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Allelic exchange

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https://www.readbyqxmd.com/read/28195318/biallelic-loss-of-function-variants-in-dock3-cause-muscle-hypotonia-ataxia-and-intellectual-disability
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28066509/development-and-implementation-of-rapid-metabolic-engineering-tools-for-chemical-and-fuel-production-in-geobacillus-thermoglucosidasius-ncimb-11955
#10
Lili Sheng, Katalin Kovács, Klaus Winzer, Ying Zhang, Nigel Peter Minton
BACKGROUND: The thermophile Geobacillus thermoglucosidasius has considerable attraction as a chassis for the production of chemicals and fuels. It utilises a wide range of sugars and oligosaccharides typical of those derived from lignocellulose and grows at elevated temperatures. The latter improves the rate of feed conversion, reduces fermentation cooling costs and minimises the risks of contamination. Full exploitation of its potential has been hindered by a dearth of effective gene tools...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28044416/identification-and-characterization-a-novel-hla-a-allele-a-02-355-by-sequence-based-typing-in-a-chinese-potential-donor
#11
X-M Nie, Y Zhang, W-B Qiao, C-F Zhu, Y-R Zhao
The new allele A*02:355 differs from A* 02:03:01 at positions 98 (T→A) and 102(A→C) resulting in an amino acid exchange F9→T. Interallelic sequence exchange is more likely the mechanism of its origination. The amino acid replacement influences the HLA peptide binding cleft and might have significant functional effects.
January 2, 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28039138/an-effective-counterselection-system-for-listeria-monocytogenes-and-its-use-to-characterize-10403s-strain-monocin-genomic-region
#12
Tal Argov, Lev Rabinovich, Nadejda Sigal, Anat A Herskovits
Construction of Listeria monocytogenes mutants by allelic exchange has been laborious and time consuming due to lack of proficient selection markers for the final recombination event. That is, a marker conveying substance sensitivity to the bacteria bearing it, enabling the exclusion of merodiploids and selection for plasmid loss. In order to address this issue, we engineered a counterselection marker based on a mutated phenylalanyl-tRNA synthetase gene (pheS*). This mutation renders the phenylalanine-binding site of the enzyme more promiscuous and allows the binding of the toxic p-chloro-phenylalanine analog (p-Cl-phe) as a substrate...
December 30, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28032472/hla-c-07-544-a-novel-hla-c-07-variant-detected-in-a-taiwanese-bone-marrow-donor
#13
K L Yang, P Y Lin
One nucleotide exchange at residue 768 of the HLA-C*07:02:01:01 results in a novel allele, HLA-C*07:544.
February 2017: HLA
https://www.readbyqxmd.com/read/28007837/the-impact-of-open-pollination-on-the-structural-evolutionary-dynamics-meiotic-behavior-and-fertility-of-resynthesized-allotetraploid-brassica-napus-l
#14
Mathieu Rousseau-Gueutin, Jérôme Morice, Olivier Coriton, Virginie Huteau, Gwenn Trotoux, Sylvie Nègre, Cyril Falentin, Gwennaëlle Deniot, Marie Gilet, Frédérique Eber, Alexandre Pelé, Sonia Vautrin, Joëlle Fourment, Maryse Lodé, Hélène Bergès, Anne-Marie Chèvre
Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination...
December 22, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28007835/paralog-specific-functions-of-rpl7a-and-rpl7b-mediated-by-ribosomal-protein-or-snorna-dosage-in-saccharomyces-cerevisiae
#15
Ryan J Palumbo, Gabriele Fuchs, Sheila Lutz, M Joan Curcio
Most ribosomal proteins in Saccharomyces cerevisiae are encoded by two paralogs that additively produce the optimal protein level for cell growth. Nonetheless, deleting one paralog of most ribosomal protein gene pairs results in a variety of phenotypes not observed when the other paralog is deleted. To determine whether paralog-specific phenotypes associated with deleting RPL7A or RPL7B stem from distinct functions or different levels of the encoded isoforms, the coding region and introns of one paralog, including an intron-embedded snoRNA (small nucleolar RNA) gene, were exchanged with that of the other paralog...
