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Human evolutionary genetics

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https://www.readbyqxmd.com/read/28446899/clonal-spread-of-16s-rrna-methyltransferase-producing-klebsiella-pneumoniae-st37-with-high-prevalence-of-esbls-from-companion-animals-in-china
#1
Jing Xia, Liang-Xing Fang, Ke Cheng, Guo-Hao Xu, Xi-Ran Wang, Xiao-Ping Liao, Ya-Hong Liu, Jian Sun
We screened 30 Klebsiella pneumoniae isolates from dogs and cats at a single animal hospital in Guangdong Province, China. Among them, 12 K. pneumoniae strains possessed high-level resistance to amikacin and gentamicin and these were screened for 16S rRNA methyltransferase (16S-RMTase) genes. And then the genes positive isolates were detected for ESBLs (extended spectrum β-lactamases) and analyzed by pulsed-field gel electrophoresis, multilocus sequence typing, PCR-based replicon typing and plasmid analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28440220/rapid-evolution-of-the-human-mutation-spectrum
#2
Kelley Harris, Jonathan K Pritchard
DNA is a remarkably precise medium for copying and storing biological information. This high fidelity results from the action of hundreds of genes involved in replication, proofreading, and damage repair. Evolutionary theory suggests that in such a system, selection has limited ability to remove genetic variants that change mutation rates by small amounts or in specific sequence contexts. Consistent with this, using SNV variation as a proxy for mutational input, we report here that mutational spectra differ substantially among species, human continental groups and even some closely-related populations...
April 25, 2017: ELife
https://www.readbyqxmd.com/read/28439010/cyclops-reveals-human-transcriptional-rhythms-in-health-and-disease
#3
Ron C Anafi, Lauren J Francey, John B Hogenesch, Junhyong Kim
Circadian rhythms modulate many aspects of physiology. Knowledge of the molecular basis of these rhythms has exploded in the last 20 years. However, most of these data are from model organisms, and translation to clinical practice has been limited. Here, we present an approach to identify molecular rhythms in humans from thousands of unordered expression measurements. Our algorithm, cyclic ordering by periodic structure (CYCLOPS), uses evolutionary conservation and machine learning to identify elliptical structure in high-dimensional data...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28438095/arcobacter-an-emerging-food-borne-zoonotic-pathogen-its-public-health-concerns-and-advances-in-diagnosis-and-control-a-comprehensive-review
#4
Thadiyam Puram Ramees, Kuldeep Dhama, Kumaragurubaran Karthik, Ramswaroop Singh Rathore, Ashok Kumar, Mani Saminathan, Ruchi Tiwari, Yashpal Singh Malik, Raj Kumar Singh
Arcobacter has emerged as an important food-borne zoonotic pathogen, causing sometimes serious infections in humans and animals. Newer species of Arcobacter are being incessantly emerging (presently 25 species have been identified) with novel information on the evolutionary mechanisms and genetic diversity among different Arcobacter species. These have been reported from chickens, domestic animals (cattle, pigs, sheep, horses, dogs), reptiles (lizards, snakes and chelonians), meat (poultry, pork, goat, lamb, beef, rabbit), vegetables and from humans in different countries...
