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Allelic exchange

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https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#1
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28320967/self-identity-reprogrammed-by-a-single-residue-switch-in-a-cell-surface-receptor-of-a-social-bacterium
#2
Pengbo Cao, Daniel Wall
The ability to recognize close kin confers survival benefits on single-celled microbes that live in complex and changing environments. Microbial kinship detection relies on perceptible cues that reflect relatedness between individuals, although the mechanisms underlying recognition in natural populations remain poorly understood. In myxobacteria, cells identify related individuals through a polymorphic cell surface receptor, TraA. Recognition of compatible receptors leads to outer membrane exchange among clonemates and fitness consequences...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28297417/description-of-a-new-hla-a-02-allele-a-02-658-in-a-russian-individual
#3
M Loginova, T Jankevich, A Goltsov, O Altukhova, D Trofimov
Sequence of the novel allele, HLA-A*02:658, differs from HLA-A*02:01:01:01 by one-nucleotide exchange in exon 2.
April 2017: HLA
https://www.readbyqxmd.com/read/28296275/the-full-length-genomic-sequence-of-a-novel-hla-a-24-allele-hla-a-24-353-identified-in-a-patient-with-hepatitis-b-infection
#4
S-Q Gao, Y-P Xu, L-M He, H Zhang, A-L Yang
HLA-A*24:353 differs from HLA-A*24:02:01 by an amino acid exchange glutamine to glutamate at position 316.
March 12, 2017: HLA
https://www.readbyqxmd.com/read/28289408/mlva-for-salmonella-enterica-subsp-enterica-serovar-dublin-development-of-a-method-suitable-for-inter-laboratory-surveillance-and-application-in-the-context-of-a-raw-milk-cheese-outbreak-in-france-in-2012
#5
Marie-Léone Vignaud, Emeline Cherchame, Muriel Marault, Emilie Chaing, Simon Le Hello, Valerie Michel, Nathalie Jourdan-Da Silva, Renaud Lailler, Anne Brisabois, Sabrina Cadel-Six
Salmonella enterica subspecies enterica serovar Dublin (S. Dublin) figures among the most frequently isolated Salmonella strains in humans in France. This serovar may affect production and animal health mainly in cattle herds with corresponding high economic losses. Given that the current gold standard method, pulsed-field gel electrophoresis (PFGE), provides insufficient discrimination for epidemiological investigations, we propose a standard operating procedure in this study for multiple-locus variable number tandem repeat analysis (MLVA) of S...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28288567/determining-clostridium-difficile-intra-taxa-diversity-by-mining-multilocus-sequence-typing-databases
#6
Marina Muñoz, Dora Inés Ríos-Chaparro, Manuel Alfonso Patarroyo, Juan David Ramírez
BACKGROUND: Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. RESULTS: Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57...
March 14, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28277220/multi-laboratory-validation-study-of-multilocus-variable-number-tandem-repeat-analysis-mlva-for-salmonella-enterica-serovar-enteritidis-2015
#7
Tansy Peters, Sophie Bertrand, Jonas T Björkman, Lin T Brandal, Derek J Brown, Tímea Erdõsi, Max Heck, Salha Ibrahem, Karin Johansson, Christian Kornschober, Saara M Kotila, Simon Le Hello, Taru Lienemann, Wesley Mattheus, Eva Møller Nielsen, Catherine Ragimbeau, Jillian Rumore, Ashley Sabol, Mia Torpdahl, Eija Trees, Alma Tuohy, Elizabeth de Pinna
Multilocus variable-number tandem repeat analysis (MLVA) is a rapid and reproducible typing method that is an important tool for investigation, as well as detection, of national and multinational outbreaks of a range of food-borne pathogens. Salmonella enterica serovar Enteritidis is the most common Salmonella serovar associated with human salmonellosis in the European Union/European Economic Area and North America. Fourteen laboratories from 13 countries in Europe and North America participated in a validation study for MLVA of S...
