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Allelic exchange

Takumi Takeuchi, Mami Hattori-Kato, Yumiko Okuno, Atsushi Kanatani, Masayoshi Zaitsu, Koji Mikami
Various conditions including distal renal tubular acidosis (dRTA) can induce stone formation in the kidney. dRTA is characterized by an impairment of urine acidification in the distal nephron. dRTA is caused by variations in genes functioning in intercalated cells including SLC4A1/AE1/Band3 transcribing two kinds of mRNAs encoding the Cl(-)/HCO3(-) exchanger in erythrocytes and that expressed in α-intercalated cells (kAE1). With the acid-loading test, 25% of urolithiasis patients were diagnosed with incomplete dRTA...
October 21, 2016: Scientific Reports
Chao Tan, Jun Wang, Yifang Hu, Peng Wang, Lili Zou
Staphylococcus aureus and Staphylococcus epidermidis are two of the most significant opportunistic human pathogens, causing medical implant and nosocomial infections worldwide. These bacteria contain surface proteins that play crucial roles in multiple biological processes. It has become apparent that they have evolved a number of unique mechanisms by which they can immobilise proteins on their surface. Notably, a conserved cell membrane-anchored enzyme, sortase A (SrtA), can catalyse the covalent attachment of precursor bacterial cell wall-attached proteins to peptidoglycan...
October 18, 2016: Antonie Van Leeuwenhoek
Fu Liang Ng, Ebbe Boedtkjer, Shu Ye, Mark Caulfield
OBJECTIVE: Chromosome 3p24.1 containing the SLC4A7 gene has been identified by genome-wide association studies as one of the genomic loci that influence blood pressure. SLC4A7 encodes electroneutral Na/HCO3 co-transporter (NBCn1) which regulates intracellular pH (pHi) in various tissues including vascular smooth muscle and endothelium, with knockout models demonstrating an altered blood pressure phenotype. We conducted a functional study of blood pressure-associated single nucleotide polymorphisms at the SLC4A7 locus in primary cultures of human vascular smooth muscle and endothelial cells...
September 2016: Journal of Hypertension
Roberto Arrigoni, Francesca Benzoni, Tullia I Terraneo, Annalisa Caragnano, Michael L Berumen
Reticulate evolution, introgressive hybridisation, and phenotypic plasticity have been documented in scleractinian corals and have challenged our ability to interpret speciation processes. Stylophora is a key model system in coral biology and physiology, but genetic analyses have revealed that cryptic lineages concealed by morphological stasis exist in the Stylophora pistillata species complex. The Red Sea represents a hotspot for Stylophora biodiversity with six morphospecies described, two of which are regionally endemic...
October 7, 2016: Scientific Reports
Erika Darrah, AeRyon Kim, Xi Zhang, Tatiana Boronina, Robert N Cole, Andrea Fava, Jon T Giles, Clifton O Bingham Iii, Michael J Chalmers, Patrick R Griffin, Scheherazade Sadegh-Nasseri, Antony Rosen
Proteolysis of autoantigens can alter normal MHC class II antigen processing and has been implicated in the induction of autoimmune diseases. Many autoantigens are substrates for the protease granzyme B (GrB), but the mechanistic significance of this association is unknown. Peptidylarginine deiminase 4 (PAD4) is a frequent target of autoantibodies in patients with rheumatoid arthritis (RA) and a substrate for GrB. RA is strongly associated with specific MHC class II alleles, and elevated levels of GrB and PAD4 are found in the joints of RA patients, suggesting that GrB may alter presentation of PAD4 by RA-associated class II alleles...
October 4, 2016: Journal of Proteome Research
Marcia F Marston, Jennifer B H Martiny
Understanding the structure and origin of natural bacteriophage genomic diversity is important in elucidating how bacteriophages influence the mortality rates and composition of their host communities. Here we examine the genetic structure and genomic diversification of naturally occurring bacteriophages by analyzing the full genomic sequences of over 100 isolates of Synechococcus-infecting cyanophages collected over 15 years from coastal waters of Southern New England, USA. Our analysis revealed well-supported cyanophage genomic clusters (genome-wide average nucleotide identity (ANI) >93%) and subclusters (genome-wide ANI >98%) that remained consistent for a decade or longer...
