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Allelic exchange

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https://www.readbyqxmd.com/read/28933689/galk-based-suicide-vector-mediated-allelic-exchange-in-mycobacterium-abscessus
#1
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
https://www.readbyqxmd.com/read/28927382/a-rapid-seamless-method-for-gene-knockout-in-pseudomonas-aeruginosa
#2
Weiliang Huang, Angela Wilks
BACKGROUND: Pseudomonas aeruginosa is a model organism for the study of quorum sensing, biofilm formation, and also leading cause of nosocomial infections in immune compromised patients. As such P. aeruginosa is one of the most well studied organisms in terms of its genetics. However, the construction of gene deletions and replacements in Pseudomonas aeruginosa is relatively time-consuming, requiring multiple steps including suicide vector construction, conjugation, inactivation with insertion of antibiotic resistance cassettes and allelic exchange...
September 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28916543/cryopyrin-associated-periodic-syndromes-in-italian-patients-evaluation-of-the-rate-of-somatic-nlrp3-mosaicism-and-phenotypic-characterization
#3
Denise Lasigliè, Anna Mensa-Vilaro, Denise Ferrera, Roberta Caorsi, Federica Penco, Giuseppe Santamaria, Marco Di Duca, Giulia Amico, Kenji Nakagawa, Francesca Antonini, Alberto Tommasini, Rita Consolini, Antonella Insalaco, Marco Cattalini, Laura Obici, Romina Gallizzi, Francesca Santarelli, Genny Del Zotto, Mariasavina Severino, Anna Rubartelli, Roberto Ravazzolo, Alberto Martini, Isabella Ceccherini, Ryuta Nishikomori, Marco Gattorno, Juan I Arostegui, Silvia Borghini
OBJECTIVE: To evaluate the rate of somatic NLRP3 mosaicism in an Italian cohort of mutation-negative patients with cryopyrin-associated periodic syndrome (CAPS). METHODS: The study enrolled 14 patients with a clinical phenotype consistent with CAPS in whom Sanger sequencing of the NLRP3 gene yielded negative results. Patients' DNA were subjected to amplicon-based NLRP3 deep sequencing. RESULTS: Low-level somatic NLRP3 mosaicism has been detected in 4 patients, 3 affected with chronic infantile neurological cutaneous and articular syndrome and 1 with Muckle-Wells syndrome...
September 15, 2017: Journal of Rheumatology
https://www.readbyqxmd.com/read/28904201/heterogeneity-of-the-epstein-barr-virus-major-internal-repeat-reveals-evolutionary-mechanisms-of-ebv-and-a-functional-defect-in-the-prototype-ebv-strain-b95-8
#4
Mohammed Ba Abdullah, Richard Palermo, Anne Palser, Nicholas E Grayson, Paul Kellam, Samantha Correia, Agnieszka Szymula, Rob White
Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified both through co-evolution with its host, and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging, because of the large number and length of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat of EBV (IR1 or BamW repeats) from over 70 strains...
September 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28889200/prevalence-of-common-hereditary-risk-factors-for-thrombophilia-in-somalia-and-identification-of-a-novel-gln544arg-mutation-in-coagulation-factor-v
#5
Abshir Ali Abdi, Abdimajid Osman
Thrombophilia, commonly manifested as venous thromboembolism (VTE), is a worldwide concern but little is known on its genetic epidemiology in many parts of the globe particularly in the developing countries. Here we employed TaqMan genotyping and pyrosequencing to evaluate the prevalence of known common nucleotide polymorphisms associated with thrombophilia in a Somali population in the Puntland region of Somalia. We also employed next generation sequencing (NGS) to investigate other genetic variants in a Somali patient with deep venous thrombosis (DVT)...
