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nonsynonymous substitution

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https://www.readbyqxmd.com/read/28431152/insights-into-the-existence-of-isomeric-plastomes-in-cupressoideae-cupressaceae
#1
Xiao-Jian Qu, Chung-Shien Wu, Shu-Miaw Chaw, Ting-Shuang Yi
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28413183/a-slc24a2-gene-variant-uncovered-in-pancreatic-ductal-adenocarcinoma-by-whole-exome-sequencing
#2
Lei Wang, Zhuo Shao, Shiyue Chen, Lu Shi, Zhaoshen Li
Pancreatic ductal adenocarcinoma (PDAC) presents as an aggressive malignancy caused by environmental and genetic factors. In order to identify causal genes for PDAC, we performed whole exome sequencing (WES) to detect gene mutations in seven pairs of PDAC tissue and adjacent non-tumor tissue samples. Finally, we found a new nonsynonymous single nucleotide variant (nsSNV) in solute carrier 24 family member 2 (SLC24A2) gene resulting in the substitution of native glutamic acid (E) into aspartic acid (D) at position of 287 amino acid (E287D) in SLC24A2 protein, and confirmed this variant by Sanger gene sequencing...
April 2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28400484/amino-acid-polymorphisms-in-the-fibronectin-binding-repeats-of-fibronectin-binding-protein-a-affect-bond-strength-and-fibronectin-conformation
#3
Nadia N Casillas-Ituarte, Carlos H B Cruz, Roberto D Lins, Alex C DiBartola, Jessica Howard, Xiaowen Liang, Magnus Höök, Isabelle F T Viana, M Roxana Sierra-Hernández, Steven K Lower
The Staphylococcus aureus cell surface contains cell wall-anchored proteins such as fibronectin-binding protein A (FnBPA) that bind to host ligands (e.g. fibronectin; Fn) present in the extracellular matrix of tissue or coatings on cardiac implants. Recent clinical studies have found a correlation between cardiovascular infections caused by S. aureus and nonsynonymous single nucleotide polymorphisms (SNPs) in FnBPA. Atomic force microscopy (AFM), surface plasmon resonance (SPR), and molecular simulations were used to investigate interactions between Fn and each of eight, 20-mer peptide variants containing amino acids A, H, I, K, N, and Q at positions equivalent to 782 and/or 786 in Fn-binding repeat-9 (FnBR-9) of FnBPA...
April 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28397003/plastome-wide-nucleotide-substitution-rates-reveal-accelerated-rates-in-papilionoideae-and-correlations-with-genome-features-across-legume-subfamilies
#4
Erika N Schwarz, Tracey A Ruhlman, Mao-Lun Weng, Mohammad A Khiyami, Jamal S M Sabir, Nahid H Hajarah, Njud S Alharbi, Samar O Rabah, Robert K Jansen
This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids...
April 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28393414/role-of-seed-germination-in-adaptation-and-reproductive-isolation-in-arabidopsis-lyrata
#5
Tuomas Hämälä, Tiina M Mattila, Päivi H Leinonen, Helmi Kuittinen, Outi Savolainen
Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North-America). Post-dormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci (QTL) mapping revealed that the trait variation is mainly controlled by two antagonistic loci...
April 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28369607/the-influence-of-hiv-on-the-evolution-of-mycobacterium-tuberculosis
#6
Anastasia Koch, Daniela Brites, David Stucki, Joanna C Evans, Ronnett Seldon, Alexa Heekes, Nicola Mulder, Mark Nicol, Tolu Oni, Digby F Warner, Valerie Mizrahi, Julian Parkhill, Sebastien Gagneux, Darren P Martin, Robert J Wilkinson
HIV significantly affects the immunological environment during tuberculosis co-infection, and therefore may influence the selective landscape upon which M. tuberculosis evolves. To test this hypothesis whole genome sequences were determined for 169 South African M. tuberculosis strains from HIV-1 co-infected and uninfected individuals and analysed using two Bayesian codon-model based selection analysis approaches: FUBAR which was used to detect persistent positive and negative selection (selection respectively favouring and disfavouring nonsynonymous substitutions); and MEDS which was used to detect episodic directional selection specifically favouring nonsynonymous substitutions within HIV-1 infected individuals...