March 2, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28275334/clinical-significance-of-an-alloantibody-against-the-kell-blood-group-glycoprotein
#8
Stella Maris Mattaloni, Carine Arnoni, Rosario Céspedes, Claudia Nonaka, Carolina Trucco Boggione, Melina Eliana Luján Brajovich, Andrea Trejo, Néstor Zani, Claudia Silvia Biondi, Lilian Castilho, Carlos Miquel Cotorruelo
BACKGROUND: Kell null (K0) individuals can produce anti-Ku, an antibody against many epitopes in the Kell glycoprotein, after transfusion and/or pregnancy. Since sensitized K0 patients are rare, little is known about anti-Ku clinical relevance and in particular about its association to hemolytic disease of the fetus and newborn. CASE REPORT: This work describes a case of neonatal hyperbilirubinemia due to immune-mediated erythrocyte destruction by an alloantibody directed against the Kell glycoprotein...
January 2017: Transfusion Medicine and Hemotherapy
https://www.readbyqxmd.com/read/28244149/eukaryotic-translation-initiation-factor-2b-beta-eif2b%C3%AE-a-new-class-of-plant-virus-resistance-gene
#9
Shopan Jannat, Haipeng Mou, Lili Zhang, Changtong Zhang, Weiwei Ma, John A Walsh, Zhongyuan Hu, Jinghua Yang, Mingfang Zhang
Recessive resistances to plant viruses in the Potyvirus genus have been found to be based on mutations in the plant eukaryotic translation initiation factors, eIF4E and eIF4G or their isoforms. Here we report that natural, monogenic recessive resistance to the potyvirus Turnip mosaic virus (TuMV) has been found in a number of mustard (Brassica juncea) accessions. Bulked segregant analysis and sequencing of resistant and susceptible plant lines indicated the resistance is controlled by a single recessive gene, recessive TuMV resistance 03 (retr03), an allele of the eukaryotic translation initiation factor 2B-beta (eIF2Bβ)...
February 28, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28237997/umtco1-a-hybrid-histidine-kinase-gene-is-essential-for-the-sexual-development-and-virulence-of-ustilago-maydis
#10
Yeo Hong Yun, Man Hwan Oh, Jun Young Kim, Seong Hwan Kim
Hybrid histidine kinase is a part of two-component system that is required for various stress responses and pathogenesis of pathogenic fungi. The Tco1 gene in human pathogen Cryptococcus neoformans encodes a hybrid histidine kinase and is important for pathogenesis. In the present study, we identified a Tco1 gene homolog, UmTco1, in the corn smut pathogen Ustilago maydis by bioinformatics analysis. To explore the role of UmTco1 in the survival of U. maydis under environmental stresses and its pathogenesis, Δumtco1 mutants were constructed by allelic exchange...
February 24, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28231283/rapid-evolution-of-distinct-helicobacter-pylori-subpopulations-in-the-americas
#11
Kaisa Thorell, Koji Yahara, Elvire Berthenet, Daniel J Lawson, Jane Mikhail, Ikuko Kato, Alfonso Mendez, Cosmeri Rizzato, María Mercedes Bravo, Rumiko Suzuki, Yoshio Yamaoka, Javier Torres, Samuel K Sheppard, Daniel Falush
For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach-dwelling bacterium Helicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence of H. pylori isolated in North, Central and South America, we found evidence for admixture between H...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28195318/biallelic-loss-of-function-variants-in-dock3-cause-muscle-hypotonia-ataxia-and-intellectual-disability
#12
Katherine L Helbig, Cameron Mroske, Divya Moorthy, Samin A Sajan, Milen Velinov
DOCK3 encodes the dedicator of cytokinesis 3 protein, a member of the DOCK180 family of proteins that are characterized by guanine nucleotide exchange factor activity. DOCK3 is expressed exclusively in the central nervous system and plays an important role in axonal outgrowth and cytoskeleton reorganization. Dock3 knockout mice exhibit motor deficiencies with abnormal ataxic gait and impaired learning. We report two siblings with biallelic loss-of-function variants in DOCK3. Diagnostic whole exome sequencing and chromosomal microarray were performed on a proband with severe intellectual disability, hypotonia, and ataxic gait...
