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synonymous substitution

Jane Hawkey, David B Ascher, Louise M Judd, Ryan R Wick, Xenia Kostoulias, Heather Cleland, Denis W Spelman, Alex Padiglione, Anton Y Peleg, Kathryn E Holt
Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A. baumannii is considered a major public-health threat and has been identified by the World Health Organization as the top priority organism requiring new antimicrobials. The most common mechanism for carbapenem resistance in A. baumannii is via horizontal acquisition of carbapenemase genes. In this study, we sampled 20 A. baumannii isolates from a patient with extensive burns, and characterized the evolution of carbapenem resistance over a 45 day period via Illumina and Oxford Nanopore sequencing...
March 16, 2018: Microbial Genomics
ChengLin Zhong, SiChen Li, JingJing Li, FengPeng Li, MingXia Ran, LingYun Qiu, DiYan Li, Qing Zhu, Yan Wang, HuaDong Yin, Gang Shu, Chaowu Yang, XiaoLing Zhao
Peroxisome proliferator activated receptor-alpha (PPARα) and Egl nine homolog 3 (EGLN3) play critical roles in facilitating the adaptation to a hypoxic environment. However, the relationship between EGLN3 and PPARα variants and hypoxic adaptation remains poorly understood in Tibetan chickens. To better understand the effects of genetic variation, we sequenced exons of PPARα and EGLN3 in 138 Lowland chickens (LC) from 7 breeds that were located in Emei, Miyi, Shimian, Wanyuan, Pengxian, and Muchuan in the Sichuan province, and Wenchang in the Hainan province (altitudes for these locations are below 1800 meters)...
2018: PloS One
Chaowen Zhang, Feifan Chen, Ziyao Zhao, Liangliang Hu, Hanqiang Liu, Zhihui Cheng, Yiqun Weng, Peng Chen, Yuhong Li
Two round-leaf mutants, rl-1 and rl-2, were identified from EMS-induced mutagenesis. High throughput sequencing and map-based cloning suggested CsPID encoding a Ser/Thr protein kinase as the most possible candidate for rl-1. Rl-2 was allelic to Rl-1. Leaf shape is an important plant architecture trait that is affected by plant hormones, especially auxin. In Arabidopsis, PINOID (PID), a regulator for the auxin polar transporter PIN (PIN-FORMED) affects leaf shape formation, but this function of PID in crop plants has not been well studied...
March 14, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Md Atique Ahmed, Muh Fauzi, Eun-Taek Han
BACKGROUND: Human infections due to the monkey malaria parasite Plasmodium knowlesi is on the rise in most Southeast Asian countries specifically Malaysia. The C-terminal 19 kDa domain of PvMSP1P is a potential vaccine candidate, however, no study has been conducted in the orthologous gene of P. knowlesi. This study investigates level of polymorphisms, haplotypes and natural selection of full-length pkmsp1p in clinical samples from Malaysia. METHODS: A total of 36 full-length pkmsp1p sequences along with the reference H-strain and 40 C-terminal pkmsp1p sequences from clinical isolates of Malaysia were downloaded from published genomes...
March 14, 2018: Malaria Journal
Pei Zhang, Kang Huang, Bingyi Zhang, Derek W Dunn, Dan Chen, Fan Li, Xiaoguang Qi, Songtao Guo, Baoguo Li
BACKGROUND: Maintaining variation in immune genes, such as those of the major histocompatibility complex (MHC), is important for individuals in small, isolated populations to resist pathogens and parasites. The golden snub-nosed monkey (Rhinopithecus roxellana), an endangered primate endemic to China, has experienced a rapid reduction in numbers and severe population fragmentation over recent years. For this study, we measured the DRB diversity among 122 monkeys from three populations in the Qinling Mountains, and estimated the relative importance of different agents of selection in maintaining variation of DRB genes...
March 13, 2018: BMC Evolutionary Biology
Michael Song, Li-Yaung Kuo, Layne Huiet, Kathleen M Pryer, Carl J Rothfels, Fay-Wei Li
PREMISE OF THE STUDY: Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS: We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF, which we now refer to as ycf94, to infer evolutionary selection pressures and assist in functional prediction...
