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Allelic exchange

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https://www.readbyqxmd.com/read/29325102/elevated-proportions-of-deleterious-genetic-variation-in-domestic-animals-and-plants
#1
Takashi Makino, Carl-Johan Rubin, Miguel Carneiro, Erik Axelsson, Leif Andersson, Matthew T Webster
A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken and silkworm) and two domestic plant species (rice and soybean) compared to their wild ancestors...
January 9, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29320565/the-absence-of-n-acetylglucosamine-in-wall-teichoic-acids-of-listeria-monocytogenes-modifies-biofilm-architecture-and-tolerance-to-rinsing-and-cleaning-procedures
#2
Thomas Brauge, Christine Faille, Irina Sadovskaya, Alain Charbit, Thierry Benezech, Yang Shen, Martin J Loessner, Jean Romain Bautista, Graziella Midelet-Bourdin
The wall teichoic acid (WTA) is the major carbohydrate found within the extracellular matrix of the Listeria monocytogenes biofilm. We first addressed the frequency of spontaneous mutations in two genes (lmo2549 and lmo2550) responsible for the GlcNAcylation in 93 serotype 1/2a strains that were mainly isolated from seafood industries. We studied the impact of mutations in lmo2549 or lmo2550 genes on biofilm formation by using one mutant carrying a natural mutation inactivating the lmo2550 gene (DSS 1130 BFA2 strain) and two EGD-e mutants that lack respective genes by in-frame deletion of lmo2549 or lmo2550 using splicing-by-overlap-extension PCR, followed by allelic exchange mutagenesis...
2018: PloS One
https://www.readbyqxmd.com/read/29316364/more-than-150-novel-variants-of-hla-class-i-genes-detected-in-german-stem-cell-donor-registry-and-ucla-international-cell-exchange-samples
#3
Vera Balz, Stefan Krause, Johannes Fischer, Jürgen Enczmann
High throughput analysis using amplicon-based next-generation sequencing (NGS) of HLA class I genes in samples of registered stem cell donors of the German Stem Cell Donor Registry Düsseldorf revealed 151 novel variants. In addition, 4 new variants were identified in well-defined samples obtained from the UCLA International Cell Exchange program. New alleles included 37 HLA-A, 57 HLA-B, and 61 HLA-C variant alleles. All variants were confirmed by NGS of HLA-A, HLA-B, and HLA-C genes including the respective 5´ and 3´ untranslated regions as well as Sanger sequence analysis...
January 8, 2018: HLA
https://www.readbyqxmd.com/read/29305877/knock-out-or-knock-in-converting-a-sacb-based-gene-disruption-system-for-site-specific-chromosomal-integration-in-pseudomonas-syringae-pv-tomato-dc3000
#4
Yun-Chen Lee, Ching-Fang Chien, Nai-Chun Lin
Recent advances in next generation sequencing technology allow us to retrieve the whole genome sequence of a requested bacterium in less than a day. Thus, development of quick, easy and efficient means to systemically analyze the functions of all genes is required in the post-genome era. Here, a procedure of finding a suitable chromosome integration site and developing a gene disruption system into a knock-in system in Gram-negative bacteria is proposed. As a proof of concept, we successfully modified a sacB-based gene knock-out strategy into a site-specific gene integration system to deliver a DNA fragment into the genome site between 313,520bp and 313,521bp of the model phytopathogenic bacterium, Pseudomonas syringae pv...
January 3, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29300677/nuclear-populations-of-the-multinucleate-fungus-of-leafcutter-ants-can-be-dekaryotized-and-recombined-to-manipulate-growth-of-nutritive-hyphal-nodules-harvested-by-the-ants
#5
Alexis L Carlson, Heather D Ishak, James Kurian, Alexander S Mikheyev, Isaac Gifford, Ulrich G Mueller
We dekaryotized the multinucleate fungus Leucocoprinus gongylophorus, a symbiotic fungus cultivated vegetatively by leafcutter ants as their food. To track genetic changes resulting from dekaryotization (elimination of some nuclei from the multinuclear population), we developed two multiplex microsatellite fingerprinting panels (15 loci total), then characterized the allele profiles of 129 accessions generated by dekaryotization treatment. Genotype profiles of the 129 accessions confirmed allele loss expected by dekaryotization of the multinucleate fungus...
