was performed on the propositus from a five-generation ADNSHL family through polymerase chain reaction amplification and Sanger sequencing. The candidate variation and the co-segregation of the phenotype were verified in all ascertained family members. Targeted genes capture and next-generation sequencing (NGS) were performed to explore additional genetic variations...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102036/combining-one-step-sanger-sequencing-with-phasing-probe-hybridization-for-hla-class-i-typing-yields-rapid-g-group-resolution-predicting-99-of-unique-full-length-protein-sequences
#5
Bin Tu, Carly Masaberg, Lihua Hou, Daniel Behm, Peter Brescia, Nuri Cha, Kanthi Kariyawasam, Jar How Lee, Thoa Nong, John Sells, Paul Tausch, Ruyan Yang, Jennifer Ng, Carolyn Katovich Hurley
BACKGROUND: Sanger-based DNA sequencing of exons 2+3 of HLA class I alleles from a heterozygote frequently results in two or more alternative genotypes. This study was undertaken to reduce the time and effort required to produce a single high resolution HLA genotype. MATERIALS AND METHODS: Samples were typed in parallel by Sanger sequencing and oligonucleotide probe hybridization. This workflow, together with optimization of analysis software, was tested and refined during the typing of over 42,000 volunteers for an unrelated hematopoietic progenitor cell donor registry...
February 2017: HLA
https://www.readbyqxmd.com/read/28101934/detection-of-neonatal-unit-clusters-of-candida-parapsilosis-fungaemia-by-microsatellite-genotyping-results-from-laboratory-based-sentinel-surveillance-south-africa-2009-2010
#6
Rindidzani E Magobo, Serisha D Naicker, Jeannette Wadula, Maphoshane Nchabeleng, Yacoob Coovadia, Anwar Hoosen, Shawn R Lockhart, Nelesh P Govender
Neonatal candidaemia is a common, deadly and costly hospital-associated disease. To determine the genetic diversity of Candida parapsilosis causing fungaemia in South African neonatal intensive care units (NICUs). From February 2009 through to August 2010, cases of candidaemia were reported through laboratory-based surveillance. C. parapsilosis isolates from neonatal cases were submitted for identification by internal transcribed spacer (ITS) region sequencing, antifungal susceptibility testing and microsatellite genotyping...
January 19, 2017: Mycoses
https://www.readbyqxmd.com/read/28101896/adaptation-of-genetically-monomorphic-bacteria-evolution-of-copper-resistance-through-multiple-horizontal-gene-transfers-of-complex-and-versatile-mobile-genetic-elements
#7
D Richard, V Ravigné, A Rieux, B Facon, C Boyer, K Boyer, P Grygiel, S Javegny, M Terville, B I Canteros, I Robène, C Vernière, A Chabirand, O Pruvost, P Lefeuvre
Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons...
January 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28101694/relationship-between-phenotypic-and-genotypic-characteristics-of-trichophyton-mentagrophytes-strains-isolated-from-patients-with-dermatophytosis
#8
I Dhib, I Khammari, A Yaacoub, F Hadj Slama, M Ben Saïd, R Zemni, A Fathallah
According to epidemiological, clinical and mycological criteria, it has long been admitted that the Trichophyton mentagrophytes species includes two varieties: a zoophilic variety (var. mentagrophytes) and an anthropophilic variety (var. interdigitale) that involve the upper and the lower part of the body, respectively. The further application of molecular techniques to the characterization of dermatophyte strains showed that this classification is unreliable. The aim of our study was to assess the usefulness of PCR-RFLP (restriction fragment length polymorphism) and sequencing in the characterization of T...
January 18, 2017: Mycopathologia
https://www.readbyqxmd.com/read/28101535/the-case-for-adopting-the-species-complex-nomenclature-for-the-etiologic-agents-of-cryptococcosis
#9
Kyung J Kwon-Chung, John E Bennett, Brian L Wickes, Wieland Meyer, Christina A Cuomo, Kurt R Wollenburg, Tihana A Bicanic, Elizabeth Castañeda, Yun C Chang, Jianghan Chen, Massimo Cogliati, Françoise Dromer, David Ellis, Scott G Filler, Matthew C Fisher, Thomas S Harrison, Steven M Holland, Shigeru Kohno, James W Kronstad, Marcia Lazera, Stuart M Levitz, Michail S Lionakis, Robin C May, Popchai Ngamskulrongroj, Peter G Pappas, John R Perfect, Volker Rickerts, Tania C Sorrell, Thomas J Walsh, Peter R Williamson, Jianping Xu, Adrian M Zelazny, Arturo Casadevall
Cryptococcosis is a potentially lethal disease of humans/animals caused by Cryptococcus neoformans and Cryptococcus gattii. Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that C. neoformans be divided into two species and C. gattii into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species...