January 2018: American Journal of Botany
Na Tian, Limin Han, Chen Chen, Zhezhi Wang
Epipremnum aureum is an important foliage plant in the Araceae family. In this study, we have sequenced the complete chloroplast genome of E. aureum by using Illumina Hiseq sequencing platforms. This genome is a double-stranded circular DNA sequence of 164,831 bp that contains 35.8% GC. The two inverted repeats (IRa and IRb; 26,606 bp) are spaced by a small single-copy region (22,868 bp) and a large single-copy region (88,751 bp). The chloroplast genome has 131 (113 unique) functional genes, including 86 (79 unique) protein-coding genes, 37 (30 unique) tRNA genes, and eight (four unique) rRNA genes...
2018: PloS One
Michael Hornsey, David W Wareham
Multidrug-resistant lineages of Acinetobacter baumannii (MDRAB) are important nosocomial pathogens. As tigecycline remains active against most MDRAB we sought to investigate whether tigecycline resistance impacts biological fitness. The effects of treatment-emergent tigecycline resistance were investigated in vitro and in vivo using two pre- (AB210; W6976) and post-therapy (AB211; W7282) clinical pairs, recovered from individual patients, where tigecycline resistance was associated with up-regulated efflux activity...
March 9, 2018: Scientific Reports
Qi-Lin Zhang, Xing-Zhuo Yang, Li Zhang, Run-Qiu Feng, Qian-Hua Zhu, Jun-Yuan Chen, Ming-Long Yuan
Given mitochondrion is the 'energy and oxygen usage factories', adaptive signatures of mitochondrial genes have been extensively investigated in vertebrates from different altitudes, but few studies focus on insects. Here, we sequenced the complete mitochondrial genome (mitogenome) of Dolycoris. baccarum living in the Tibetan Plateau (DBHC, ∼3200 m above sea level (asl)) and conducted a detailed comparative analysis with another D. baccarum mitogenome (DBQY) from relatively low altitude (∼1300 m asl)...
March 9, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Rolando Robert, Kenneth Francis Rodrigues, Zarinah Waheed, Subbiah Vijay Kumar
This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts /Tv ), synonymous-to-nonsynonymous rate ratio (dN /dS ), and substitution patterns at the three codon positions...
March 9, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
P Fasura Amorim
The Jenynsia lineata species complex comprises J. lineata from Montevideo, Uruguay and Jenynsia multidentata, from coastal basins of Brazil, Uruguay and Argentina up to 1200 m a.s.l. Taxonomic divisions within this group were tested using three different species delimitation methods, which found the two existing names to be synonyms and revealed a new cryptic species. Jenynsia darwini sp. nov. is distinguished from all congeners by having a unique combination of character states, including the shape of the dorsal postcleithrum (three times higher than wide v...
March 7, 2018: Journal of Fish Biology
Donhyun Shin, Jae-Don Oh, Kyung-Hye Won, Ki-Duk Song
Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified nsSNPs in Berkshire selective sweep regions and investigated Berkshire-specific nsSNPs to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: NsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs...
March 2, 2018: Asian-Australasian Journal of Animal Sciences
Naoya Shinohara, Chieko Matsumoto, Keiji Matsubayashi, Tadashi Nagai, Masahiro Satake
There are few reports on HIV-1 intra-host evolutionary rate in asymptomatic treatment-naïve patients. Here, the HIV-1 intra-host evolutionary rate was estimated based on HIV-1 RNA sequences from plasma samples of blood donors in Japan. Blood donors were assumed to have received no treatment for and have no symptoms of HIV-1 infection because they were healthy, and declared no risky behaviors of HIV-1 infection on a self-reported questionnaire or interview followed by donation. HIV-1 RNA was obtained from 85 plasma samples from 36 blood donors who donated blood multiple times and were HIV-1-positive...
March 7, 2018: Virus Genes
Yuanting Jin, Yubin Wo, Haojie Tong, Sen Song, Lixun Zhang, Richard P Brown
BACKGROUND: Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover a broad altitudinal gradient of over 4000 m and are useful models for studies of such adaptive responses. In one of the first studies to have considered selection on mitochondrial protein-coding regions in an ectothermic group distributed over such a wide range of environments, we analysed nineteen complete mitochondrial genomes from all Chinese Phrynocephalus (including eight genomes sequenced for the first time)...