November 10, 2017: Mycologia
https://www.readbyqxmd.com/read/29286340/slc9a3-protein-is-critical-for-acrosomal-formation-in-postmeiotic-male-germ-cells
#6
Ya-Yun Wang, Han-Sun Chiang, Chiao-Yin Cheng, Yi-No Wu, Yung-Chih Lin, Hsuan-Che Liu, Wei-Kung Tsai, Yen-Lin Chen, Ying-Hung Lin
Solute carrier family 9 isoform 3 (SLC9A3), a Na⁺/H⁺ exchanger, regulates the transepithelial absorption of Na⁺ and water and is primarily expressed on the apical membranes of the intestinal epithelium, renal proximal tubule, epididymis, and vas deferens. Loss of the Slc9a3 allele in mice enhances intestinal fluid and causes diarrhoea as a consequence of diminished Na⁺ and HCO₃- absorption. Hence, the loss also causes male infertility and reveals the abnormal dilated lumen of the rete testis and calcification in efferent ductules...
December 29, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29247835/amlexanox-provides-a-potential-therapy-for-nonsense-mutations-in-the-lysosomal-storage-disorder-aspartylglucosaminuria
#7
Antje Banning, Manuel Schiff, Ritva Tikkanen
Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by mutations in the gene for aspartylglucosaminidase (AGA). This enzyme participates in glycoprotein degradation in lysosomes. AGU results in progressive mental retardation, and no curative therapy is currently available. We have here characterized the consequences of AGA gene mutations in a compound heterozygous patient who exhibits a missense mutation producing a Ser72Pro substitution in one allele, and a nonsense mutation Trp168X in the other...
December 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29247682/collection-and-storage-of-hla-ngs-genotyping-data-for-the-17th-international-hla-and-immunogenetics-workshop
#8
Chia-Jung Chang, Kazutoyo Osoegawa, Robert P Milius, Martin Maiers, Wenzhong Xiao, Marcelo Fernandez-Viňa, Steven J Mack
For over 50 years, the International HLA and Immunogenetics Workshops (IHIW) have advanced the fields of histocompatibility and immunogenetics (H&I) via community sharing of technology, experience and reagents, and the establishment of ongoing collaborative projects. Held in the fall of 2017, the 17th IHIW focused on the application of next generation sequencing (NGS) technologies for clinical and research goals in the H&I fields. NGS technologies have the potential to allow dramatic insights and advances in these fields, but the scope and sheer quantity of data associated with NGS raise challenges for their analysis, collection, exchange and storage...
December 13, 2017: Human Immunology
https://www.readbyqxmd.com/read/29245274/rad52-gene-polymorphisms-are-associated-with-risk-of-colorectal-cancer-in-a-chinese-han-population
#9
Longyi Zhang, Yongjun Zhang, Chih-Hsin Tang, Chen-Ming Su
Upward trends in the incidence and mortality rates of colorectal cancer (CRC) in China over the past decade mean that it is critical to improve survival outcomes for patients with this malignancy. Analysis of genetic variants may identify biomarkers that have a role in CRC susceptibility and clinical outcomes in Chinese patients with CRC. RAD52 is a key mediator during DNA strand exchange and homologous recombination within mammalian cells. In this study, we explored the effects of RAD52 single nucleotide polymorphisms (SNPs) in the susceptibility and clinicopathological characteristics of Chinese Han patients with CRC...
