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https://www.readbyqxmd.com/read/29147935/nucleotide-and-octapeptide-repeat-variations-of-the-prion-protein-coding-gene-prnp-in-anatolian-murrah-and-crossbred-water-buffaloes
#1
Yalçın Yaman, Cemal Ün
Resistance to bovine spongiform encephalopathy (BSE) that is significantly associated with insertion/deletion (indel) polymorphisms at two loci (putative promoter and intron 1) on the prion protein gene (PRNP) in cattle has been well documented. Studies suggest that the insertion alleles are related to BSE resistance. Until recently, BSE has never been reported in water buffaloes (unlike cattle). Previous studies have demonstrated that the PRNP gene in water buffalo consists mostly of insertion alleles at both loci; nevertheless, whether or not water buffaloes are genetically resistant to BSE and the role of indel polymorphisms in their resistance status is not clear...
November 16, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/29143187/multi-locus-sequence-typing-of-african-swine-fever-viruses-from-endemic-regions-of-kenya-and-eastern-uganda-2011-2013-reveals-rapid-b602l-central-variable-region-evolution
#2
C K Onzere, A D Bastos, E A Okoth, J K Lichoti, E N Bochere, M G Owido, G Ndambuki, M Bronsvoort, R P Bishop
The central variable region (CVR) within the B602L gene of the African swine fever virus (ASFV) is highly polymorphic within the 23 ASFV genotypes defined by sequencing of the C-terminal end of the p72 locus. Sequencing the p54 gene further discriminates ASFV genotypes that are conserved at the p72 locus. Variation in the thymidine kinase locus is a novel additional tool for ASFV genotyping whose application for this purpose is described for the first time herein. We evaluated genetic variation at these four polymorphic loci in 39 ASFV isolates obtained from outbreaks in Kenya and a region of Eastern Uganda between 2011 and 2013...
November 15, 2017: Virus Genes
https://www.readbyqxmd.com/read/29132312/genomic-analysis-of-endemic-clones-of-toxigenic-and-non-toxigenic-corynebacterium-diphtheriae-in-belarus-during-and-after-the-major-epidemic-in-1990s
#3
Steffen Grosse-Kock, Valentina Kolodkina, Edward C Schwalbe, Jochen Blom, Andreas Burkovski, Paul A Hoskisson, Sylvain Brisse, Darren Smith, Iain C Sutcliffe, Leonid Titov, Vartul Sangal
BACKGROUND: Diphtheria remains a major public health concern with multiple recent outbreaks around the world. Moreover, invasive non-toxigenic strains have emerged globally causing severe infections. A diphtheria epidemic in the former Soviet Union in the 1990s resulted in ~5000 deaths. In this study, we analysed the genome sequences of a collection of 93 C. diphtheriae strains collected during and after this outbreak (1996 - 2014) in a former Soviet State, Belarus to understand the evolutionary dynamics and virulence capacities of these strains...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29116063/-myc-gene-family-in-cereals-transformations-during-evolution-of-hexaploid-bread-wheat-and-its-relatives
#4
K V Strygina, E K Khlestkina
The transcription factors of the MYC gene family are an integral part of the MYB + MYC + WD40 regulatory complex required to activate the genes of plant flavonoid biosynthesis. The TaMyc1 gene, which controls the synthesis of flavonoid pigments in the grain pericarp, is known in bread wheat (Triticum aestivum L., BBAADD genome, 2n = 6x = 42). In the present work, we identified 10 copies of this gene in the T. aestivum genome, 22 copies in the nearest bread wheat relatives (T. durum, T. urartu, T. monococcum, Aegilops speltoides, Ae...
September 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29114575/prediction-of-a-highly-deleterious-mutation-e17k-in-akt-1-gene-an-in-silico-approach
#5
Imran Khan, Irfan A Ansari
The AKT1 (v-akt murine thymoma viral oncogene homologue 1) kinase is a member of most frequently activated proliferation and survival signaling pathway in cancer. Recently, hyperactivation of AKT1, due to functional point mutation in the pleckstrin homology (PH) domain of AKT1 gene, has been found to be associated with human colorectal, breast and ovarian cancer. Thus, considering its crucial role in cellular signaling pathway, a functional analysis of missense mutations of AKT1 gene was undertaken in this study...
