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Allelic exchange

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https://www.readbyqxmd.com/read/28087731/increased-nbcn1-expression-na-hco3-co-transport-and-intracellular-ph-in-human-vascular-smooth-muscle-cells-with-a-risk-allele-for-hypertension
#1
Fu Liang Ng, Ebbe Boedtkjer, Katarzyna Witkowska, Meixia Ren, Ruoxin Zhang, Arthur Tucker, Christian Aalkjær, Mark J Caulfield, Shu Ye
Genome-wide association studies have revealed an association between variation at the SLC4A7 locus and blood pressure. SLC4A7 encodes the electroneutral Na(+)/HCO3 co-transporter NBCn1 which regulates intracellular pH (pHi). We conducted a functional study of variants at this locus in primary cultures of vascular smooth muscle and endothelial cells. In both cell types, we found genotype-dependent differences for rs13082711 in DNA-nuclear protein interactions, where the risk allele is associated with increased SLC4A7 expression level, NBCn1 availability and function as reflected in elevated steady-state pHi and accelerated recovery from intracellular acidosis...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28077981/dna-polymerase-kappa-protects-human-cells-against-mmc-induced-genotoxicity-through-error-free-translesion-dna-synthesis
#2
Yuki Kanemaru, Tetsuya Suzuki, Akira Sassa, Kyomu Matsumoto, Noritaka Adachi, Masamitsu Honma, Satoshi Numazawa, Takehiko Nohmi
BACKGROUND: Interactions between genes and environment are critical factors for causing cancer in humans. The genotoxicity of environmental chemicals can be enhanced via the modulation of susceptible genes in host human cells. DNA polymerase kappa (Pol κ) is a specialized DNA polymerase that plays an important role in DNA damage tolerance through translesion DNA synthesis. To better understand the protective roles of Pol κ, we previously engineered two human cell lines either deficient in expression of Pol κ (KO) or expressing catalytically dead Pol κ (CD) in Nalm-6-MSH+ cells and examined cytotoxic sensitivity against various genotoxins...
2017: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
https://www.readbyqxmd.com/read/28068993/improvement-of-yeast-tolerance-to-acetic-acid-through-haa1-transcription-factor-engineering-towards-the-underlying-mechanisms
#3
Steve Swinnen, Sílvia F Henriques, Ranjan Shrestha, Ping-Wei Ho, Isabel Sá-Correia, Elke Nevoigt
BACKGROUND: Besides being a major regulator of the response to acetic acid in Saccharomyces cerevisiae, the transcription factor Haa1 is an important determinant of the tolerance to this acid. The engineering of Haa1 either by overexpression or mutagenesis has therefore been considered to be a promising avenue towards the construction of more robust strains with improved acetic acid tolerance. RESULTS: By applying the concept of global transcription machinery engineering to the regulon-specific transcription factor Haa1, a mutant allele containing two point mutations could be selected that resulted in a significantly higher acetic acid tolerance as compared to the wild-type allele...
January 9, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28066509/development-and-implementation-of-rapid-metabolic-engineering-tools-for-chemical-and-fuel-production-in-geobacillus-thermoglucosidasius-ncimb-11955
#4
Lili Sheng, Katalin Kovács, Klaus Winzer, Ying Zhang, Nigel Peter Minton
BACKGROUND: The thermophile Geobacillus thermoglucosidasius has considerable attraction as a chassis for the production of chemicals and fuels. It utilises a wide range of sugars and oligosaccharides typical of those derived from lignocellulose and grows at elevated temperatures. The latter improves the rate of feed conversion, reduces fermentation cooling costs and minimises the risks of contamination. Full exploitation of its potential has been hindered by a dearth of effective gene tools...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28044416/identification-and-characterization-a-novel-hla-a-allele-a-02-355-by-sequence-based-typing-in-a-chinese-potential-donor
#5
X-M Nie, Y Zhang, W-B Qiao, C-F Zhu, Y-R Zhao
The new allele A*02:355 differs from A* 02:03:01 at positions 98 (T→A) and 102(A→C) resulting in an amino acid exchange F9→T. Interallelic sequence exchange is more likely the mechanism of its origination. The amino acid replacement influences the HLA peptide binding cleft and might have significant functional effects.