September 9, 2017: Journal of Thrombosis and Thrombolysis
https://www.readbyqxmd.com/read/28888135/strseq-a-catalog-of-sequence-diversity-at-human-identification-short-tandem-repeat-loci
#6
Katherine Butler Gettings, Lisa A Borsuk, David Ballard, Martin Bodner, Bruce Budowle, Laurence Devesse, Jonathan King, Walther Parson, Christopher Phillips, Peter M Vallone
The STR Sequencing Project (STRSeq) was initiated to facilitate the description of sequence-based alleles at the Short Tandem Repeat (STR) loci targeted in human identification assays. This international collaborative effort, which has been endorsed by the ISFG DNA Commission, provides a framework for communication among laboratories. The initial data used to populate the project are the aggregate alleles observed in targeted sequencing studies across four laboratories: National Institute of Standards and Technology (N=1786), Kings College London (N=1043), University of North Texas Health Sciences Center (N=839), and University of Santiago de Compostela (N=944), for a total of 4612 individuals...
September 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28874406/revisiting-the-role-of-csp-family-proteins-in-regulating-clostridium-difficile-spore-germination
#7
Yuzo Kevorkian, Aimee Shen
Clostridium difficile causes considerable healthcare-associated gastrointestinal disease that is transmitted by its metabolically dormant spore form. Upon entering the gut, C. difficile spores germinate and outgrow to produce vegetative cells that release disease-causing toxins. C. difficile spore germination depends on the Csp family of (pseudo)proteases and the cortex hydrolase, SleC. The CspC pseudoprotease functions as a bile salt germinant receptor that activates the protease CspB, which in turn proteolytically activates SleC zymogen...
September 5, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28860155/protoplast-swelling-and-hypocotyl-growth-depend-on-different-auxin-signaling-pathways
#8
Renate Irmgard Dahlke, Simon Fraas, Kristian K Ullrich, Kirka Heinemann, Maren Romeiks, Thomas Rickmeyer, Gerhard Klebe, Klaus Palme, Hartwig Lüthen, Bianka Steffens
Members of the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX PROTEIN (TIR1/AFB) family are known auxin receptors. To analyze the possible receptor function of AUXIN BINDING PROTEIN1 (ABP1), an auxin receptor currently under debate, we performed different approaches. We performed a pharmacological approach using α-(2,4-dimethylphenylethyl-2-oxo)-indole-3-acetic acid (auxinole), α-(phenylethyl-2-oxo)-indole-3-acetic acid (PEO-IAA) and 5-fluoroindole-3-acetic acid (5-F-IAA) to discriminate between ABP1 and TIR1/AFB mediated processes...
August 31, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28833204/simultaneous-evaluation-of-the-effects-of-geographic-environmental-and-temporal-isolation-in-ecotypic-populations-of-solidago-virgaurea
#9
Shota Sakaguchi, Kenji Horie, Naoko Ishikawa, Atsushi J Nagano, Masaki Yasugi, Hiroshi Kudoh, Motomi Ito
Early stages of ecological speciation can create populations with an ecology and reproduction timing distinct from those of related populations. Landscape genetic models incorporating environmental heterogeneity and population-specific reproductive traits enable the processes of population genetic differentiation to be inferred. We investigated genome-wide genetic variation in ecotypic populations of Solidago virgaurea sensu lato, a herbaceous plant inhabiting a wide range of habitats (woodlands, serpentine barrens and alpine grasslands) and displaying remarkable variation in flowering time...
August 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28830938/clathrin-heavy-chain-subunits-coordinate-endo-and-exocytic-traffic-and-affect-stomatal-movement
#10
Emily R Larson, Eva Van Zelm, Camille Roux, Annie Marion-Poll, Michael R Blatt
The current model for vesicular traffic to and from the plasma membrane is accepted but the molecular requirements for this coordination are not well defined. We have identified the has1 mutant, which has a stomatal function defect, as a clathrin heavy chain 1 (CHC1) mutant allele and show that it has a decreased rate of endocytosis and growth defects that are shared with other chc1 mutant alleles. We used chc1 alleles and the related chc2 mutant as tools to investigate the effects clathrin defects have on secretion pathways and plant growth...