February 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28184216/porphyromonas-gingivalis-uses-specific-domain-rearrangements-and-allelic-exchange-to-generate-diversity-in-surface-virulence-factors
#13
Stuart G Dashper, Helen L Mitchell, Christine A Seers, Simon L Gladman, Torsten Seemann, Dieter M Bulach, P Scott Chandry, Keith J Cross, Steven M Cleal, Eric C Reynolds
Porphyromonas gingivalis is a keystone pathogen of chronic periodontitis. The virulence of P. gingivalis is reported to be strain related and there are currently a number of strain typing schemes based on variation in capsular polysaccharide, the major and minor fimbriae and adhesin domains of Lys-gingipain (Kgp), amongst other surface proteins. P. gingivalis can exchange chromosomal DNA between strains by natural competence and conjugation. The aim of this study was to determine the genetic variability of P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28157227/association-of-vav2-and-vav3-polymorphisms-with-cardiovascular-risk-factors
#14
Nuria Perretta-Tejedor, Javier Fernández-Mateos, Luis García-Ortiz, Manuel A Gómez-Marcos, José I Recio-Rodríguez, Cristina Agudo-Conde, Emiliano Rodriguez-Sánchez, Ana I Morales, Francisco J López-Hernández, José M López-Novoa, Rogelio González-Sarmiento, Carlos Martínez-Salgado
Hypertension, diabetes and obesity are cardiovascular risk factors closely associated to the development of renal and cardiovascular target organ damage. VAV2 and VAV3, members of the VAV family proto-oncogenes, are guanosine nucleotide exchange factors for the Rho and Rac GTPase family, which is related with cardiovascular homeostasis. We have analyzed the relationship between the presence of VAV2 rs602990 and VAV3 rs7528153 polymorphisms with cardiovascular risk factors and target organ damage (heart, vessels and kidney) in 411 subjects...
February 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28132693/biallelic-mutation-of-arhgef18-involved-in-the-determination-of-epithelial-apicobasal-polarity-causes-adult-onset-retinal-degeneration
#15
Gavin Arno, Keren J Carss, Sarah Hull, Ceniz Zihni, Anthony G Robson, Alessia Fiorentino, Alison J Hardcastle, Graham E Holder, Michael E Cheetham, Vincent Plagnol, Anthony T Moore, F Lucy Raymond, Karl Matter, Maria S Balda, Andrew R Webster
Mutations in more than 250 genes are implicated in inherited retinal dystrophy; the encoded proteins are involved in a broad spectrum of pathways. The presence of unsolved families after highly parallel sequencing strategies suggests that further genes remain to be identified. Whole-exome and -genome sequencing studies employed here in large cohorts of affected individuals revealed biallelic mutations in ARHGEF18 in three such individuals. ARHGEF18 encodes ARHGEF18, a guanine nucleotide exchange factor that activates RHOA, a small GTPase protein that is a key component of tight junctions and adherens junctions...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28127254/genetic-separation-of-southern-and-northern-soybean-breeding-programs-in-north-america-and-their-associated-allelic-variation-at-four-maturity-loci
#16
Goettel Wolfgang, Yong-Qiang Charles An
North American soybean breeders have successfully developed a large number of elite cultivars with diverse maturity groups (MG) from a small number of ancestral landraces. To understand molecular and genetic basis underlying the large variation in their maturity and flowering times, we integrated pedigree and maturity data of 166 cultivars representing North American soybean breeding. Network analysis and visualization of their pedigree relationships revealed a clear separation of southern and northern soybean breeding programs, suggesting that little genetic exchange occurred between northern (MG 0-IV) and southern cultivars (MG V-VIII)...