January 2, 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28039138/an-effective-counterselection-system-for-listeria-monocytogenes-and-its-use-to-characterize-10403s-strain-monocin-genomic-region
#6
Tal Argov, Lev Rabinovich, Nadejda Sigal, Anat A Herskovits
Construction of Listeria monocytogenes mutants by allelic exchange has been laborious and time consuming due to lack of proficient selection markers for the final recombination event. That is, a marker conveying substance sensitivity to the bacteria bearing it, enabling the exclusion of merodiploids and selection for plasmid loss. In order to address this issue, we engineered a counterselection marker based on a mutated phenylalanyl-tRNA synthetase gene (pheS*). This mutation renders the phenylalanine-binding site of the enzyme more promiscuous and allows the binding of the toxic p-chloro-phenylalanine analog (p-Cl-phe) as a substrate...
December 30, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28032472/hla-c-07-544-a-novel-hla-c-07-variant-detected-in-a-taiwanese-bone-marrow-donor
#7
K L Yang, P Y Lin
One nucleotide exchange at residue 768 of the HLA-C*07:02:01:01 results in a novel allele, HLA-C*07:544.
December 29, 2016: HLA
https://www.readbyqxmd.com/read/28007837/the-impact-of-open-pollination-on-the-structural-evolutionary-dynamics-meiotic-behavior-and-fertility-of-resynthesized-allotetraploid-brassica-napus-l
#8
Mathieu Rousseau-Gueutin, Jérôme Morice, Olivier Coriton, Virginie Huteau, Gwenn Trotoux, Sylvie Nègre, Cyril Falentin, Gwennaëlle Deniot, Marie Gilet, Frédérique Eber, Alexandre Pelé, Sonia Vautrin, Joëlle Fourment, Maryse Lodé, Hélène Bergès, Anne-Marie Chèvre
Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination...
December 22, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28007835/paralog-specific-functions-of-rpl7a-and-rpl7b-mediated-by-ribosomal-protein-or-snorna-dosage-in-saccharomyces-cerevisiae
#9
Ryan J Palumbo, Gabriele Fuchs, Sheila Lutz, M Joan Curcio
Most ribosomal proteins in Saccharomyces cerevisiae are encoded by two paralogs that additively produce the optimal protein level for cell growth. Nonetheless, deleting one paralog of most ribosomal protein gene pairs results in a variety of phenotypes not observed when the other paralog is deleted. To determine whether paralog-specific phenotypes associated with deleting RPL7A or RPL7B stem from distinct functions or different levels of the encoded isoforms, the coding region and introns of one paralog, including an intron-embedded snoRNA (small nucleolar RNA) gene, were exchanged with that of the other paralog...
December 22, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27998798/recursions-for-the-exchangeable-partition-function-of-the-seedbank-coalescent
#10
Noemi Kurt, Mathias Rafler
For the seedbank coalescent with mutation under the infinite alleles assumption, which describes the gene genealogy of a population with a strong seedbank effect subject to mutations, we study the distribution of the final partition with mutation. This generalizes the coalescent with freeze by Dong et al. (2007) to coalescents where ancestral lineages are blocked from coalescing. We derive an implicit recursion which we show to have a unique solution and give an interpretation in terms of absorption problems of a random walk...
December 18, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27990727/coupling-sensitive-nucleic-acid-amplification-with-commercial-pregnancy-test-strips
#11
Yan Du, Arti Pothukuchy, Jimmy D Gollihar, Armin Nourani, Bingling Li, Andrew D Ellington
The detection of nucleic acid biomarkers for point-of-care (POC) diagnostics is currently limited by technical complexity, cost, and time constraints. To overcome these shortcomings, we have combined loop-mediated isothermal amplification (LAMP), programmable toehold-mediated strand-exchange signal transduction, and standard pregnancy test strips. The incorporation of an engineered hCG-SNAP fusion reporter protein (human chorionic gonadotropin-O(6) -alkylguanine-DNA alkyltransferase) led to LAMP-to-hCG signal transduction on low-cost, commercially available pregnancy test strips...