August 22, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28830922/deletion-of-11q-in-neuroblastomas-drives-sensitivity-to-parp-inhibition
#11
Elena Sanmartín, Lisandra Muñoz, Marta Piqueras, J Antoni Sirerol, Pablo Berlanga, Adela Cañete, Victoria Castel, Jaime Font de Mora
PURPOSE: Despite advances in multimodal therapy, neuroblastomas with hemizygous deletion in chromosome 11q (20-30%) undergo consecutive recurrences with poor outcome. We hypothesized that patients with 11q loss may share a druggable molecular target(s) that can be exploited for a precision medicine strategy to improve treatment outcome. EXPERIMENTAL DESIGN: SNP arrays were combined with next generation sequencing (NGS) to precisely define the deleted region in 17 primary 11q-loss neuroblastomas and identify allelic variants in genes relevant for neuroblastoma aetiology...
August 22, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28822129/targeted-isolation-and-characterization-of-t-dna-mutants-defective-in-photorespiration
#12
Stefan Timm, Katharina Modde, Hermann Bauwe
Transfer DNA (T-DNA) insertional lines have facilitated reverse genetic approaches in plant science and considerably accelerated the functional characterization of genes. Typically, online databases of mutant collections are searched for suitable mutant alleles of the gene of interest (GOI). Before such lines can be characterized physiologically, the genotype of the respective mutant has to be verified followed by the quantitative examination of downstream effects on the levels of the respective mRNA and the encoded protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28797792/specific-status-of-echinococcus-canadensis-cestoda-taeniidae-inferred-from-nuclear-and-mitochondrial-gene-sequences
#13
Tetsuya Yanagida, Antti Lavikainen, Eric P Hoberg, Sergey Konyaev, Akira Ito, Marcello Otake Sato, Vladimir A Zaikov, Kimberlee Beckmen, Minoru Nakao
The specific status of Echinococcus canadensis has long been controversial, mainly because it consists of the mitochondrial lineages G6, G7, G8 and G10 with different host affinity: G6 (camel strain) and G7 (pig strain) with domestic cycles and G8 (cervid strain) and G10 (Fennoscandian cervid strain) with sylvatic or semi-domestic cycles. There is an argument whether the mitochondrial lineages should be recognised as separate species which correspond to the biological or epidemiological aggregation. In the present study, the specific status of E...
August 7, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28795321/nkg2d-gene-polymorphisms-are-associated-with-disease-control-of-chronic-myeloid-leukemia-by-dasatinib
#14
Ryujiro Hara, Makoto Onizuka, Erika Matsusita, Eri Kikkawa, Yoshihiko Nakamura, Hiromichi Matsushita, Daisuke Ohgiya, Hiromichi Murayama, Shinichiro Machida, Ken Ohmachi, Yukari Shirasugi, Yoshiaki Ogawa, Hiroshi Kawada, Kiyoshi Ando
A recent study reported that treatment-free remission (TFR) of chronic myeloid leukemia (CML) after dasatinib (Das) treatment was significantly associated with natural killer (NK) cell proliferation in the peripheral blood. However, biomarkers to predict lymphocytosis or successful TFR are not well characterized. In order to clarify individual differences in NK cell responses among patients treated with Das, we retrospectively analyzed the association between polymorphisms in the natural killer group 2D receptor [NKG2D; also known as killer cell lectin like receptor K1 (KLRK1)] gene and clinical outcomes in 31 patients treated with Das as first-line treatment for CML...