October 1, 2016: Environmental Microbiology
T Brooke McClendon, Rana Mainpal, Francis Raj Gandhi Amrit, Michael W Krause, Arjumand Ghazi, Judith L Yanowitz
The germ line efficiently combats numerous genotoxic insults to ensure the high fidelity propagation of unaltered genomic information across generations. Yet, germ cells in most metazoans also intentionally create double-strand breaks (DSBs) to promote DNA exchange between parental chromosomes, a process known as crossing over. Homologous recombination is employed in the repair of both genotoxic lesions and programmed DSBs and many of the core DNA repair proteins function in both processes. In addition, DNA repair efficiency and crossover distribution are both influenced by local and global differences in chromatin structure, yet the interplay between chromatin structure, genome integrity, and meiotic fidelity is still poorly understand...
October 5, 2016: G3: Genes—Genomes—Genetics
Christina C Saak, Karine A Gibbs
Proteus mirabilis is a social bacterium that is capable of self (kin) versus non-self recognition. Swarming colonies of this bacterium expand outward on surfaces at centimeter-scale distances due to the collective motility of individual cells. Colonies of genetically distinct populations remain separate while those of identical populations merge. Ids proteins are essential for this recognition behavior. Two of these proteins, IdsD and IdsE, encode identity information for each strain. These two proteins bind in vitro in an allele-restrictive manner, and IdsD-IdsE binding is correlated with populations merging whereas a lack of binding correlates with populations separating...
September 26, 2016: Journal of Bacteriology
Selorme Adukpo, Ben A Gyan, Michael F Ofori, Daniel Dodoo, Thirumalaisamy P Velavan, Christian G Meyer
BACKGROUND: Malaria elicits inflammatory responses, which, if not well regulated, may exert detrimental effects. When activated, triggering receptor expressed on myeloid cells (TREM)-1 enhances inflammatory responses by increasing secretion of IL-8 and other Th1 cytokines. In contrast, TREM-like transcript 1 (TREML-1) promotes anti-inflammatory responses by binding to TREM-1 ligands and competing with TREM-1, thus antagonizing TREM-1 activation to reduce inflammation. Endothelial protein C receptor (EPCR) also mediates anti-inflammatory responses by activating endothelial protein C (PC)...
September 27, 2016: Tropical Medicine & International Health: TM & IH
Y F Pei, H N Huang, H C Li, G G Wu
HLA-A*33:88 differs from HLA-A*33:03:01 by one nucleotide exchange at position 475, G>A (codon 135 GCG>ACG).
November 2016: HLA
Fu Liang Ng, Ebbe Boedtkjer, Shu Ye, Mark Caulfield
OBJECTIVE: Chromosome 3p24.1 containing the SLC4A7 gene has been identified by genome-wide association studies as one of the genomic loci that influence blood pressure. SLC4A7 encodes electroneutral Na/HCO3 co-transporter (NBCn1) which regulates intracellular pH (pHi) in various tissues including vascular smooth muscle and endothelium, with knockout models demonstrating an altered blood pressure phenotype. We conducted a functional study of blood pressure-associated single nucleotide polymorphisms at the SLC4A7 locus in primary cultures of human vascular smooth muscle and endothelial cells...
September 2016: Journal of Hypertension
John Chattaway, R Andrei Ramirez-Valdez, Paul E Chappell, Joseph J E Caesar, Susan M Lea, Jim Kaufman
Mammalian butyrophilins have various important functions, one for lipid binding but others as ligands for co-inhibition of αβ T cells or for stimulation of γδ T cells in the immune system. The chicken BG homologues are dimers, with extracellular immunoglobulin variable (V) domains joined by cysteines in the loop equivalent to complementarity-determining region 1 (CDR1). BG genes are found in three genomic locations: BG0 on chromosome 2, BG1 in the classical MHC (the BF-BL region) and many BG genes in the BG region just outside the MHC...
September 2016: Open Biology
Moses C Wambulwa, Muditha K Meegahakumbura, Samson Kamunya, Alice Muchugi, Michael Möller, Jie Liu, Jian-Chu Xu, Sailesh Ranjitkar, De-Zhu Li, Lian-Ming Gao
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa...