January 2017: MSphere
https://www.readbyqxmd.com/read/28101439/development-of-highly-variable-microsatellite-markers-for-the-tetraploid-silene-stellata-caryophyllaceae
#10
Juannan Zhou, Michele R Dudash, Charles B Fenster, Elizabeth A Zimmer
PREMISE OF THE STUDY: We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success. METHODS AND RESULTS: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats...
December 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28100546/accuracy-of-line-probe-assays-for-the-diagnosis-of-pulmonary-and-multidrug-resistant-tuberculosis-a-systematic-review-and-meta-analysis
#11
Ruvandhi R Nathavitharana, Patrick G T Cudahy, Samuel G Schumacher, Karen R Steingart, Madhukar Pai, Claudia M Denkinger
Only 25% of multidrug-resistant tuberculosis (MDR-TB) cases are currently diagnosed. Line probe assays (LPAs) enable rapid drug-susceptibility testing for rifampicin (RIF) and isoniazid (INH) resistance and Mycobacterium tuberculosis detection. Genotype MTBDRplusV1 was WHO-endorsed in 2008 but newer LPAs have since been developed.This systematic review evaluated three LPAs: Hain Genotype MTBDRplusV1, MTBDRplusV2 and Nipro NTM+MDRTB. Study quality was assessed with QUADAS-2. Bivariate random-effects meta-analyses were performed for direct and indirect testing...
January 2017: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/28100473/delineating-the-phenotypic-spectrum-of-bainbridge-ropers-syndrome-12-new-patients-with-de-novo-heterozygous-loss-of-function-mutations-in-asxl3-and-review-of-published-literature
#12
M Balasubramanian, J Willoughby, A E Fry, A Weber, H V Firth, C Deshpande, J N Berg, K Chandler, K A Metcalfe, W Lam, D Pilz, S Tomkins
BACKGROUND: Bainbridge-Ropers syndrome (BRPS) is a recently described developmental disorder caused by de novo truncating mutations in the additional sex combs like 3 (ASXL3) gene. To date, there have been fewer than 10 reported patients. OBJECTIVES: Here, we delineate the BRPS phenotype further by describing a series of 12 previously unreported patients identified by the Deciphering Developmental Disorders study. METHODS: Trio-based exome sequencing was performed on all 12 patients included in this study, which found a de novo truncating mutation in ASXL3...
January 18, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28100385/-phylogenetic-analysis-of-envelope-gene-of-dengue-virus-serotype-2-in-guangzhou-2001-2015
#13
Y Liu, L Y Jiang, L Luo, Y M Cao, Q L Jing, Z C Yang
Objective: To investigate the molecular characteristics of dengue virus serotype 2 (DENV2) in Guangzhou during 2001-2015, and analyze the E gene of the strains isolated, the phylogenetic tree and molecular clock were constructed to know about the evolution of the strains. Methods: The serum samples of the patients were detected by real time PCR, and positive samples were used to isolate dengue virus by using C6/36 cells. The E gene of the isolated strains were sequenced. The phylogenetic tree was constructed by using software Mega 4...
January 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28100344/-recurrent-syncope-related-to-catecholaminergic-polymorphic-ventricular-tachycardia-due-to-de-novo-ryr2-r2401h-mutation
#14
X Liu, J X Li, J Z Hu, Y Shen, R Wan, Q M Xiong, Q Q Zhou, J Y Xie, J J Jin, X Yan, J H Yu, K Hong
Objective: To explore the clinical and molecular genetic features of a Chinese patient with catecholaminergic polymorphic ventricular tachycardia (CPVT). Methods: Clinical data including resting electrocardiography, echocardiography and treadmill exercise testing of a patient with CPVT admitted to our department in March 2013 were analyzed, and the peripheral venous blood samples of the patient and his family members and 400 ethnicity-matched healthy controls were obtained. All exons and exon-intron boundaries of the six CPVT-related genes including RYR2, CASQ2, TRDN, CALM1, KCNJ2 and ANKB were sequenced to detect the variants related to CPVT...
