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Allelic exchange

Ye Li, Jihong Zeng, Yujiang Fan, Guanglin He, Mingkun Xie, Tianzhen Gao, Shouyu Wang, Jin Wu
The X chromosome has a special mode of inheritance, and is thus a rich resource for population studies. In this study, the allele frequencies and forensic statistics of the 19 X chromosomal short tandem repeat loci were evaluated in 500 Uyghur individuals from Aksu Prefecture in northwest China. We further aimed to study whether the Uyghur populations located in various regions of Xinjiang share similar allele and haplotype frequency distributions, as they have experienced genetic exchanges. Population comparisons, PCA and MDS were performed for the Uyghurs and 27 populations and the results indicate that the Uyghur minority in Aksu has a relatively close phylogenetic relationship with East Asians, especially the Kazakh minority...
May 19, 2018: International Journal of Legal Medicine
Hirotsugu Banno, Kouji Kimura, Tomomi Seki, Wanchun Jin, Jun-Ichi Wachino, Keiko Yamada, Noriyuki Nagano, Yoshichika Arakawa
Group B Streptococcus (GBS) clinical isolates with reduced penicillin susceptibility (PRGBS) have emerged through acquisition of amino acid substitutions in penicillin-binding protein 2X (PBP2X). Moreover, we also reported the emergence of penicillin-susceptible GBS clinical isolates with reduced ceftibuten susceptibility (CTBr PSGBS) due to amino acid substitutions in PBPs. However, whether or not these amino acid substitutions are responsible for the reduced ceftibuten susceptibility (RCTBS) profile remains unclear...
May 17, 2018: European Journal of Clinical Microbiology & Infectious Diseases
Lisa Tymensen, Rahat Zaheer, Shaun R Cook, Kingsley K Amoako, Noriko Goji, Ron Read, Calvin W Booker, Sherry J Hannon, Norman Neumann, Tim A McAllister
Livestock wastewater lagoons represent important environmental reservoirs of antibiotic resistance genes (ARGs), although factors contributing to their proliferation within these reservoirs remain poorly understood. Here, we characterized Escherichia coli from feedlot cattle feces and associated wastewater lagoons using CRISPR1 subtyping, and demonstrated that while generic E. coli were genetically diverse, populations were dominated by several 'feedlot-adapted' CRISPR types (CTs) that were widely distributed throughout the feedlot...
May 11, 2018: Science of the Total Environment
Steven M Hrycaj, Leilani Marty-Santos, Andrew J Rasky, Nicholas W Lukacs, Deneen M Wellik
Alveologenesis is the final stage of lung development and is responsible for the formation of the principle gas exchange units called alveoli. The lung mesenchyme, in particular the alveolar myofibroblasts, are drivers of alveolar development, however, few key regulators that govern the proper distribution and behavior of these cells in the distal lung during alveologenesis have been identified. While Hox5 triple mutants (Hox5 aabbcc) exhibit neonatal lethality, four-allele, compound mutant mice (Hox5 AabbCc) are born in Mendelian ratios and are phenotypically normal at birth...
April 27, 2018: Science China. Life Sciences
Fábio B Britto, Anders J Schmidt, Adriana M F Carvalho, Carolina C M P Vasconcelos, Antonia M Farias, Paul Bentzen, Fábio M Diniz
Background: The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear...
2018: PeerJ
Ingar Olsen, Tsute Chen, Gena D Tribble
Porphyromonas gingivalis is considered a keystone pathogen in adult periodontitis but has also been associated with systemic diseases. It has a myriad of virulence factors that differ between strains. Genetic exchange and intracellular genome rearrangements may be responsible for the variability in the virulence of P. gingivalis . The present review discusses how the exchange of alleles can convert this bacterium from commensalistic to pathogenic and potentially shapes the host-microbe environment from homeostasis to dysbiosis...
2018: Journal of Oral Microbiology
Eduardo P C Rocha
Kimura's outstanding contributions to population genetics included many elegant theoretical results on the vagaries of alleles in populations. Once polymorphism data showed extensive variation in natural populations, these results led naturally to the Neutral Theory. In this article, I'll depart from some of these results to focus on four major open problems in microbial population genetics with direct implications to the study of molecular evolution: the lack of neutral polymorphism, the modeling of genetic exchanges, the population genetics of ill-defined populations, and the difficulty of untangling selection and demography in the light of the previous issues...