2016: Frontiers in Plant Science
Pawel Bialk, Brett Sansbury, Natalia Rivera-Torres, Kevin Bloh, Dula Man, Eric B Kmiec
The repair of a point mutation can be facilitated by combined activity of a single-stranded oligonucleotide and a CRISPR/Cas9 system. While the mechanism of action of combinatorial gene editing remains to be elucidated, the regulatory circuitry of nucleotide exchange executed by oligonucleotides alone has been largely defined. The presence of the appropriate CRISPR/Cas9 system leads to an enhancement in the frequency of gene editing directed by single-stranded DNA oligonucleotides. While CRISPR/Cas9 executes double-stranded DNA cleavage efficiently, closure of the broken chromosomes is dynamic, as varying degrees of heterogeneity of the cleavage products appear to accompany the emergence of the corrected base pair...
2016: Scientific Reports
Candice Heath, Christine M Gillen, Panagiotis Chrysanthopoulos, Mark J Walker, Andrew C Barnes
Streptococcus iniae causes septicaemia and meningitis in marine and freshwater fish wherever they are farmed in warm-temperate and tropical regions. Although serotype specific, vaccination with bacterins (killed bacterial cultures) is largely successful and vaccine failure occurs only occasionally through emergence of new capsular serotypes. Previously we showed that mutations in vaccine escapes are restricted to a limited repertoire of genes within the 20-gene capsular polysaccharide (cps) operon. cpsG, a putative UDP-galactose 4-epimerase, has three sequence types based on the insertion or deletion of the three amino acids leucine, serine and lysine in the substrate binding site of the protein...
September 25, 2016: Veterinary Microbiology
Hans-Rolf Gregorius
: Admissible measures of diversity allow specification of the number of types (species, alleles, etc.) that are "effectively" involved in producing the diversity (the "diversity effective number", also referred to as "true diversity") of a community or population. In metacommunities, effective numbers additionally serve in partitioning the total diversity (symbolized by γ) into one component summarizing the diversity within communities (symbolized by α) and an independent component summarizing the differences between communities (symbolized by β)...
November 21, 2016: Journal of Theoretical Biology
Johanna Acevedo-Garcia, David Spencer, Hannah Thieron, Anja Reinstädler, Kim Hammond-Kosack, Andrew L Phillips, Ralph Panstruga
Wheat is one of the most widely grown cereal crops in the world and is an important food grain source for humans. However, wheat yields can be reduced by many abiotic and biotic stress factors, including powdery mildew disease caused by Blumeria graminis f.sp. tritici (Bgt). Generating resistant varieties is thus a major effort in plant breeding. Here, we took advantage of the non-transgenic Targeted Induced Lesions IN Genomes (TILLING) technology to select partial loss-of-function alleles of TaMlo, the orthologue of the barley Mlo (Mildew resistance locus o) gene...
August 27, 2016: Plant Biotechnology Journal
S Nadri, P Zamani, A Ahmadi
The BMP15 gene is a growth factor and a member of the transforming growth factor β (TGFβ) superfamily, specifically expressed in oocytes. In the present study, polymorphism of BMP15 gene exon 1 was studied using single strand conformational polymorphism (SSCP) and direct DNA sequencing methods in 170 Mehraban and Lori sheep ewes. A 231-bp fragment in BMP15 exon 1 was amplified by PCR reactions. Two genotypes (GG and AG) with a new point mutation at position 121 bp of the studied fragment (c.379G>A in reference GenBank number AF236078...
October 2016: Animal Biotechnology
Miguel Alvaro-Benito, Eliot Morrison, Marek Wieczorek, Jana Sticht, Christian Freund
Classical MHC class II (MHCII) proteins present peptides for CD4(+) T-cell surveillance and are by far the most prominent risk factor for a number of autoimmune disorders. To date, many studies have shown that this link between particular MHCII alleles and disease depends on the MHCII's particular ability to bind and present certain peptides in specific physiological contexts. However, less attention has been paid to the non-classical MHCII molecule human leucocyte antigen-DM, which catalyses peptide exchange on classical MHCII proteins acting as a peptide editor...
August 2016: Open Biology
Charles Darkoh, Chioma Odo, Herbert L DuPont
UNLABELLED: Clostridium difficile infection (CDI) is responsible for most of the definable cases of antibiotic- and hospital-associated diarrhea worldwide and is a frequent cause of morbidity and mortality in older patients. C. difficile, a multidrug-resistant anaerobic pathogen, causes disease by producing toxins A and B, which are controlled by an accessory gene regulator (Agr) quorum signaling system. Some C. difficile strains encode two Agr loci in their genomes, designated agr1 and agr2 The agr1 locus is present in all of the C...
2016: MBio
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