December 19, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27965242/genome-wide-genotyping-by-sequencing-data-provide-a-high-resolution-view-of-wild-helianthus-diversity-genetic-structure-and-interspecies-gene-flow
#12
Gregory J Baute, Gregory L Owens, Dan G Bock, Loren H Rieseberg
PREMISE: Wild sunflowers harbor considerable genetic diversity and are a major resource for improvement of the cultivated sunflower, Helianthus annuus. The Helianthus genus is also well known for its propensity for gene flow between taxa. METHODS: We surveyed genomic diversity of 292 samples of wild Helianthus from 22 taxa that are cross-compatible with the cultivar using genotyping by sequencing. With these data, we derived a high-resolution phylogeny of the taxa, interrogated genome-wide levels of diversity, explored H...
December 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27931869/a-genetic-overview-of-atlantic-coastal-populations-from-europe-and-north-west-africa-based-on-a-17-x-str-panel
#13
Endika Prieto-Fernández, Ana Díaz-de Usera, Miriam Baeta, Carolina Núñez, Faiza Chbel, Sellama Nadifi, Karen Rouault, Claude Férec, Orla Hardiman, Fátima Pinheiro, Marian M de Pancorbo
The forensic use of X-STRs requires the creation of allele and haplotype frequency databases in the populations where they are going to be used. Recently, an updated Spanish allele and haplotype frequency database for the new 17 X-STR panel has been created, being the only database available up to now for this new multiplex. In order to broaden the forensic applicability of the 17 X-STR panel, 513 individuals from four different populations located on the Atlantic Coast of Europe and North-West Africa have been studied, i...
November 30, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27907066/b-cell-based-seamless-engineering-of-antibody-fc-domains
#14
Koji Hashimoto, Kohei Kurosawa, Akiho Murayama, Hidetaka Seo, Kunihiro Ohta
Engineering of monoclonal antibodies (mAbs) enables us to obtain mAbs with additional functions. In particular, modifications in antibody's Fc (fragment, crystallizable) region can provide multiple benefits such as added toxicity by drug conjugation, higher affinity to Fc receptors on immunocytes, or the addition of functional modules. However, the generation of recombinant antibodies requires multiple laborious bioengineering steps. We previously developed a technology that enables rapid in vitro screening and isolation of specific mAb-expressing cells from the libraries constructed with chicken B-cell line DT40 (referred to as the 'ADLib system')...
2016: PloS One
https://www.readbyqxmd.com/read/27884809/construction-of-a-streptococcus-agalactiae-phob-mutant-and-evaluation-of-its-potential-as-an-attenuated-modified-live-vaccine-in-golden-pompano-trachinotus-ovatus
#15
Xiaohui Cai, Bei Wang, Yinhui Peng, Yuan Li, Yishan Lu, Yucong Huang, Jichang Jian, Zaohe Wu
Streptococcus agalactiae is a Gram-positive pathogen that can survive inside professional phagocytes and nonphagocytic cells to cause septicemia and meningoencephalitis in freshwater and marine fish. However, vaccines based on extracellular products (ECP) and formalin-killed whole S. agalactiae cells, as well as subunit vaccine are unable to protect fish from infection by variant serotypes S. agalactiae. The search for live attenuated vaccine with highly conserved and virulent-related genes is essential for producing a vaccine to help understand and control streptococcosis In this study, the phoB gene was cloned from pathogenic S...
November 21, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27879314/genetic-variation-in-the-slc8a1-calcium-signaling-pathway-is-associated-with-susceptibility-to-kawasaki-disease-and-coronary-artery-abnormalities
#16
Chisato Shimizu, Hariklia Eleftherohorinou, Victoria J Wright, Jihoon Kim, Martin P Alphonse, James C Perry, Rolando Cimaz, David Burgner, Nagib Dahdah, Long T Hoang, Chiea Chuen Khor, Andrea Salgado, Adriana H Tremoulet, Sonia Davila, Taco W Kuijpers, Martin L Hibberd, Todd A Johnson, Atsushi Takahashi, Tatsuhiko Tsunoda, Michiaki Kubo, Toshihiro Tanaka, Yoshihiro Onouchi, Rae S M Yeung, Lachlan J M Coin, Michael Levin, Jane C Burns
BACKGROUND: Kawasaki disease (KD) is an acute pediatric vasculitis in which host genetics influence both susceptibility to KD and the formation of coronary artery aneurysms. Variants discovered by genome-wide association studies and linkage studies only partially explain the influence of genetics on KD susceptibility. METHODS AND RESULTS: To search for additional functional genetic variation, we performed pathway and gene stability analysis on a genome-wide association study data set...