December 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29226520/a-novel-homozygous-slc25a1-mutation-with-impaired-mitochondrial-complex-v-possible-phenotypic-expansion
#10
Idan Cohen, Orna Staretz-Chacham, Ohad Wormser, Yonatan Perez, Ann Saada, Rotem Kadir, Ohad S Birk
SLC25A1 mutations are associated with combined D,L-2-hydroxyglutaric aciduria (DL- 2HGA; OMIM #615182), characterized by muscular hypotonia, severe neurodevelopmental dysfunction and intractable seizures. SLC25A1 encodes the mitochondrial citrate carrier (CIC), which mediates efflux of the mitochondrial tricarboxylic acid (TCA) cycle intermediates citrate and isocitrate in exchange for cytosolic malate. Only a single family with an SLC25A1 mutation has been described in which mitochondrial respiratory chain dysfunction was documented, specifically in complex IV...
December 11, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29223136/allele-exchange-at-the-epsps-locus-confers-glyphosate-tolerance-in-cassava
#11
Aaron W Hummel, Raj Deepika Chauhan, Tomas Cermak, Andrew M Mutka, Anupama Vijayaraghavan, Adam Boyher, Colby G Starker, Rebecca Bart, Daniel F Voytas, Nigel J Taylor
Effective weed control can protect yields of cassava (Manihot esculenta) storage roots (Doll and Piedrahita Cañola, 1978). Farmers could benefit from using herbicide with a tolerant cultivar. We applied traditional transgenesis and gene editing to generate robust glyphosate tolerance in cassava. By comparing promoters regulating expression of transformed 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) genes with various paired amino acid substitutions, we found that strong constitutive expression is required to achieve glyphosate tolerance during in vitro selection and in whole cassava plants...
December 9, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29201383/an-autosomal-recessive-mutation-in-scl24a4-causing-enamel-hypoplasia-in-samoyed-and-its-relationship-to-breed-wide-genetic-diversity
#12
Niels C Pedersen, Bonnie Shope, Hongwei Liu
Background: Pure breeding of dogs has led to over 700 heritable disorders, of which almost 300 are Mendelian in nature. Seventy percent of the characterized mutations have an autosomal recessive mode of inheritance, indicative of positive selection during bouts of inbreeding primarily for new desired conformational traits. Samoyed suffer from several common complex genetic disorders, but up to this time only two X-linked and one autosomal dominant disorder have been identified. Previous studies based on pedigrees and SNP arrays have concluded that Samoyed breeders have done a good job in maintaining genetic diversity and avoiding excessive inbreeding...
2017: Canine Genetics and Epidemiology
https://www.readbyqxmd.com/read/29196271/gibson-assembly-facilitates-bacterial-allelic-exchange-mutagenesis
#13
Oleksandra Silayeva, Andrew C Barnes
Allelic exchange mutagenesis that relies on RecA-mediated homologous recombination up- and downstream from the targeted gene is a generalizable method of site-specific bacterial gene knock-out and knock-in. However, generation of a mutagenic DNA construct (alternative allele flanked by regions surrounding the gene target) and subsequent mutant selection are laborious procedures. Here we demonstrate allelic exchange knock-out facilitated by Gibson Assembly in Streptococcus iniae. Gibson Assembly allows rapid construction of a mutagenic DNA sequence simultaneous with cloning, as well as rapid reconstruction of complete recombinant vector sequence when required...
November 28, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29183972/unleashing-meiotic-crossovers-in-hybrid-plants
#14
Joiselle Blanche Fernandes, Mathilde Seguéla-Arnaud, Cécile Larchevêque, Andrew H Lloyd, Raphael Mercier
Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713-4718], and FIGL1 [Girard C, et al...