December 22, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27998798/recursions-for-the-exchangeable-partition-function-of-the-seedbank-coalescent
#16
Noemi Kurt, Mathias Rafler
For the seedbank coalescent with mutation under the infinite alleles assumption, which describes the gene genealogy of a population with a strong seedbank effect subject to mutations, we study the distribution of the final partition with mutation. This generalizes the coalescent with freeze by Dong et al. (2007) to coalescents where ancestral lineages are blocked from coalescing. We derive an implicit recursion which we show to have a unique solution and give an interpretation in terms of absorption problems of a random walk...
December 18, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27990727/coupling-sensitive-nucleic-acid-amplification-with-commercial-pregnancy-test-strips
#17
Yan Du, Arti Pothukuchy, Jimmy D Gollihar, Armin Nourani, Bingling Li, Andrew D Ellington
The detection of nucleic acid biomarkers for point-of-care (POC) diagnostics is currently limited by technical complexity, cost, and time constraints. To overcome these shortcomings, we have combined loop-mediated isothermal amplification (LAMP), programmable toehold-mediated strand-exchange signal transduction, and standard pregnancy test strips. The incorporation of an engineered hCG-SNAP fusion reporter protein (human chorionic gonadotropin-O(6) -alkylguanine-DNA alkyltransferase) led to LAMP-to-hCG signal transduction on low-cost, commercially available pregnancy test strips...
January 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/27965242/genome-wide-genotyping-by-sequencing-data-provide-a-high-resolution-view-of-wild-helianthus-diversity-genetic-structure-and-interspecies-gene-flow
#18
Gregory J Baute, Gregory L Owens, Dan G Bock, Loren H Rieseberg
PREMISE: Wild sunflowers harbor considerable genetic diversity and are a major resource for improvement of the cultivated sunflower, Helianthus annuus. The Helianthus genus is also well known for its propensity for gene flow between taxa. METHODS: We surveyed genomic diversity of 292 samples of wild Helianthus from 22 taxa that are cross-compatible with the cultivar using genotyping by sequencing. With these data, we derived a high-resolution phylogeny of the taxa, interrogated genome-wide levels of diversity, explored H...
December 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27931869/a-genetic-overview-of-atlantic-coastal-populations-from-europe-and-north-west-africa-based-on-a-17-x-str-panel
#19
Endika Prieto-Fernández, Ana Díaz-de Usera, Miriam Baeta, Carolina Núñez, Faiza Chbel, Sellama Nadifi, Karen Rouault, Claude Férec, Orla Hardiman, Fátima Pinheiro, Marian M de Pancorbo
The forensic use of X-STRs requires the creation of allele and haplotype frequency databases in the populations where they are going to be used. Recently, an updated Spanish allele and haplotype frequency database for the new 17 X-STR panel has been created, being the only database available up to now for this new multiplex. In order to broaden the forensic applicability of the 17 X-STR panel, 513 individuals from four different populations located on the Atlantic Coast of Europe and North-West Africa have been studied, i...
November 30, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27907066/b-cell-based-seamless-engineering-of-antibody-fc-domains
#20
Koji Hashimoto, Kohei Kurosawa, Akiho Murayama, Hidetaka Seo, Kunihiro Ohta
Engineering of monoclonal antibodies (mAbs) enables us to obtain mAbs with additional functions. In particular, modifications in antibody's Fc (fragment, crystallizable) region can provide multiple benefits such as added toxicity by drug conjugation, higher affinity to Fc receptors on immunocytes, or the addition of functional modules. However, the generation of recombinant antibodies requires multiple laborious bioengineering steps. We previously developed a technology that enables rapid in vitro screening and isolation of specific mAb-expressing cells from the libraries constructed with chicken B-cell line DT40 (referred to as the 'ADLib system')...
2016: PloS One
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