March 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28369510/antagonistic-coevolution-of-mer-tyrosine-kinase-expression-and-function
#7
Amanda L Evans, Jack W D Blackburn, Kyle Taruc, Angela Kipp, Brennan S Dirk, Nina R Hunt, Stephen D Barr, Jimmy D Dikeakos, Bryan Heit
TYRO3, AXL, and MERTK (TAM) receptors are a family of receptor tyrosine kinases that maintain homeostasis through the clearance of apoptotic cells, and when defective, contribute to chronic inflammatory and autoimmune diseases such as atherosclerosis, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and Crohn's disease. In addition, certain enveloped viruses utilize TAM receptors for immune evasion and entry into host cells, with several viruses preferentially hijacking MERTK for these purposes...
March 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28332757/selective-modes-determine-evolutionary-rates-gene-compactness-and-expression-patterns-in-brassica
#8
Yue Guo, Jing Liu, Jiefu Zhang, Shengyi Liu, Jianchang Du
It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories, i.e., positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (Ka) and the synonymous substitution (Ks) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa, and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs...
March 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28296211/deleterious-effects-of-nonsynonymous-single-nucleotide-variants-of-human-il-1%C3%AE-gene
#9
Yue-Hui Zhang, Jia Song, Jing Zhang, Jiang Shao
The IL-1β gene is currently topic of interest for its important role in the pathogenesis of intervertebral disc degeneration. The new sequencing technology makes it crucial to study the effects of variants in IL-1β. Thus, 714 IL-1β variants with evidence supporting were collected from the EMBL database. Among them, 62 were nonsynonymous single nucleotide variants (nsSNVs). Furthermore, six common nsSNVs were predicted to have damaging effects by SIFT, PolyPhen, PROVEAN and SNPs&GO. Based on the constructed three-dimensional structure of pro-IL-1β, rs375479974 with a mutation of Phe to Ser was proposed to reduce the stability of the pro-IL-1β protein...
March 15, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28288365/dexd-h-box-rna-helicase-genes-are-differentially-expressed-between-males-and-females-during-the-critical-period-of-male-sex-differentiation-in-channel-catfish
#10
Changxu Tian, Suxu Tan, Lisui Bao, Qifan Zeng, Shikai Liu, Yujia Yang, Xiaoxiao Zhong, Zhanjiang Liu
DExD/H-box RNA helicases are motor proteins participating in nearly all aspects of cellular processes, especially in RNA metabolism. In this study, a total of 54 DExD/H-box RNA helicase genes including 37 DDX (DEAD-box) and 17 DHX (DEAH-box) genes were characterized in channel catfish (Ictalurus punctatus), and annotated through phylogenetic and syntenic analyses. All the catfish RNA helicases contained conserved helicase signature motifs, demonstrating that the RNA helicase gene family was highly conserved...
March 1, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28282490/gene-augmentation-therapy-for-a-missense-substitution-in-the-cgmp-binding-domain-of-ovine-cnga3-gene-restores-vision-in-day-blind-sheep
#11
Elisha Gootwine, Mazen Abu-Siam, Alexey Obolensky, Alex Rosov, Hen Honig, Tali Nitzan, Andrey Shirak, Raaya Ezra-Elia, Esther Yamin, Eyal Banin, Edward Averbukh, William W Hauswirth, Ron Ofri, Eyal Seroussi
Purpose: Applying CNGA3 gene augmentation therapy to cure a novel causative mutation underlying achromatopsia (ACHM) in sheep. Methods: Impaired vision that spontaneously appeared in newborn lambs was characterized by behavioral, electroretinographic (ERG), and histologic techniques. Deep-sequencing reads of an affected lamb and an unaffected lamb were compared within conserved genomic regions orthologous to human genes involved in similar visual impairment. Observed nonsynonymous amino acid substitutions were classified by their deleteriousness score...