April 19, 2018: Molecular Biology and Evolution
Maria R Servedio, Reinhard Bürger
Attempts to uncover the genetic basis of female mating preferences and male signals involved in reproductive isolation have discovered intriguing cases in which loci contributing to these traits co-localize in their chromosomal positions. Such discoveries raise the question of whether alleles at certain loci contribute pleiotropically to male and female components of premating reproductive isolation, versus whether these loci are merely tightly linked. Here we use population genetic models to assess the degree to which these alternatives affect both short term and equilibrium patterns of trait (signal) and preference divergence...
April 17, 2018: Genes
David Roy, Daisuke Takamatsu, Masatoshi Okura, Guillaume Goyette-Desjardins, Marie-Rose Van Calsteren, Audrey Dumesnil, Marcelo Gottschalk, Mariela Segura
The capsular polysaccharide (CPS) represents a key virulence factor for most encapsulated streptococci. Streptococcus suis and Group B Streptococcus (GBS) are both well-encapsulated pathogens of clinical importance in veterinary and/or human medicine and responsible for invasive systemic diseases. S. suis and GBS are the only Gram-positive bacteria which express a sialylated CPS at their surface. An important difference between these two sialylated CPSs is the linkage between the side-chain terminal galactose and sialic acid, being α-2,6 for S...
2018: Frontiers in Microbiology
Ziv Lifshitz, Na'ama Sturlesi, Miriam Parizade, Shlomo E Blum, Michal Gordon, Diana Taran, Amos Adler
The goal of this study was to compare the molecular features of bovine- and human community-acquired extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Israel. Bovine ESBL-producing E. coli were isolated during a point-prevalence study from the main farming locations throughout Israel. Human ESBL-producing E. coli isolates were collected from community-acquired urinary tract infection cases. Molecular typing was done initially by repetitive extragenic palindromic-PCR. Representative isolates were subjected to next-generation sequencing (NGS) and analyzed for multilocus sequence typing (MLST), core genome MLST (cgMLST), blaCTX-M gene allele, and mobile genetic elements (MGEs) surrounding it...
April 17, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
Gareth T Little, Benjamin J Willson, John T Heap, Klaus Winzer, Nigel P Minton
The solventogenic anaerobe Clostridium beijerinckii has potential for use in the sustainable bioconversion of plant-derived carbohydrates into solvents, such as butanol or acetone. However, relatively few strains have been extensively characterised either at the genomic level or through exemplification of a complete genetic toolkit. To remedy this situation, a new strain of C. beijerinckii, NCIMB 14988, was selected from amongst a total of 55 new clostridial isolates capable of growth on hexose and pentose sugars...
April 16, 2018: Biotechnology Journal
Leah R Vincent, Samuel R Kerr, Yang Tan, Joshua Tomberg, Erica L Raterman, Julie C Dunning Hotopp, Magnus Unemo, Robert A Nicholas, Ann E Jerse
Resistance to ceftriaxone in Neisseria gonorrhoeae is mainly conferred by mosaic penA alleles that encode penicillin-binding protein 2 (PBP2) variants with markedly lower rates of acylation by ceftriaxone. To assess the impact of these mosaic penA alleles on gonococcal fitness, we introduced the mosaic penA alleles from two ceftriaxone-resistant (Cror ) clinical isolates (H041 and F89) into a Cros strain (FA19) by allelic exchange and showed that the resultant Cror mutants were significantly outcompeted by the Cros parent strain in vitro and in a murine infection model...
April 3, 2018: MBio
Alexander A Celik, Gwendolin S Simper, Trevor Huyton, Rainer Blasczyk, Christina Bade-Döding
The trade-off from HLA class I expression to HLA-G expression support the immune evasion of malignant cells. The essential role of the virtually invariant HLA-G in immune tolerance, tumor immunology and its expression frequency in immune privileged tissues is known; however the specific importance of allelic subtypes in immune responses is still not well understood. HLA-G∗01:01, ∗01:03 and ∗01:04 are the most prevalent allelic variants differing at residues 31 and 110, respectively. In cytotoxicity assays applying K562 cells transduced with the HLA-G variants as targets and NK cells as effectors the differential protective potential of HLA-G variants was analyzed...
March 29, 2018: Human Immunology
Chiara Bortoluzzi, Richard P M A Crooijmans, Mirte Bosse, Sipke Joost Hiemstra, Martien A M Groenen, Hendrik-Jan Megens
Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60 K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams...
March 28, 2018: Heredity
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)...
May 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 Huan, Kousuke Shimazaki, Huangqi Qu, Yoshinao Mori, Yosuke 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...
June 2018: New Phytologist
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