December 2016: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/27836845/development-of-a-high-efficiency-transformation-method-and-implementation-of-rational-metabolic-engineering-for-the-industrial-butanol-hyperproducer-clostridium-saccharoperbutylacetonicum-strain-n1-4
#17
Nicolaus A Herman, Jeffrey Li, Ripika Bedi, Barbara Turchi, Xiaoji Liu, Michael J Miller, Wenjun Zhang
: While a majority of academic studies concerning acetone, butanol, and ethanol (ABE) production by Clostridium have focused on Clostridium acetobutylicum, other members of this genus have proven to be effective industrial workhorses despite the inability to perform genetic manipulations on many of these strains. To further improve the industrial performance of these strains in areas such as substrate usage, solvent production, and end product versatility, transformation methods and genetic tools are needed to overcome the genetic intractability displayed by these species...
January 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27833122/re-visiting-the-protamine-2-locus-deletion-but-not-haploinsufficiency-renders-male-mice-infertile
#18
Simon Schneider, Melanie Balbach, Jan F Jikeli, Daniela Fietz, Daniel Nettersheim, Sina Jostes, Rovenna Schmidt, Monika Kressin, Martin Bergmann, Dagmar Wachten, Klaus Steger, Hubert Schorle
Protamines are arginine-rich DNA-binding proteins that replace histones in elongating spermatids. This leads to hypercondensation of chromatin and ensures physiological sperm morphology, thereby protecting DNA integrity. In mice and humans, two protamines, protamine-1 (Prm1) and protamine-2 (Prm2) are expressed in a species-specific ratio. In humans, alterations of this PRM1/PRM2 ratio is associated with subfertility. By applying CRISPR/Cas9 mediated gene-editing in oocytes, we established Prm2-deficient mice...
November 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27827392/mhc-class-ii-complexes-sample-intermediate-states-along-the-peptide-exchange-pathway
#19
Marek Wieczorek, Jana Sticht, Sebastian Stolzenberg, Sebastian Günther, Christoph Wehmeyer, Zeina El Habre, Miguel Álvaro-Benito, Frank Noé, Christian Freund
The presentation of peptide-MHCII complexes (pMHCIIs) for surveillance by T cells is a well-known immunological concept in vertebrates, yet the conformational dynamics of antigen exchange remain elusive. By combining NMR-detected H/D exchange with Markov modelling analysis of an aggregate of 275 microseconds molecular dynamics simulations, we reveal that a stable pMHCII spontaneously samples intermediate conformations relevant for peptide exchange. More specifically, we observe two major peptide exchange pathways: the kinetic stability of a pMHCII's ground state defines its propensity for intrinsic peptide exchange, while the population of a rare, intermediate conformation correlates with the propensity of the HLA-DM-catalysed pathway...
November 9, 2016: Nature Communications
https://www.readbyqxmd.com/read/27827008/homologous-recombination-and-xylella-fastidiosa-host-pathogen-associations-in-south-america
#20
Helvecio Coletta-Filho, Carolina Francisco, Joao Lopes, Christiane Muller, Rodrigo Almeida
Homologous recombination impacts the evolution of bacteria such as Xylella fastidiosa, a naturally competent plant pathogen that requires insect vectors for dispersal. This bacterial species is taxonomically divided into subspecies, with phylogenetic clusters within subspecies that are host specific. One subspecies, pauca, is primarily limited to South America, with the exception of recently reported strains in Europe and Costa Rica. Despite the economic importance of X. fastidiosa subsp. pauca in South America, little is known about its genetic diversity...
November 9, 2016: Phytopathology
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