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https://www.readbyqxmd.com/read/29150636/a-genetic-system-for-targeted-mutations-to-disrupt-and-restore-genes-in-the-obligate-bacterium-ehrlichia-chaffeensis
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/29120483/azospirillum-brasilense-laboratory-maintenance-and-genetic-manipulation
#5
Jessica Gullett, Lindsey O'Neal, Tanmoy Mukherjee, Gladys Alexandre
Bacteria of the genus Azospirillum, including the most comprehensively studied Azospirillum brasilense, are non-pathogenic soil bacteria that promote the growth of diverse plants, making them an attractive model to understand non-symbiotic, beneficial plant-bacteria associations. Research into the physiology and genetics of these organisms spans decades and a range of molecular tools and protocols have been developed for allelic exchange mutagenesis, in trans expression of genes, and fusions to reporter genes...
November 9, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/29114020/identification-of-novel-alleles-conferring-superior-production-of-rose-flavor-phenylethyl-acetate-using-polygenic-analysis-in-yeast
#6
Bruna Trindade de Carvalho, Sylvester Holt, Ben Souffriau, Rogelio Lopes Brandão, Maria R Foulquié-Moreno, Johan M Thevelein
Flavor compound metabolism is one of the last areas in metabolism where multiple genes encoding biosynthetic enzymes are still unknown. A major challenge is the involvement of side activities of enzymes having their main function in other areas of metabolism. We have applied pooled-segregant whole-genome sequence analysis to identify novel Saccharomyces cerevisiae genes affecting production of phenylethyl acetate (2-PEAc). This is a desirable flavor compound of major importance in alcoholic beverages imparting rose- and honey-like aromas, with production of high 2-PEAc levels considered a superior trait...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29079820/the-phe362tyr-mutation-conveying-resistance-to-organophosphates-occurs-in-high-frequencies-in-salmon-lice-collected-from-wild-salmon-and-trout
#7
Helene Børretzen Fjørtoft, Francois Besnier, Anne Stene, Frank Nilsen, Pål Arne Bjørn, Ann-Kristin Tveten, Bengt Finstad, Vidar Aspehaug, Kevin Alan Glover
The parasitic salmon louse, and its resistance to chemical delousing agents, represents one of the largest challenges to the salmon aquaculture industry. We genotyped lice sampled from wild salmon and sea trout throughout Norway with the recently identified Phe362Tyr mutation that conveys resistance to organophosphates. These results were compared to data from lice sampled on farmed salmon in the same regions. The resistant (R) allele was observed in salmon lice from wild salmon and sea trout throughout Norway, although its frequency was highest in farming-intense regions...
October 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29079751/a-missense-mutation-in-slc26a3-is-associated-with-human-male-subfertility-and-impaired-activation-of-cftr
#8
Satu Wedenoja, Ahlam Khamaysi, Liana Shimshilashvili, Shireen Anbtawe-Jomaa, Outi Elomaa, Jorma Toppari, Pia Höglund, Kristiina Aittomäki, Christer Holmberg, Outi Hovatta, Juha S Tapanainen, Ehud Ohana, Juha Kere
Chloride absorption and bicarbonate excretion through exchange by the solute carrier family 26 member 3 (SLC26A3) and cystic fibrosis transmembrane conductance regulator (CFTR) are crucial for many tissues including sperm and epithelia of the male reproductive tract. Homozygous SLC26A3 mutations cause congenital chloride diarrhea with male subfertility, while homozygous CFTR mutations cause cystic fibrosis with male infertility. Some homozygous or heterozygous CFTR mutations only manifest as male infertility...
October 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29066090/genetic-variants-associated-with-susceptibility-to-idiopathic-pulmonary-fibrosis-in-people-of-european-ancestry-a-genome-wide-association-study
#9
Richard J Allen, Joanne Porte, Rebecca Braybrooke, Carlos Flores, Tasha E Fingerlin, Justin M Oldham, Beatriz Guillen-Guio, Shwu-Fan Ma, Tsukasa Okamoto, Alison E John, Ma'en Obeidat, Ivana V Yang, Amanda Henry, Richard B Hubbard, Vidya Navaratnam, Gauri Saini, Norma Thompson, Helen L Booth, Simon P Hart, Mike R Hill, Nik Hirani, Toby M Maher, Robin J McAnulty, Ann B Millar, Philip L Molyneaux, Helen Parfrey, Doris M Rassl, Moira K B Whyte, William A Fahy, Richard P Marshall, Eunice Oballa, Yohan Bossé, David C Nickle, Don D Sin, Wim Timens, Nick Shrine, Ian Sayers, Ian P Hall, Imre Noth, David A Schwartz, Martin D Tobin, Louise V Wain, R Gisli Jenkins
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with high mortality, uncertain cause, and few treatment options. Studies have identified a significant genetic risk associated with the development of IPF; however, mechanisms by which genetic risk factors promote IPF remain unclear. We aimed to identify genetic variants associated with IPF susceptibility and provide mechanistic insight using gene and protein expression analyses. METHODS: We used a two-stage approach: a genome-wide association study in patients with IPF of European ancestry recruited from nine different centres in the UK and controls selected from UK Biobank (stage 1) matched for age, sex, and smoking status; and a follow-up of associated genetic variants in independent datasets of patients with IPF and controls from two independent US samples from the Chicago consortium and the Colorado consortium (stage 2)...