April 25, 2017: Veterinary Quarterly
https://www.readbyqxmd.com/read/28436429/human-fetal-heart-specific-coexpression-network-involves-congenital-heart-disease-defect-candidate-genes
#5
Bo Wang, Guoling You, Qihua Fu
Heart development is a complex process requiring dynamic transcriptional regulation. Disturbance of this process will lead to severe developmental defects such as congenital heart disease/defect (CHD). CHD is a group of complex disorder with high genetic heterogeneity, common pathways associated with CHD remains largely unknown. In the manuscript, we focused on the tissue specific genes in human fetal heart samples to explore such pathways. We used the RNA microarray dataset of human fetal tissues from ENCODE project to identify genes with heart tissue specific expression...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28435878/evolutionary-dynamics-of-crispr-gene-drives
#6
Charleston Noble, Jason Olejarz, Kevin M Esvelt, George M Church, Martin A Nowak
The alteration of wild populations has been discussed as a solution to a number of humanity's most pressing ecological and public health concerns. Enabled by the recent revolution in genome editing, clustered regularly interspaced short palindromic repeats (CRISPR) gene drives-selfish genetic elements that can spread through populations even if they confer no advantage to their host organism-are rapidly emerging as the most promising approach. However, before real-world applications are considered, it is imperative to develop a clear understanding of the outcomes of drive release in nature...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28434972/one-bacillus-to-rule-them-all-investigating-broad-range-host-adaptation-in-mycobacterium-bovis
#7
REVIEW
Adrian R Allen
Recent advances are permitting researchers to undertake largescale comparative genomics studies within and between bacterial species to determine the types of genetic change that underpin the phenotypic spectrum that runs from strict host adaptation to generalist. Within the Mycobacterium tuberculosis complex (MTBC) of bacilli, there is much heterogeneity in host specificity. Globally, Mycobacterium bovis exhibits a broad host range encompassing domesticated bovine and wildlife animals unlike the human adapted specialist M...
April 20, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28426741/as3mt-mediated-tolerance-to-arsenic-evolved-by-multiple-independent-horizontal-gene-transfers-from-bacteria-to-eukaryotes
#8
Michael Palmgren, Karin Engström, Björn M Hallström, Karin Wahlberg, Dan Ariel Søndergaard, Torbjörn Säll, Marie Vahter, Karin Broberg
Organisms have evolved the ability to tolerate toxic substances in their environments, often by producing metabolic enzymes that efficiently detoxify the toxicant. Inorganic arsenic is one of the most toxic and carcinogenic substances in the environment, but many organisms, including humans, metabolise inorganic arsenic to less toxic metabolites. This multistep process produces mono-, di-, and trimethylated arsenic metabolites, which the organism excretes. In humans, arsenite methyltransferase (AS3MT) appears to be the main metabolic enzyme that methylates arsenic...
2017: PloS One
https://www.readbyqxmd.com/read/28424085/the-within-host-population-dynamics-of-mycobacterium-tuberculosis-vary-with-treatment-efficacy
#9
Andrej Trauner, Qingyun Liu, Laura E Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England, Guolong Zhang, Sebastien Gagneux, Clifton E Barry, Qian Gao
BACKGROUND: Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics...
April 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28421323/gene-expression-nucleotide-composition-and-codon-usage-bias-of-genes-associated-with-human-y-chromosome
#10
Monisha Nath Choudhury, Arif Uddin, Supriyo Chakraborty
Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position...
April 18, 2017: Genetica
https://www.readbyqxmd.com/read/28416820/contrasting-evolutionary-genome-dynamics-between-domesticated-and-wild-yeasts
#11
Jia-Xing Yue, Jing Li, Louise Aigrain, Johan Hallin, Karl Persson, Karen Oliver, Anders Bergström, Paul Coupland, Jonas Warringer, Marco Cosentino Lagomarsino, Gilles Fischer, Richard Durbin, Gianni Liti
Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics...
April 17, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28414106/molecular-evolution-of-the-fusion-protein-f-gene-in-human-respiratory-syncytial-virus-subgroup-b
#12
Hirokazu Kimura, Koo Nagasawa, Ryusuke Kimura, Hiroyuki Tsukagoshi, Yuki Matsushima, Kiyotaka Fujita, Eiko Hirano, Naruhiko Ishiwada, Takako Misaki, Kazunori Oishi, Makoto Kuroda, Akihide Ryo
In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes...