March 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28264646/strain-dependent-mutational-effects-for-pepino-mosaic-virus-in-a-natural-host
#12
Julia Minicka, Santiago F Elena, Natasza Borodynko-Filas, Błażej Rubiś, Beata Hasiów-Jaroszewska
BACKGROUND: Pepino mosaic virus (PepMV) is an emerging plant pathogen that infects tomatoes worldwide. Understanding the factors that influence its evolutionary success is essential for developing new control strategies that may be more robust against the evolution of new viral strains. One of these evolutionary factors is the distribution of mutational fitness effect (DMFE), that is, the fraction of mutations that are lethal, deleterious, neutral, and beneficial on a given viral strain and host species...
March 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28253868/selections-frameshift-mutations-and-copy-number-variation-detected-on-the-surf-4-1-gene-in-the-western-kenyan-plasmodium-falciparum-population
#13
Jesse N Gitaka, Mika Takeda, Masatsugu Kimura, Zulkarnain Md Idris, Chim W Chan, James Kongere, Kazuhide Yahata, Francis W Muregi, Yoshio Ichinose, Akira Kaneko, Osamu Kaneko
BACKGROUND: Plasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the infected red blood cell, whose gene was suggested to be under directional selection in the eastern Kenyan population, but under balancing selection in the Thai population. To understand this difference, surf 4.1 sequences of western Kenyan P. falciparum isolates were analysed. Frameshift mutations and copy number variation (CNV) were also examined for the parasites from western Kenya and Thailand...
March 2, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28253282/identification-of-extensive-drug-resistant-pseudomonas-aeruginosa-strains-new-clone-st1725-and-high-risk-clone-st233
#14
Pamela Aguilar-Rodea, Gerardo Zúñiga, Benjamín Antonio Rodríguez-Espino, Alma Lidia Olivares Cervantes, Ana Estela Gamiño Arroyo, Sarbelio Moreno-Espinosa, Daniela de la Rosa Zamboni, Briceida López Martínez, María Del Carmen Castellanos-Cruz, Israel Parra-Ortega, Verónica Leticia Jiménez Rojas, Juan Carlos Vigueras Galindo, Norma Velázquez-Guadarrama
Several microorganisms produce nosocomial infections (NIs), among which Pseudomonas aeruginosa stands out as an opportunist pathogen with the capacity to develop multiresistance to first-choice antibiotics. From 2007 to 2013, forty-six NIs produced by P. aeruginosa were detected at a pediatric tertiary care hospital in Mexico with a significant mortality rate (17.39%). All isolates (n = 58/46 patients) were characterized by evaluating their response to several antibiotics as panresistant (PDR), extensively resistant (XDR), multiresistant (MDR) or sensitive (S)...
2017: PloS One
https://www.readbyqxmd.com/read/28242674/in-vitro-activity-of-bedaquiline-against-nontuberculous-mycobacteria-in-china
#15
Yu Pang, Huiwen Zheng, Yaoju Tan, Yuanyuan Song, Yanlin Zhao
The main goal of our study was to evaluate in vitro drug susceptibility of bedaquiline against six prevalent pathogenic nontuberculous mycobacteria (NTM) diseases in China. In addition, we investigated the potential molecular mechanism contributing to the bedaquiline resistance in these different NTM species. For slowly growing mycobacteria (SGM), bedaquiline exhibited the highest activity against Mycobacterium avium, the MIC50 and MIC90 were 0.03 and 16 mg/L, respectively. Of rapidly growing mycobacteria (RGM), Mycobacterium abscessus subsp...