July 2017: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/29109707/genomic-comparisons-reveal-microevolutionary-differences-in-mycobacterium-abscessus-subspecies
#6
Joon L Tan, Kee P Ng, Chia S Ong, Yun F Ngeow
Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29106622/a-light-sensitive-mutation-in-arabidopsis-lew3-reveals-the-important-role-of-n-glycosylation-in-root-growth-and-development
#7
Concepción Manzano, Mercedes Pallero-Baena, J Silva-Navas, Sara Navarro Neila, Ilda Casimiro, Pedro Casero, Jose M Garcia-Mina, Roberto Baigorri, Lourdes Rubio, Jose A Fernandez, Matthew Norris, Yiliang Ding, Miguel A Moreno-Risueno, Juan C Del Pozo
Plant roots have the potential capacity to grow almost indefinitely if meristematic and lateral branching is sustained. In a genetic screen we identified an Arabidopsis mutant showing limited root growth (lrg1) due to defects in cell division and elongation in the root meristem. Positional cloning determined that lrg1 affects an alpha-1,2-mannosyltransferase gene, LEW3, involved in protein N-glycosylation. The lrg1 mutation causes a synonymous substitution that alters the correct splicing of the fourth intron in LEW3, causing a mix of wild-type and truncated protein...
November 2, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29090506/-minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding
#8
Anabel Rodriguez, Gabriel Wright, Scott Emrich, Patricia L Clark
Most amino acids can be encoded by more than one synonymous codon, but these are rarely used with equal frequency. In many coding sequences the usage patterns of rare versus common synonymous codons is non-random and under selection. Moreover, synonymous substitutions that alter these patterns can have a substantial impact on the folding efficiency of the encoded protein. This has ignited broad interest in exploring synonymous codon usage patterns. For many protein chemists, biophysicists and structural biologists, the primary motivation for codon analysis is identifying and preserving usage patterns most likely to impact high-yield production of functional proteins...
November 1, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29089942/the-possible-influence-of-non-synonymous-point-mutations-within-the-fima-adhesin-of-non-typhoidal-salmonella-nts-isolates-in-the-process-of-host-adaptation
#9
Sahar Alshalchi, Shivdeep S Hayer, Ran An, Jeannette Munoz-Aguayo, Christian Flores-Figueroa, Ryan Nguyen, Dale Lauer, Karen Olsen, Julio Alvarez, David Boxrud, Carol Cardona, Sinisa Vidovic
Non-typhoidal Salmonella (NTS) remains a global pathogen that affects a wide range of animal species. We analyzed a large number of NTS isolates of different host origins, including Salmonella Heidelberg (n = 80, avian), S. Dublin (50, bovine), S. Typhimurium var 5- (n = 40, porcine), S. 4,5,12,:i:- (n = 40, porcine), S. Cerro (n = 16, bovine), and S. Montevideo (n = 14, bovine), using virulence profiling of the bcfC, mgtC, ssaC, invE, pefA, stn, sopB, and siiE virulence-associated genes, a biofilm production assay, pulsed field gel electrophoresis, and the full-length sequencing of the fimA (adhesin) and iroN (receptor) genes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29084015/molecular-characterization-of-glanzmann-s-thrombasthenia-in-iran-identification-of-three-novel-mutations
#10
Ahmad Kazemi, Hassan Abolghasemi, Shima Kazemzadeh, Reza Vahidi, Mohammad Faranoush, Alireza Farsinejad, Fereydoun Ala
: Quantitative and/or qualitative defects of the platelet membrane glycoprotein IIb/IIIa complex lead to the clinical entity of Glanzmann's thrombasthenia. A large variety of mutations and polymorphisms are responsible for the aberrant expression and defective activity of this heterodimeric complex. The current study aimed to determine the pattern of mutations among Iranian population with Glanzmann's thrombasthenia. A total of 20 patients with Glanzmann's thrombasthenia have been evaluated. All exons and splice sites of ITGA2B and ITGB3 genes were amplified using touchdown PCR...
October 27, 2017: Blood Coagulation & Fibrinolysis: An International Journal in Haemostasis and Thrombosis
https://www.readbyqxmd.com/read/29073068/evidence-of-evolutionary-selection-for-cotranslational-folding
#11
William M Jacobs, Eugene I Shakhnovich
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from cotranslational folding remain open questions. Here we report a genome-wide analysis that uncovers evidence of evolutionary selection for cotranslational folding. We describe a robust statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved. Surprisingly, we find that domain boundaries can explain only a small fraction of these conserved loci...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29052764/fine-mapping-and-candidate-gene-analysis-of-the-virescent-gene-v-1-in-upland-cotton-gossypium-hirsutum
#12
Guangzhi Mao, Qiang Ma, Hengling Wei, Junji Su, Hantao Wang, Qifeng Ma, Shuli Fan, Meizhen Song, Xianlong Zhang, Shuxun Yu
The young leaves of virescent mutants are yellowish and gradually turn green as the plants reach maturity. Understanding the genetic basis of virescent mutants can aid research of the regulatory mechanisms underlying chloroplast development and chlorophyll biosynthesis, as well as contribute to the application of virescent traits in crop breeding. In this study, fine mapping was employed, and a recessive gene (v 1) from a virescent mutant of Upland cotton was narrowed to an 84.1-Kb region containing ten candidate genes...