January 25, 2017: Zhonghua Xin Xue Guan Bing za Zhi
https://www.readbyqxmd.com/read/28100324/-characteristics-of-duoxa2-gene-mutation-in-children-with-congenital-hypothyroidism
#15
Min-Yi Tan, Yong-Lan Huang, Bei Li, Xiang Jiang, Qian-Yu Chen, Xue-Fang Jia, Cheng-Fang Tang, Li Liu
OBJECTIVE: To investigate the characteristics of DUOXA2 gene mutation and the genotype-phenotype relationship in children with congenital hypothyroidism (CH) in Guangzhou, China. METHODS: A total of 20 CH patients with suspected thyroid dyshormonogenesis who had no DUOX2 gene mutation were enrolled. These patients who were born between 2011 and 2012 were screened and diagnosed with CH in the Guangzhou Newborn Screening Center. PCR and direct sequencing were used to analyze DUOXA2 gene mutation...
January 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/28100302/fecal-virome-of-healthy-chickens-reveals-a-large-diversity-of-the-eukaryote-viral-community-including-novel-circular-single-stranded-dna-viruses
#16
Diane Lima, Samuel Paulo Cibulski, Fabrine Finkler, Thais Teixeira, Ana Paula Varela, Cristine Cerva, Márcia Loiko, Camila Scheffer, Helton Dos Santos, Fabiana Mayer, Paulo Roehe
This study is focused on the identification of the fecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7,743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with BLASTx revealed that 279 contigs (4%) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes...
January 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28100189/an-snp-based-saturated-genetic-map-and-qtl-analysis-of-fruit-related-traits-in-zucchini-using-genotyping-by-sequencing
#17
Javier Montero-Pau, José Blanca, Cristina Esteras, Eva Ma Martínez-Pérez, Pedro Gómez, Antonio J Monforte, Joaquín Cañizares, Belén Picó
BACKGROUND: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100010/fine-scale-genetic-structure-analyses-reveal-dispersal-patterns-in-a-critically-endangered-primate-trachypithecus-leucocephalus
#18
Weiran Wang, Meng Yao
Dispersal is a critically important life history trait of social organisms that has a major impact on the population genetic structure and social relationships within groups. Primates exhibit highly diversified dispersal and philopatry patterns, but knowledge of these patterns is difficult to obtain and usually limited to observations of a small number of focal social groups or individuals. Here, we investigated the dispersal pattern of a critically endangered colobine monkey, the white-headed langur (Trachypithecus leucocephalus), using molecular approaches, and sex-specific population genetic structure analyses at fine geographical scales...
January 18, 2017: American Journal of Primatology
https://www.readbyqxmd.com/read/28099951/complex-x-chromosomal-rearrangements-in-two-women-with-ovarian-dysfunction-implications-of-chromothripsis-chromoanasynthesis-dependent-and-independent-origins-of-complex-genomic-alterations
#19
Erina Suzuki, Hirohito Shima, Machiko Toki, Kunihiko Hanew, Keiko Matsubara, Hiroki Kurahashi, Satoshi Narumi, Tsutomu Ogata, Tsutomu Kamimaki, Maki Fukami
Our current understanding of the phenotypic consequences and the molecular basis of germline complex chromosomal rearrangements remains fragmentary. Here, we report the clinical and molecular characteristics of 2 women with germline complex X-chromosomal rearrangements. Patient 1 presented with nonsyndromic ovarian dysfunction and hyperthyroidism; patient 2 exhibited various Turner syndrome- associated symptoms including ovarian dysfunction, short stature, and autoimmune hypothyroidism. The genomic abnormalities of the patients were characterized by array-based comparative genomic hybridization, high-resolution karyotyping, microsatellite genotyping, X-inactivation analysis, and bisulfite sequencing...
January 19, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28099825/transmission-of-extensively-drug-resistant-tuberculosis-in-south-africa
#20
N Sarita Shah, Sara C Auld, James C M Brust, Barun Mathema, Nazir Ismail, Pravi Moodley, Koleka Mlisana, Salim Allana, Angela Campbell, Thuli Mthiyane, Natashia Morris, Primrose Mpangase, Hermina van der Meulen, Shaheed V Omar, Tyler S Brown, Apurva Narechania, Elena Shaskina, Thandi Kapwata, Barry Kreiswirth, Neel R Gandhi
Background Drug-resistant tuberculosis threatens recent gains in the treatment of tuberculosis and human immunodeficiency virus (HIV) infection worldwide. A widespread epidemic of extensively drug-resistant (XDR) tuberculosis is occurring in South Africa, where cases have increased substantially since 2002. The factors driving this rapid increase have not been fully elucidated, but such knowledge is needed to guide public health interventions. Methods We conducted a prospective study involving 404 participants in KwaZulu-Natal Province, South Africa, with a diagnosis of XDR tuberculosis between 2011 and 2014...
19, 2017: New England Journal of Medicine
keyword
keyword
43250
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"