2017: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/28111249/metabolic-engineering-of-clostridium-autoethanogenum-for-selective-alcohol-production
#17
Fungmin Liew, Anne M Henstra, Michael Kӧpke, Klaus Winzer, Sean D Simpson, Nigel P Minton
Gas fermentation using acetogenic bacteria such as Clostridium autoethanogenum offers an attractive route for production of fuel ethanol from industrial waste gases. Acetate reduction to acetaldehyde and further to ethanol via an aldehyde: ferredoxin oxidoreductase (AOR) and alcohol dehydrogenase has been postulated alongside the classic pathway of ethanol formation via a bi-functional aldehyde/alcohol dehydrogenase (AdhE). Here we demonstrate that AOR is critical to ethanol formation in acetogens and inactivation of AdhE led to consistently enhanced autotrophic ethanol production (up to 180%)...
January 19, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28087731/increased-nbcn1-expression-na-hco3-co-transport-and-intracellular-ph-in-human-vascular-smooth-muscle-cells-with-a-risk-allele-for-hypertension
#18
Fu Liang Ng, Ebbe Boedtkjer, Katarzyna Witkowska, Meixia Ren, Ruoxin Zhang, Arthur Tucker, Christian Aalkjær, Mark J Caulfield, Shu Ye
Genome-wide association studies have revealed an association between variation at the SLC4A7 locus and blood pressure. SLC4A7 encodes the electroneutral Na(+)/HCO3 co-transporter NBCn1 which regulates intracellular pH (pHi). We conducted a functional study of variants at this locus in primary cultures of vascular smooth muscle and endothelial cells. In both cell types, we found genotype-dependent differences for rs13082711 in DNA-nuclear protein interactions, where the risk allele is associated with increased SLC4A7 expression level, NBCn1 availability and function as reflected in elevated steady-state pHi and accelerated recovery from intracellular acidosis...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28077981/dna-polymerase-kappa-protects-human-cells-against-mmc-induced-genotoxicity-through-error-free-translesion-dna-synthesis
#19
Yuki Kanemaru, Tetsuya Suzuki, Akira Sassa, Kyomu Matsumoto, Noritaka Adachi, Masamitsu Honma, Satoshi Numazawa, Takehiko Nohmi
BACKGROUND: Interactions between genes and environment are critical factors for causing cancer in humans. The genotoxicity of environmental chemicals can be enhanced via the modulation of susceptible genes in host human cells. DNA polymerase kappa (Pol κ) is a specialized DNA polymerase that plays an important role in DNA damage tolerance through translesion DNA synthesis. To better understand the protective roles of Pol κ, we previously engineered two human cell lines either deficient in expression of Pol κ (KO) or expressing catalytically dead Pol κ (CD) in Nalm-6-MSH+ cells and examined cytotoxic sensitivity against various genotoxins...
2017: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
https://www.readbyqxmd.com/read/28068993/improvement-of-yeast-tolerance-to-acetic-acid-through-haa1-transcription-factor-engineering-towards-the-underlying-mechanisms
#20
Steve Swinnen, Sílvia F Henriques, Ranjan Shrestha, Ping-Wei Ho, Isabel Sá-Correia, Elke Nevoigt
BACKGROUND: Besides being a major regulator of the response to acetic acid in Saccharomyces cerevisiae, the transcription factor Haa1 is an important determinant of the tolerance to this acid. The engineering of Haa1 either by overexpression or mutagenesis has therefore been considered to be a promising avenue towards the construction of more robust strains with improved acetic acid tolerance. RESULTS: By applying the concept of global transcription machinery engineering to the regulon-specific transcription factor Haa1, a mutant allele containing two point mutations could be selected that resulted in a significantly higher acetic acid tolerance as compared to the wild-type allele...
January 9, 2017: Microbial Cell Factories
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