October 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29052098/comparative-transcriptome-analysis-reveals-whole-genome-duplications-and-gene-selection-patterns-in-cultivated-and-wild-chrysanthemum-species
#13
So Youn Won, Soo-Jin Kwon, Tae-Ho Lee, Jae-A Jung, Jung Sun Kim, Sang-Ho Kang, Seong-Han Sohn
Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species. Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C...
October 19, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29043885/first-report-of-hb-kent-%C3%AE-37-c3-trp%C3%A2-cys-tgg-tgc-hbb-c-114g-c-in-a-chinese-family
#14
Nelson C N Chan, King-Ho Chow, Rico F Y Leung, Sequence S H Tang, Michelle F W Chiu, Rosalind Lie, Kelvin C K Cheng, Kin-Mang Lau, Natalie P H Chan, Margaret H L Ng
We report a novel HBB: c.114G>C mutation in a Chinese family. This mutation resulted in a β37(C3)Trp→Cys amino acid substitution and was synonymous with Hb Kent, a hemoglobin (Hb) variant that was reported exclusively in patients of European descent. Though Hb Kent has a normal oxygen affinity and molecular stability, it has a characteristic dual variant appearance on cellulose acetate electrophoresis (CAE) and high performance liquid chromatography (HPLC) caused by the posttranslational modification of cysteine...
October 18, 2017: Hemoglobin
https://www.readbyqxmd.com/read/29042507/selection-of-functional-2a-sequences-within-foot-and-mouth-disease-virus-requirements-for-the-npgp-motif-with-a-distinct-codon-bias
#15
Jonas Kjær, Graham J Belsham
Foot-and-mouth disease virus (FMDV) has a positive-sense ssRNA genome including a single, large, open reading frame. Splitting of the encoded polyprotein at the 2A/2B junction is mediated by the 2A peptide (18 residues long) which induces a non-proteolytic, co-translational, "cleavage" at its own C-terminus. A conserved feature among variants of 2A is the C-terminal motif N16P17G18/P19 where P19 is the first residue of 2B. It has been shown previously that certain amino acid substitutions can be tolerated at residues E14, S15 and N16 within the 2A sequence of infectious FMDVs but no variants at residues P17, G18 or P19 have been identified...
October 17, 2017: RNA
https://www.readbyqxmd.com/read/29040697/mapping-selection-within-drosophila-melanogaster-embryo-s-anatomy
#16
Irepan Salvador-Martínez, Marta Coronado-Zamora, David Castellano, Antonio Barbadilla, Isaac Salazar-Ciudad
We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns and development, with the aim of mapping adaptation over the entire embryo's anatomy. Our adaptation map is based on analyzing spatial gene expression information for 5,969 genes (from text-based annotations of in situ hybridization data directly from the BDGP database, Tomancak et al. 2007) and the polymorphism and divergence in these genes (from the project DGRP, Mackay et al...
October 10, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29037158/genomic-divergence-and-cohesion-in-a-species-of-pelagic-freshwater-bacteria
#17
Matthias Hoetzinger, Martin W Hahn
BACKGROUND: In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity - i.e. elevated geographic barriers to gene flow - is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29026650/accurate-quantification-of-within-and-between-host-hbv-evolutionary-rates-requires-explicit-transmission-chain-modelling
#18
Bram Vrancken, Marc A Suchard, Philippe Lemey
Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/29026213/genomic-divergence-within-non-photosynthetic-cyanobacterial-endosymbionts-in-rhopalodiacean-diatoms
#19
Takuro Nakayama, Yuji Inagaki
Organelle acquisitions via endosymbioses with prokaryotes were milestones in the evolution of eukaryotes. Still, quite a few uncertainties have remained for the evolution in the early stage of organellogenesis. In this respect, rhopalodiacean diatoms and their obligate cyanobacterial endosymbionts, called spheroid bodies, are emerging as new models for the study of organellogenesis. The genome for the spheroid body of Epithemia turgida, a rhopalodiacean diatom, has unveiled its unique metabolic nature lacking the photosynthetic ability...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29022133/arginine-kinases-from-the-precious-corals-corallium-rubrum-and-paracorallium-japonicum-presence-of-two-distinct-arginine-kinase-gene-lineages-in-cnidarians
#20
Tomoka Matsuo, Daichi Yano, Kouji Uda, Nozomu Iwasaki, Tomohiko Suzuki
The cDNA sequence of arginine kinase (AK) from the precious coral Corallium rubrum was assembled from transcriptome sequence data, and the deduced amino acid sequence of 364 residues was shown to conserve the structural features characteristic of AK. Based on the amino acid sequence, the DNA coding C. rubrum AK was synthesized by overlap extension PCR to prepare the recombinant enzyme. The following kinetic parameters were determined for the C. rubrum enzyme: K a(Arg) (0.10 mM), K ia(Arg) (0.79 mM), K a(ATP) (0...
October 11, 2017: Protein Journal
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