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Debi Prasad Mohapatra, Santosh Kumar Singh, Minu Sahoo, Shashank Patole, Mitali Mishra, Nagen Kumar Debata, Harapriya Mohapatra
PURPOSE: Antibiotic resistance patterns often exhibit geographical variations. Periodic analyses of resistance spectra and phylogenetic trends are important guides for facilitating judicious use of therapeutic interventions. The present study retrospectively analysed the infection trends, resistance patterns, and clonal relationships between isolates of Klebsiella spp. from a tertiary care hospital. METHODOLOGY: Bacterial isolates were collected from January 2013 to June 2014 and their resistance profiles were identified using an automated bacterial identification system...
March 9, 2018: Journal of Medical Microbiology
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
Drozdstoy Stoyanov, Sevdalina Kandilarova, Stefan Borgwardt, Rolf-Dieter Stieglitz, Kenneth Hugdahl, Stefan Kostianev
We present in this article a study design that combines clinical self-assessment scale, simultaneously administered with fMRI data acquisition. We have used a standard block-design with two different conditions. Each active block consisted of four text statements (items), alternating diagnostically specific (DS) blocks comprising items from von Zerssen depression scale and diagnostically neutral (DN) blocks with items from a questionnaire about general interests. All items were rated on four degree Likert scale, and patients provided responses with corresponding four buttons during the fMRI session...
2018: Frontiers in Psychiatry
Sahar Parto, Nicolas Lartillot
Rubisco (Ribulose-1, 5-biphosphate carboxylase/oxygenase) is the most important enzyme on earth, catalyzing the first step of photosynthetic CO2 fixation. So, without it, there would be no storing of the sun's energy in plants. Molecular adaptation of Rubisco to C4 photosynthetic pathway has attracted a lot of attention. C4 plants, which comprise less than 5% of land plants, have evolved more efficient photosynthesis compared to C3 plants. Interestingly, a large number of independent transitions from C3 to C4 phenotype have occurred...
2018: PloS One
Sara Domínguez-Rodríguez, Patricia Rojas, Carolina Fernández McPhee, Israel Pagán, María Luisa Navarro, José Tomás Ramos, África Holguín
This pilot study evaluates in pediatric patients the impact of HIV/HCV coinfection in the molecular evolution of the HIV-1 subtype B protease (HIV-1BPR). For this study, HIV-1B/HCV coinfected (15) and HIV-1B monoinfected (56) patients with available HIV-1B pol sequences were enrolled. Both groups of patients had comparable gender frequencies and average age, time of infection, antiretroviral treatment (ART) exposure and time under ART. Prevalence of drug resistance mutations (DRM), genetic diversity, number of synonymous (dS) and non-synonymous (dN) mutations per site and selection pressures (dN - dS) in the HIV-1BPR were estimated and compared between mono- and coinfected patients...
February 5, 2018: Scientific Reports
M Cortázar-Chinarro, Y Meyer-Lucht, A Laurila, J Höglund
MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient...
February 1, 2018: Immunogenetics
Mario A Cerón-Romero, Esther Nwaka, Zuliat Owoade, Laura A Katz
The genome of P. falciparum, the causative agent of malaria in Africa, has been extensively studied since it was first fully sequenced in 2002. However, many open questions remain, including understanding the chromosomal context of molecular evolutionary changes (e.g. relationship between chromosome map and phylogenetic conservation, patterns of gene duplication, and patterns of selection). Here we present PhyloChromoMap, a method that generates a phylogenomic map of chromosomes from a custom-built bioinformatics pipeline...
January 22, 2018: Genome Biology and Evolution
J Jaquiéry, J Peccoud, T Ouisse, F Legeai, N Prunier-Leterme, A Gouin, P Nouhaud, J A Brisson, R Bickel, S Purandare, J Poulain, C Battail, C Lemaitre, L Mieuzet, G Le Trionnaire, J C Simon, C Rispe
The faster evolution of X chromosomes has been documented in several species, and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X evolution because their peculiar life cycle and unusual inheritance of sex chromosomes should generally lead to equivalent effective population sizes for X and autosomes...
January 19, 2018: Genome Biology and Evolution
Yiyuan Li, Rui Zhang, Shanlin Liu, Alexander Donath, Ralph S Peters, Jessica Ware, Bernhard Misof, Oliver Niehuis, Michael E Pfrender, Xin Zhou
BACKGROUND: The primary energy-producing pathway in eukaryotic cells, the oxidative phosphorylation (OXPHOS) system, comprises proteins encoded by both mitochondrial and nuclear genes. To maintain the function of the OXPHOS system, the pattern of substitutions in mitochondrial and nuclear genes may not be completely independent. It has been suggested that slightly deleterious substitutions in mitochondrial genes are compensated by substitutions in the interacting nuclear genes due to positive selection...
December 28, 2017: BMC Evolutionary Biology
Xianyan Zou, Zhang Zhen, Qun Ge, Senmiao Fan, Aiying Liu, Wankui Gong, Junwen Li, Juwu Gong, Yuzhen Shi, Yanling Wang, Ruixian Liu, Li Duan, Kang Lei, Qi Zhang, Xiao Jiang, Shuya Zhang, Tingting Jia, Lipeng Zhang, Haihong Shang, Youlu Yuan
The cellulose synthase gene superfamily, which includes the cellulose synthase (Ces) and cellulose synthase-like (Csl) families, is involved in the synthesis of cellulose and hemicellulose. This superfamily is critical for cotton fiber development in Gossypium species. Applying a series of bioinformatic methods, we identified 228 Ces/Csl genes from four Gossypium species (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii). These genes were then grouped into 11 subfamilies based on phylogenetic relationships...