February 27, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28220980/the-fire-ant-social-chromosome-supergene-variant-sb-shows-low-diversity-but-high-divergence-from-sb
#16
Rodrigo Pracana, Anurag Priyam, Ilya Levantis, Richard A Nichols, Yannick Wurm
Variation in social behaviour is common, yet little is known about the genetic architectures underpinning its evolution. A rare exception is in the fire ant Solenopsis invicta: Alternative variants of a supergene region determine whether a colony will have exactly one or up to dozens of queens. The two variants of this region are carried by a pair of 'social chromosomes', SB and Sb, which resemble a pair of sex chromosomes. Recombination is suppressed between the two chromosomes in the supergene region. While the X-like SB can recombine with itself in SB/SB queens, recombination is effectively absent in the Y-like Sb because Sb/Sb queens die before reproducing...
February 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28198556/comparison-of-genetic-characteristics-in-the-evolution-of-norovirus-gii-4-and-gii-17
#17
Kohji Mori, Kazushi Motomura, Yoshiko Somura, Kana Kimoto, Tetsuya Akiba, Kenji Sadamasu
The genetic characteristics of Norovirus GII.17 were evaluated. Phylogenetic analysis and comparisons of amino acid (Aa) substitutions and nonsynonymous (NS) substitutions/site/year were performed. The complete VP1 sequence of Tokyo/27-3/1976 clustered independently with GII.P17_GII.17 strains. Aa substitutions were mainly accumulated in the P2 domain. NS substitutions/site/year for Tokyo/27-3/1976 compared to Kawasaki323/2014 and Kawasaki308/2015 were 0.57 × 10(-3) and 0.78 × 10(-3) , respectively; for GII...
February 15, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28185042/phylogenomic-relationship-of-feijoa-acca-sellowiana-o-berg-burret-with-other-myrtaceae-based-on-complete-chloroplast-genome-sequences
#18
Lilian de Oliveira Machado, Leila do Nascimento Vieira, Valdir Marcos Stefenon, Fábio de Oliveira Pedrosa, Emanuel Maltempi de Souza, Miguel Pedro Guerra, Rubens Onofre Nodari
Given their distribution, importance, and richness, Myrtaceae species comprise a model system for studying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an efficient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and northern Uruguay. Feijoa is known for its exquisite perfume and flavorful fruits, pharmacological properties, ornamental value and increasing economic relevance...
April 2017: Genetica
https://www.readbyqxmd.com/read/28161810/mutation-screening-of-gata4-gene-in-ctd-patients-within-chinese-han-population
#19
Yang Liu, Bojian Li, Yuejuan Xu, Kun Sun
Conotruncal heart defect is a complex form of congenital heart disease and usually has a poor prognosis. Although previous studies have identified several missense variants in GATA4 gene that may cause CTD, it remains unclear whether they are involved in CTD pathogenesis because the study population was limited. The aim of the study was to investigate the mutations of GATA4 gene in isolated CTD Chinese Han patients and identify the pathomechanism of the missense mutations. In this report, the coding exons and exon-intron boundaries of the GATA4 gene were sequenced in 600 CTD patients and 300 controls...
March 2017: Pediatric Cardiology
https://www.readbyqxmd.com/read/28115489/functional-validation-of-a-common-nonsynonymous-coding-variant-in-zc3hc1-associated-with-protection-from-coronary-artery-disease
#20
Tara Linseman, Sébastien Soubeyrand, Amy Martinuk, Majid Nikpay, Paulina Lau, Ruth McPherson
BACKGROUND: Although virtually all coronary artery disease associated single-nucleotide polymorphisms identified by genome-wide association studies (GWAS) are in noncoding regions of the genome, a common polymorphism in ZC3HC1 (rs11556924), resulting in an arginine (Arg) to histidine (His) substitution in its encoded protein, NIPA (Nuclear Interacting Partner of Anaplastic Lyphoma Kinase) is linked to a protection from coronary artery disease. NIPA plays a role in cell cycle progression, but the functional consequences of this polymorphism have not been established...
January 2017: Circulation. Cardiovascular Genetics
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