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Allelic exchange

Kevin Brick, Florencia Pratto, Chi-Yu Sun, Rafael D Camerini-Otero, Galina Petukhova
The repair of programmed DNA double-strand breaks (DSBs) physically tethers homologous chromosomes in meiosis to allow for accurate segregation through meiotic cell divisions. This process, known as recombination, also results in the exchange of alleles between parental chromosomes and contributes to genetic diversity. In mammals, meiotic DSBs occur predominantly in a small fraction of the genome, at sites known as hotspots. Studies of the formation and repair of meiotic DSBs in mammals are challenging, because few cells undergo meiotic DSB formation at a given time...
2018: Methods in Enzymology
Shannon Owens, Shangming Tang, Neil Hunter
Homologous recombination is fundamental to sexual reproduction, facilitating accurate segregation of homologous chromosomes at the first division of meiosis, and creating novel allele combinations that fuel evolution. Following initiation of meiotic recombination by programmed DNA double-strand breaks (DSBs), homologous pairing and DNA strand exchange form joint molecule (JM) intermediates that are ultimately resolved into crossover and noncrossover repair products. Physical monitoring of the DNA steps of meiotic recombination in Saccharomyces cerevisiae (budding yeast) cultures undergoing synchronous meiosis has provided seminal insights into the molecular basis of meiotic recombination and affords a powerful tool for dissecting the molecular roles of recombination factors...
2018: Methods in Enzymology
Marina O Cesar, Eliana R Matushima, Ticiana Zwarg, Alice S de Oliveira, Thaís C Sanches, Adriana M Joppert, Lara B Keid, Trícia Maria F S Oliveira, Helena L Ferreira, Horwald Alexander Bedoya Llano, Guilherme Konradt, Matheus Viezzer Bianchi, Fábio Gregori, Luís Fernando P Gondim, Rodrigo M Soares
In a previous study in Brazil, six isolates of Sarcocystis spp. recovered from budgerigars fed sporocysts excreted by opossums of the genus Didelphis were characterized by means of sequencing fragments of gene coding cytochrome B (CYTB), internal transcribed spacer 1 (ITS1), and surface antigen genes (SAG2, SAG3 and SAG4). The isolates shared identical ITS1 and CYTB sequences, but differed at SAG2, SAG3 and SAG4: three allele variants of SAG2, 3 allele variants of SAG3 and 2 allele variants of SAG4 were encountered in three multilocus genotypes (MLGs) (MLG1, MLG2, and MLG3)...
March 6, 2018: Experimental Parasitology
Kouhei Kishida, Natsumi Ogawa, Eikichi Ichihashi, Hiromi Kato, Yuji Nagata, Yoshiyuki Ohtsubo, Masataka Tsuda
Plasmid vector and allelic exchange mutagenesis systems were established for the genetic analysis of a phenanthrene-degrading mycobacterial strain, Mycobacterium sp. EPa45. Successful application of these systems revealed the necessity of the EPa45 phdI gene for the degradation of 1-hydroxy-2-naphthoate, which has been proposed to be an intermediate product in the degradation pathway of phenanthrene.
March 9, 2018: Bioscience, Biotechnology, and Biochemistry
J Pruszak, M Bernheiden, F Emmerich
HLA-B*50:01:09 differs by a synonymous nucleotide exchange in codon 17 from B*50:01:01.
March 9, 2018: HLA
Yusuke Kurokawa, Keisuke Nagai, Phung Danh Hung, Kousuke Shimazaki, Huangqi Qu, Yoshinao Mori, Yusuke Toda, Takeshi Kuroha, Nagao Hayashi, Saori Aiga, Jun-Ichi Itoh, Atsushi Yoshimura, Yuko Sasaki-Sekimoto, Hiroyuki Ohta, Mie Shimojima, Al Imran Malik, Ole Pedersen, Timothy David Colmer, Motoyuki Ashikari
Floods impede gas (O2 and CO2 ) exchange between plants and the environment. A mechanism to enhance plant gas exchange under water comprises gas films on hydrophobic leaves, but the genetic regulation of this mechanism is unknown. We used a rice mutant (dripping wet leaf 7, drp7) which does not retain gas films on leaves, and its wild-type (Kinmaze), in gene discovery for this trait. Gene complementation was tested in transgenic lines. Functional properties of leaves as related to gas film retention and underwater photosynthesis were evaluated...
March 2, 2018: New Phytologist
Ariadna E Morales, Bryan C Carstens
While genetic exchange between non-sister species was traditionally considered to be rare in mammals, analyses of molecular data in multiple systems suggest that it may be common. Interspecific gene flow, if present, is problematic for phylogenetic inference, particularly for analyses near the species level. Here, we explore how to detect and account for gene flow during phylogeny estimation using data from a clade of North American Myotis bats where previous results have led researchers to suspect that gene flow among lineages is present...
February 15, 2018: Systematic Biology
Tiantian Wang, Dongshu Wang, Yufei Lyu, Erling Feng, Zhu Li, Chunjie Liu, Yanchun Wang, Xiankai Liu, Hengliang Wang
To investigate gene function in Bacillus anthracis, a high-efficiency cloning system is required with an increased rate of allelic exchange. Golden Gate cloning is a molecular cloning strategy allowing researchers to simultaneously and directionally assemble multiple DNA fragments to construct target plasmids using type IIs restriction enzymes and T4 DNA ligase in the same reaction system. Here, a B. anthracis S-layer protein EA1 allelic exchange vector was successfully constructed using the Golden Gate method...
February 10, 2018: Journal of Biotechnology
A Edrees, H Abdelhamed, S W Nho, S B Park, A Karsi, F W Austin, M Essa, T Pechan, M L Lawrence
Catfish is the largest aquaculture industry in the United States. Edwardsiellosis is considered one of the most significant problems affecting this industry. Edwardsiella piscicida is a newly described species within the genus Edwardsiella, and it was previously classified as Edwardsiella tarda. It causes gastrointestinal septicaemia, primarily in summer months, in farmed channel catfish in the south-eastern United States. In the current study, we adapted gene deletion methods used for Edwardsiella to E. piscicida strain C07-087, which was isolated from a disease outbreak in a catfish production pond...
February 9, 2018: Journal of Fish Diseases
Kazuhisa Okada, Warawan Wongboot, Siriporn Chantaroj, Wirongrong Natakuathung, Amonrattana Roobthaisong, Watcharaporn Kamjumphol, Fumito Maruyama, Taichiro Takemura, Ichiro Nakagawa, Makoto Ohnishi, Shigeyuki Hamada
Vibrio cholerae inhabits aquatic environments worldwide and has over 200 recognized serogroups classified by O-polysaccharide specificity. Here, we report that V. cholerae selects either of two genetic traits during their evolution. Sequencing of the specific gene locus MS6_A0927 revealed that 339 of 341 strains of V. cholerae and closely related Vibrio species originating from 34 countries over a century carried either metY (M) (~1,269 bp) or luxR-hchA (LH) (~1,600 bp) genes, and consequently those vibrios were separated into two clusters, M (45...
January 26, 2018: Scientific Reports
Kevin H-C Wei, Sarah E Lower, Ian V Caldas, Trevor J Sless, Daniel A Barbash, Andrew G Clark
Simple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through non-allelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly...
January 19, 2018: Molecular Biology and Evolution
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
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
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
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
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
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
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
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
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)
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