November 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/29046578/a-sex-linked-supergene-controls-sperm-morphology-and-swimming-speed-in-a-songbird
#10
Kang-Wook Kim, Clair Bennison, Nicola Hemmings, Lola Brookes, Laura L Hurley, Simon C Griffith, Terry Burke, Tim R Birkhead, Jon Slate
Sperm competition is an important selective force in many organisms. As a result, sperm have evolved to be among the most diverse cells in the animal kingdom. However, the relationship between sperm morphology, sperm motility and fertilization success is only partially understood. The extent to which between-male variation is heritable is largely unknown, and remarkably few studies have investigated the genetic architecture of sperm traits, especially sperm morphology. Here we use high-density genotyping and gene expression profiling to explore the considerable sperm trait variation that exists in the zebra finch Taeniopygia guttata...
August 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29044609/phenomics-allows-identification-of-genomic-regions-affecting-maize-stomatal-conductance-with-conditional-effects-of-water-deficit-and-evaporative-demand
#11
Santiago Alvarez Prado, Llorenç Cabrera-Bosquet, Antonin Grau, Aude Coupel-Ledru, Emilie J Millet, Claude Welcker, François Tardieu
Stomatal conductance is central for the trades-off between hydraulics and photosynthesis. We aimed at deciphering its genetic control and that of its responses to evaporative demand and water deficit, a nearly impossible task with gas exchanges measurements. Whole-plant stomatal conductance was estimated via inversion of the Penman Monteith equation from data of transpiration and plant architecture collected in a phenotyping platform. We have analyzed jointly four experiments with contrasting environmental conditions imposed to a panel of 254 maize hybrids...
October 17, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29038948/molecular-characterization-of-nbs-lrr-genes-in-the-soybean-rsv3-locus-reveals-several-divergent-alleles-that-likely-confer-resistance-to-the-soybean-mosaic-virus
#12
Fang-Fang Ma, Mian Wu, Ying-Na Liu, Xue-Ying Feng, Xun-Zong Wu, Jian-Qun Chen, Bin Wang
The divergence patterns of NBS - LRR genes in soybean Rsv3 locus were deciphered and several divergent alleles ( NBS_C, NBS_D and Columbia NBS_E ) were identified as the likely functional candidates of Rsv3. The soybean Rsv3 locus, which confers resistance to the soybean mosaic virus (SMV), has been previously mapped to a region containing five nucleotide binding site-leucine-rich repeats (NBS-LRR) genes (referred to as nbs_A-E) in Williams 82. In resistant cultivars, however, the number of NBS-LRR genes in this region and their divergence from susceptible alleles remain unclear...
October 16, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29028881/snp-genotyping-and-parameter-estimation-in-polyploids-using-low-coverage-sequencing-data
#13
Paul D Blischak, Laura S Kubatko, Andrea D Wolfe
Motivation: Genotyping and parameter estimation using high throughput sequencing data are everyday tasks for population geneticists, but methods developed for diploids are typically not applicable to polyploid taxa. This is due to their duplicated chromosomes, as well as the complex patterns of allelic exchange that often accompany whole genome duplication (WGD) events. For WGDs within a single lineage (autopolyploids), inbreeding can result from mixed mating and/or double reduction. For WGDs that involve hybridization (allopolyploids), alleles are typically inherited through independently segregating subgenomes...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29024923/a-ghep-isfg-collaborative-study-on-the-genetic-variation-of-38-autosomal-indels-for-human-identification-in-different-continental-populations
#14
R Pereira, C Alves, M Aler, A Amorim, C Arévalo, E Betancor, D Braganholi, M L Bravo, P Brito, J J Builes, G Burgos, E F Carvalho, A Castillo, C I Catanesi, R M B Cicarelli, P Coufalova, P Dario, M E D'Amato, S Davison, J Ferragut, M Fondevila, S Furfuro, O García, A Gaviria, I Gomes, E González, A Gonzalez-Liñan, T E Gross, A Hernández, Q Huang, S Jiménez, L F Jobim, A M López-Parra, M Marino, S Marques, G Martínez-Cortés, V Masciovecchio, D Parra, G Penacino, M F Pinheiro, M J Porto, Y Posada, C Restrepo, T Ribeiro, L Rubio, A Sala, A Santurtún, L S Solís, L Souto, E Streitemberger, A Torres, C Vilela-Lamego, J J Yunis, I Yurrebaso, L Gusmão
A collaborative effort was carried out by the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) to promote knowledge exchange between associate laboratories interested in the implementation of indel-based methodologies and build allele frequency databases of 38 indels for forensic applications. These databases include populations from different countries that are relevant for identification and kinship investigations undertaken by the participating laboratories...