March 6, 2018: BMC Genomics
Junyi Wang, Zongyu Li, Liling Xu, Hengwen Yang, Wanli Liu
FcγRIIB, the only inhibitory IgG Fc receptor, functions to suppress the hyper-activation of immune cells. Numerous studies have illustrated its inhibitory function through the ITIM motif in the cytoplasmic tail of FcγRIIB. However, later studies revealed that in addition to the ITIM, the transmembrane (TM) domain of FcγRIIB is also indispensable for its inhibitory function. Indeed, recent epidemiological studies revealed that a non-synonymous single nucleotide polymorphism (rs1050501) within the TM domain of FcγRIIB, responsible for the I232T substitution, is associated with the susceptibility to systemic lupus erythematosus (SLE)...
March 1, 2018: Protein & Cell
Hamid Reza Maghamnia, Mohammad Hajizadeh, Abdolbaset Azizi
The complete genome sequence of Zucchini yellow mosaic virus strain Kurdistan (ZYMV-Kurdistan) infecting squash from Iran was determined from 13 overlapping fragments. Excluding the poly (A) tail, ZYMV-Kurdistan genome consisted of 9593 nucleotides (nt), with 138 and 211 nt at the 5' and 3' non-translated regions, respectively. It contained two open-reading frames (ORFs), the large ORF encoding a polyprotein of 3080 amino acids (aa) and the small overlapping ORF encoding a P3N-PIPO protein of 74 aa. This isolate had six unique aa differences compared to other ZYMV isolates and shared 79...
March 2018: 3 Biotech
Kousuke Hanada, Ayumi Tezuka, Masafumi Nozawa, Yutaka Suzuki, Sumio Sugano, Atsushi J Nagano, Motomi Ito, Shin-Ichi Morinaga
Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae...
February 21, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Xiao Lei, Yi Kou, Yang Fu, Niroop Rajashekar, Haoran Shi, Fang Wu, Jiang Xu, Yibing Luo, Lin Chen
MEF2B is a major target of somatic mutations in non-Hodgkin lymphoma. Most of these mutations are non-synonymous substitutions of surface residues in the MADS-box/MEF2 domain. Among them, D83V is the most frequent mutation found in tumor cells. The link between this hotspot mutation and cancer is not well understood. Here we show that the D83V mutation induces a dramatic α-helix to β-strand switch in the MEF2 domain. Located in an α-helix region rich in β-branched residues, the D83V mutation not only removes the extensive helix stabilization interactions but also introduces an additional β-branched residue that further shifts the conformation equilibrium from α-helix to β-strand...
February 22, 2018: Journal of Molecular Biology
Sooyeon Lee, Yandong Zhou, Donald L Gill, Shannon L Kelleher
SLC30A2 encodes a zinc (Zn) transporter (ZnT2) that imports Zn into vesicles in highly-specialized secretory cells. Numerous mutations and non-synonymous variants in ZnT2 have been reported in humans and in breastfeeding women; ZnT2 variants are associated with abnormally low milk Zn levels and can lead to severe infantile Zn deficiency. However, ZnT2-null mice have profound defects in mammary epithelial cell (MEC) polarity and vesicle secretion, indicating that normal ZnT2 function is critical for MEC function...
February 23, 2018: Scientific Reports
Li Qian, Wang Xiaoxi, Chen Xuexin, Han Baoyu
The complete mitochondrial genome (mitogenome) of the Ectropis obliqua (Lepidoptera: Geometridae) was sequenced and compared with other species of Geometridae. The mitochondrial genome of E. obliqua is 15,475 bp long and contains 37 genes including 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region. Gene cluster trnI-trnQ-trnM rearranged to trnM-trnI-trnQ comparing with the ancestral mitogenome of insects. All tRNA genes have typical cloverleaf secondary structure except for trnS (AGN)...
February 20, 2018: International Journal of Biological Macromolecules
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