December 23, 2017: Gene
Mark S Springer, John Gatesy
MC5R is one of five melanocortin receptor genes found in placental mammals. MC5R plays an important role in energy homeostasis and is also expressed in the terminal differentiation of sebaceous glands. Among placental mammals there are multiple lineages that either lack or have degenerative sebaceous glands including Cetacea (whales, dolphins, and porpoises), Hippopotamidae (hippopotamuses), Sirenia (manatees and dugongs), Proboscidea (elephants), Rhinocerotidae (rhinos), and Heterocephalus glaber (naked mole rat)...
December 19, 2017: Molecular Phylogenetics and Evolution
Verma Subhash, Sodhi Monika, Salwan Richa, Shekhar Chander, Singh Geetanjali, Sharma Mandeep
Distribution of polymorphism in TLR2 gene was studied in Pahari (Indian non-descript indigenous breed) cattle of Himachal Pradesh. The complete sequence of TLR2 gene consisted of 136bp 5'-UTR, 2355bp CDS and 1316bp 3'UTR. The phylogenetic analysis revealed clustering of Indian Zebu with Bos taurus as the nearest neighbour. The nucleotide sequences of TLR2 revealed the occurrence of 19 SNPs including 47% non-synonymous and 53% synonymous SNPs within TLR domain among all bovines. The dS/dN ratio (ω)<1 at polymorphic sites revealed purifying selection and thus, indicating the presence of highly conserved domains...
December 15, 2017: Research in Veterinary Science
Hyeonju Ahn, Chul Lee, Bo-Hye Nam, Eun Bae Kim, Kelsey Caetano-Anolles, Heebal Kim
The pufferfish accumulates neurotoxic tetrodotoxin in its body and inflates by filling its stomach with water. These traits are unique to this species, and may be a result of adaptation post-divergence of Tetraodontidae. However, evolution of the protein-coding genes in the pufferfish has not yet been well elucidated. Detection of positive selection on these genes can help us understand the mechanisms associated with functional evolution. We downloaded well-annotated gene information of two pufferfish species, Takifugu rubripes and Tetraodon nigroviridis, from the public ENSEMBL database...
December 19, 2017: Marine Genomics
Hong-Yi Liu, Fei Xue, Jie Gong, Qiu-Hong Wan, Sheng-Guo Fang
Amphibians can be more vulnerable to environmental changes and diseases than other species because of their complex life cycle and physiological requirements. Therefore, understanding the adaptation of amphibians to environmental changes is crucial for their conservation. Major histocompatibility complex (MHC) presents an excellent tool for the investigation of adaptive variations and the assessment of adaptive potential because it can be under strong diversifying selection. Here, we isolated the MHC class II B (MHCIIB) gene from cDNA sequences of the black-spotted frog (Pelophylax nigromaculatus), a widespread amphibian species in China, and designed locus-specific primers to characterize adaptive variability of this amphibian...
December 2017: Ecology and Evolution
Wentao Fan, Yuliang Xu, Pu Zhang, Peng Chen, Yiran Zhu, Ziqiang Cheng, Xiaona Zhao, Yongxia Liu, Jianzhu Liu
The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes. The evolutionary timescale and rate were estimated using the Bayesian Markov chain Monte Carlo (MCMC) method. The p-distance, Bayesian skyline plot (BSP), and positively selected sites were also analyzed. The MCMC tree indicated that NDV diverged about 250 years ago with a rapid evolution rate (1.059 × 10-2 substitutions/site/year) and that different NDV genotypes formed three lineages...
November 14, 2017: Oncotarget
Laurent Guéeguen, Laurent Duret
The measurement of synonymous and non-synonymous substitution rates (dS and dN) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio dNdS is expected to be a good proxy for ω, the ratio of fixation robabilities of non-synonymous mutations relative to that of neutral mutations. Standard methods for estimating dN, dS or ω rely on the assumption that the base composition of sequences is at the equilibrium of the evolutionary process...
December 6, 2017: Molecular Biology and Evolution
Angela K Hawkins, Elyssa R Garza, Valerie A Dietz, Oscar J Hernandez, W Daryl Hawkins, A Millie Burrell, Alan E Pepper
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var...
December 1, 2017: Genome Biology and Evolution
Chao Tong, Fei Tian, Kai Zhao
BACKGROUND: Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. The Schizothoracine fish, Gymnocypris przewalskii ganzihonensis had underwent the ecological niche shift from salt water to freshwater, and also experienced a recent split from Gymnocypris przewalskii przewalskii. In addition, G. p. ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined...
December 6, 2017: BMC Genomics
Frances K Shepherd, Michael P Murtaugh, Fangzhou Chen, Marie R Culhane, Douglas G Marthaler
Rotavirus B (RVB) is an important swine pathogen, but control and prevention strategies are limited without an available vaccine. To develop a subunit RVB vaccine with maximal effect, we characterized the amino acid sequence variability and predicted antigenicity of RVB viral protein 7 (VP7), a major neutralizing antibody target, from clinically infected pigs in the United States and Canada. We identified genotype-specific antigenic sites that may be antibody neutralization targets. While some antigenic sites had high amino acid functional group diversity, nine antigenic sites were completely conserved...
December 3, 2017: Pathogens
Ke-Yi Tang, Xin Wang, Qiu-Hong Wan, Sheng-Guo Fang
The β-defensin, one of the antimicrobial peptides (AMPs), is a significant component of the innate immune with a broad range of antimicrobial activities. Differing from the widely-studied mammals and birds, limited information about β-defensins has been reported in reptiles, especially in crocodilians. As a same ancient species as dinosaurs and the most endangered species of 23 crocodilians, the survival of Chinese alligator (Alligator sinensis) means a powerful immune system and possible involvement of AMPs in its immune resistance...
April 2018: Developmental and Comparative Immunology
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