September 22, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29016860/primary-angle-closure-glaucoma-pacg-susceptibility-gene-plekha7-encodes-a-novel-rac1-cdc42-gap-that-modulates-cell-migration-and-blood-aqueous-barrier-function
#15
Mei-Chin Lee, William Shei, Anita S Chan, Boon-Tin Chua, Shuang-Ru Goh, Yaan-Fun Chong, Maryam H Hilmy, Monisha E Nongpiur, Mani Baskaran, Chiea-Chuen Khor, Tin Aung, Walter Hunziker, Eranga N Vithana
PLEKHA7, a gene recently associated with primary angle closure glaucoma (PACG), encodes an apical junctional protein expressed in components of the blood aqueous barrier (BAB). We found that PLEKHA7 is down-regulated in lens epithelial cells and in iris tissue of PACG patients. PLEKHA7 expression also correlated with the C risk allele of the sentinel SNP rs11024102 with the risk allele carrier groups having significantly reduced PLEKHA7 levels compared to non-risk allele carriers. Silencing of PLEKHA7 in human immortalized non-pigmented ciliary epithelium (h-iNPCE) and primary trabecular meshwork cells, which are intimately linked to BAB and aqueous humor outflow respectively, affected actin cytoskeleton organization...
October 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28985418/the-systemhc-atlas-project
#16
Wenguang Shao, Patrick G A Pedrioli, Witold Wolski, Cristian Scurtescu, Emanuel Schmid, Juan A Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S L Arlehamn, Kerrie Vaughan, Bjoern Peters, Alessandro Sette, Tom H M Ottenhoff, Krista E Meijgaarden, Natalie Nieuwenhuizen, Stefan H E Kaufmann, Ralph Schlapbach, John C Castle, Alexey I Nesvizhskii, Morten Nielsen, Eric W Deutsch, David S Campbell, Robert L Moritz, Roman A Zubarev, Anders Jimmy Ytterberg, Anthony W Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E Costello, Nicola Ternette, Peter A van Veelen, Cécile A C M van Els, Albert J R Heck, Gustavo A de Souza, Ludvig M Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron
Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets...
July 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28970272/fraem-reveals-a-role-for-c-trachomatis-tmea-in-invasion-that-is-independent-of-host-ahnak
#17
M J McKuen, K E Mueller, Y S Bae, K A Fields
Development of approaches to genetically manipulate Chlamydia is fostering important advances in understanding pathogenesis. Fluorescence-reported allelic exchange mutagenesis (FRAEM) now enables the complete deletion of specific genes in C. trachomatis L2. We have leveraged this technology to delete the coding sequences for a known type III effector. The evidence provided herein indicates that CT694/CTL0063 is a virulence protein involved in chlamydial invasion. Based on our findings, we designate the gene product corresponding to ct694/ctl0063 as translocated membrane-associated effector A (TmeA)...
October 2, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28968440/genetic-structure-in-the-southernmost-populations-of-black-and-gold-howler-monkeys-alouatta-caraya-and-its-conservation-implications
#18
Luciana Inés Oklander, Carolina Isabel Miño, Gabriela Fernández, Mariela Caputo, Daniel Corach
Black-and-gold howler monkeys Alouatta caraya, are arboreal primates, inhabitants of Neotropical forests, highly susceptible to the yellow fever virus, considered early 'sentinels' of outbreaks, and thus, of major epidemiological importance. Currently, anthropogenic habitat loss and modifications threatens their survival. Habitat modification can prevent, reduce or change dispersal behavior, which, in turn, may influence patterns of gene flow. We explored past and contemporary levels of genetic diversity, elucidated genetic structure and identified its possible drivers, in ten populations (n = 138) located in the southernmost distribution range of the species in South America, in Argentina and Paraguay...
2017: PloS One
https://www.readbyqxmd.com/read/28947214/dominance-of-yeast-aac2-r96h-and-aac2-r252g-mutations-equivalent-to-pathological-mutations-in-ant1-is-due-to-gain-of-function
#19
Cristina Dallabona, Enrico Baruffini, Paola Goffrini, Tiziana Lodi
The mitochondrial ADP/ATP carrier is a nuclear encoded protein, which catalyzes the exchange of ATP generated in mitochondria with ADP produced in the cytosol. In humans, mutations in the major ADP/ATP carrier gene, ANT1, are involved in several degenerative mitochondrial pathologies, leading to instability of mitochondrial DNA. Recessive mutations have been associated with mitochondrial myopathy and cardiomyopathy whereas dominant mutations have been associated with autosomal dominant Progressive External Ophtalmoplegia (adPEO)...
November 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28933689/galk-based-suicide-vector-mediated-allelic-exchange-in-mycobacterium-abscessus
#20
Stacy A Gregoire, Joel Byam, Martin S Pavelka
Mycobacterium abscessus is a fast-growing environmental organism and an important emerging pathogen. It is highly resistant to many antibiotics and undergoes a smooth to rough colony morphology change that appears to be important for pathogenesis. Smooth environmental strains have a glycopeptidolipid (GPL) on the surface, while certain types of clinical strains are often rough and lack this GPL, due to mutations in biosynthetic genes or the mmpL4b transporter gene. We report here the development and evaluation of an allelic exchange system for unmarked alleles in M...
September 21, 2017: Microbiology
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