November 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29164142/pathogenesis-molecular-genetics-and-genomics-of-mycobacterium-avium-subsp-paratuberculosis-the-etiologic-agent-of-johne-s-disease
#15
REVIEW
Govardhan Rathnaiah, Denise K Zinniel, John P Bannantine, Judith R Stabel, Yrjö T Gröhn, Michael T Collins, Raúl G Barletta
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne's disease in ruminants causing chronic diarrhea, malnutrition, and muscular wasting. Neonates and young animals are infected primarily by the fecal-oral route. MAP attaches to, translocates via the intestinal mucosa, and is phagocytosed by macrophages. The ensuing host cellular immune response leads to granulomatous enteritis characterized by a thick and corrugated intestinal wall. We review various tissue culture systems, ileal loops, and mice, goats, and cattle used to study MAP pathogenesis...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29162625/sgs1-binding-to-rad51-stimulates-homology-directed-dna-repair-in-saccharomyces-cerevisiae
#16
Lillian Campos-Doerfler, Salahuddin Syed, Kristina H Schmidt
Accurate repair of DNA breaks is essential for maintaining genome integrity and cellular fitness. Sgs1, the sole member of the RecQ family of DNA helicases in Saccharomyces cerevisiae, is important for both early and late stages of homology-dependent repair. Its large number of physical and genetic interactions with DNA recombination, repair and replication factors has established Sgs1 as a key player in the maintenance of genome integrity. To determine the significance of Sgs1 binding to the strand exchange factor Rad51 we have identified a single amino acid change C-terminal of the helicase core of Sgs1 that disrupts Rad51 binding...
November 21, 2017: Genetics
https://www.readbyqxmd.com/read/29150636/a-genetic-system-for-targeted-mutations-to-disrupt-and-restore-genes-in-the-obligate-bacterium-ehrlichia-chaffeensis
#17
Ying Wang, Lanjing Wei, Huitao Liu, Chuanmin Cheng, Roman R Ganta
Obligate intracellular bacteria (obligates) belonging to Rickettsiales and Chlamydiales cause diseases in hundreds of millions of people worldwide and in many animal species. Lack of an efficient system for targeted mutagenesis in obligates remains a major impediment in understanding microbial pathogenesis. Challenges in creating targeted mutations may be attributed to essential nature of majority of the genes and intracellular replication dependence. Despite success in generating random mutations, a method that works well in creating mutations in specific genes of interest followed by complementation remains problematic for obligates and is a highly sought-after goal...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29134729/maintaining-their-genetic-distance-little-evidence-for-introgression-between-widely-hybridising-species-of-geum-with-contrasting-mating-systems
#18
Crispin Y Jordan, Konrad Lohse, Frances Turner, Marian Thomson, Karim Gharbi, Richard A Ennos
Within the plant kingdom many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridise. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing G. urbanum, sister species that hybridise in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2-3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations)...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29133559/mutations-in-gene-fusa1-as-a-novel-mechanism-of-aminoglycoside-resistance-in-clinical-strains-of-pseudomonas-aeruginosa
#19
Arnaud Bolard, Patrick Plesiat, Katy Jeannot
Resistance of clinical strains of Pseudomonas aeruginosa to aminoglycosides can result from production of transferable aminoglycoside-modifying enzymes, of 16S rRNA methylases, and/or mutational derepression of intrinsic multidrug efflux pump MexXY(OprM). The present study reports on characterization of a new type of mutants 4- to 8-fold more resistant to 2-deoxystreptamine derivatives (e.g., gentamicin, amikacin, tobramycin), as compared with wild-type strain PAO1. The genetic alterations of three in vitro mutants were mapped on fusA1, and found to result in single amino acid substitutions in domains II, III and V of elongation factor G (EF-G1A), a key component of translational machinery...
November 13, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29123253/the-gene-fmt-encoding-trna-fmet-formyl-transferase-is-essential-for-normal-growth-of-m-bovis-but-not-for-viability
#20
Miriam Vanunu, Ziv Lang, Daniel Barkan
Mycobacterium tuberculosis is a major health threat, necessitating novel drug targets. Protein synthesis in bacteria uses initiator tRNAi charged with formylated methionine residue. Deletion of the formylase gene, tRNA(fMet)-formyl transferase (fmt), causes severe growth-retardation in E. coli and in S. pneumoniae, but not in P. aeruginosa or S. aureus. fmt was predicted to be essential in M. tuberculosis by transposon library analysis, but this was never formally tested in any mycobacteria. We performed a targeted deletion of fmt in M...
November 9, 2017: Scientific Reports
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