August 9, 2017: International Journal of Hematology
https://www.readbyqxmd.com/read/28794482/the-white-gene-controls-copulation-success-in-drosophila-melanogaster
#15
Chengfeng Xiao, Shuang Qiu, R Meldrum Robertson
Characteristics of male courtship behavior in Drosophila melanogaster have been well-described, but the genetic basis of male-female copulation is largely unknown. Here we show that the white (w) gene, a classical gene for eye color, is associated with copulation success. 82.5% of wild-type Canton-S flies copulated within 60 minutes in circular arenas, whereas few white-eyed mutants mated successfully. The w (+) allele exchanged to the X chromosome or duplicated to the Y chromosome in the white-eyed genetic background rescued the defect of copulation success...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790327/natural-history-of-the-narrow-endemics-ipomoea-cavalcantei-and-i-marabaensis-from-amazon-canga-savannahs
#16
Elena Babiychuk, Sergei Kushnir, Santelmo Vasconcelos, Mariana Costa Dias, Nelson Carvalho-Filho, Gisele Lopes Nunes, Jorge Filipe Dos Santos, Lourival Tyski, Delmo Fonseca da Silva, Alexandre Castilho, Vera Lucia Imperatriz Fonseca, Guilherme Oliveira
Amazon comprises a vast variety of ecosystems, including savannah-like Canga barrens that evolved on iron-lateritic rock plateaus of the Carajás Mountain range. Individual Cangas are enclosed by the rain forest, indicating insular isolation that enables speciation and plant community differentiation. To establish a framework for the research on natural history and conservation management of endemic Canga species, seven chloroplast DNA loci and an ITS2 nuclear DNA locus were used to study natural molecular variation of the red flowered Ipomoea cavalcantei and the lilac flowered I...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790316/a-plasmodium-yoelii-hect-like-e3-ubiquitin-ligase-regulates-parasite-growth-and-virulence
#17
Sethu C Nair, Ruixue Xu, Sittiporn Pattaradilokrat, Jian Wu, Yanwei Qi, Martine Zilversmit, Sundar Ganesan, Vijayaraj Nagarajan, Richard T Eastman, Marlene S Orandle, John C Tan, Timothy G Myers, Shengfa Liu, Carole A Long, Jian Li, Xin-Zhuan Su
Infection of mice with strains of Plasmodium yoelii parasites can result in different pathology, but molecular mechanisms to explain this variation are unclear. Here we show that a P. yoelii gene encoding a HECT-like E3 ubiquitin ligase (Pyheul) influences parasitemia and host mortality. We genetically cross two lethal parasites with distinct disease phenotypes, and identify 43 genetically diverse progeny by typing with microsatellites and 9230 single-nucleotide polymorphisms. A genome-wide quantitative trait loci scan links parasite growth and host mortality to two major loci on chromosomes 1 and 7 with LOD (logarithm of the odds) scores = 6...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28790145/inter-chromosomal-transfer-of-immune-regulation-during-infection-of-barley-with-the-powdery-mildew-pathogen
#18
Priyanka Surana, Ruo Xu, Gregory Fuerst, Antony Ve Chapman, Dan Nettleton, Roger P Wise
Powdery mildew pathogens colonize over 9,500 plant species, causing critical yield loss. The Ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causes powdery mildew disease in barley (Hordeum vulgare L.). Successful infection begins with penetration of host epidermal cells, culminating in haustorial feeding structures, facilitating delivery of fungal effectors to the plant and exchange of nutrients from host to pathogen. We used expression Quantitative Trait Locus (eQTL) analysis to dissect the temporal control of immunity-associated gene expression in a doubled haploid barley population challenged with Bgh Two highly significant regions possessing trans eQTL were identified near the telomeric ends of chromosomes 2HL and 1HS...
August 8, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28769970/genetic-diversity-within-a-global-panel-of-durum-wheat-triticum-durum-landraces-and-modern-germplasm-reveals-the-history-of-alleles-exchange
#19
Hafssa Kabbaj, Amadou T Sall, Ayed Al-Abdallat, Mulatu Geleta, Ahmed Amri, Abdelkarim Filali-Maltouf, Bouchra Belkadi, Rodomiro Ortiz, Filippo M Bassi
Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28769912/xanthomonas-citri-minc-oscillates-from-pole-to-pole-to-ensure-proper-cell-division-and-shape
#20
André S G Lorenzoni, Giordanni C Dantas, Tessa Bergsma, Henrique Ferreira, Dirk-Jan Scheffers
Xanthomonas citri (Xac) is the causal agent of citrus canker, a disease that affects citrus crops and causes economic impact worldwide. To further characterize cell division in this plant pathogen, we investigated the role of the protein MinC in cell division, chromosome segregation, and peptidoglycan incorporation by deleting the gene minC using allele exchange. Xac with minC deleted exhibited the classic Δmin phenotype observed in other bacteria deleted for min components: minicells and short filamentation...
2017: Frontiers in Microbiology
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