April 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28405014/update-of-the-gjb2-dfnb1-mutation-spectrum-in-russia-a-founder-ingush-mutation-del-gjb2-d13s175-is-the-most-frequent-among-other-large-deletions
#13
Elena A Bliznetz, Maria R Lalayants, Tatiana G Markova, Oleg P Balanovsky, Elena V Balanovska, Roza A Skhalyakho, Elvira A Pocheshkhova, Natalya V Nikitina, Sergey V Voronin, Elena K Kudryashova, Oleg S Glotov, Alexander V Polyakov
Although mutations in the GJB2 gene sequence make up the majority of variants causing autosomal-recessive non-syndromic hearing loss, few large deletions have been shown to contribute to DFNB1 deafness. Currently, genetic testing for DFNB1 hearing loss includes GJB2 sequencing and DFNB1 deletion analysis for two common large deletions, del(GJB6-D13S1830) and del(GJB6-D13S1854). Here, we report frequency in Russia, clinical significance and evolutionary origins of a 101 kb deletion, del(GJB2-D13S175), recently identified by us...
April 13, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28404845/molecular-evolution-and-emergence-of-h5n6-avian-influenza-virus-in-central-china
#14
Yingying Du, Mingyue Chen, Jiayun Yang, Yane Jia, Shufang Han, Edward C Holmes, Jie Cui
H5N6 avian influenza virus (AIV) has posed a potential threat to public health since its emergence in China in 2013. To understand the evolution and emergence of H5N6 in the avian population we performed molecular surveillance of live poultry markets (LPMs) in Wugang prefecture, Hunan province, in central China during 2014-2015. Wugang prefecture is located on the Eastern Asian-Australian migratory bird flyway and a human death due to an H5N6 virus was reported in the prefecture on 21(th) November 2016. In total, we sampled and sequenced the complete genomes of 175 H5N6 AIVs...
April 12, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28404241/discrete-morphological-variants-of-human-cervical-vertebrae-exploring-pattern-of-distribution-and-biological-significance
#15
M K Karapetian
Studies on discrete traits of the human cervical vertebrae, appearing at certain intervals during the last century, posed some questions regarding evolutionary processes that human cervical spine underwent during phylogenesis. To address questions of significance of these morphological traits we need first a good knowledge of the extent of their variation in modern humans. The aim of the current work was to integrate available data on the occurrence of various non-metric traits in the human cervical spine and search for the pattern of their distribution on intra- and inter-population levels...
March 9, 2017: Homo: Internationale Zeitschrift Für die Vergleichende Forschung Am Menschen
https://www.readbyqxmd.com/read/28401898/a-unique-haplotype-of-rccx-copy-number-variation-from-the-clinics-of-congenital-adrenal-hyperplasia-to-evolutionary-genetics
#16
Márton Doleschall, Andrea Luczay, Klára Koncz, Kinga Hadzsiev, Éva Erhardt, Ágnes Szilágyi, Zoltán Doleschall, Krisztina Németh, Dóra Török, Zoltán Prohászka, Balázs Gereben, György Fekete, Edit Gláz, Péter Igaz, Márta Korbonits, Miklós Tóth, Károly Rácz, Attila Patócs
There is a difficulty in the molecular diagnosis of congenital adrenal hyperplasia (CAH) due to the c.955C>T (p.(Q319*), formerly Q318X, rs7755898) variant of the CYP21A2 gene. Therefore, a systematic assessment of the genetic and evolutionary relationships between c.955C>T, CYP21A2 haplotypes and the RCCX copy number variation (CNV) structures, which harbor CYP21A2, was performed. In total, 389 unrelated Hungarian individuals with European ancestry (164 healthy subjects, 125 patients with non-functioning adrenal incidentaloma and 100 patients with classical CAH) as well as 34 adrenocortical tumor specimens were studied using a set of experimental and bioinformatic methods...
April 12, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28400513/determining-the-factors-driving-selective-effects-of-new-nonsynonymous-mutations
#17
Christian D Huber, Bernard Y Kim, Clare D Marsden, Kirk E Lohmueller
The distribution of fitness effects (DFE) of new mutations plays a fundamental role in evolutionary genetics. However, the extent to which the DFE differs across species has yet to be systematically investigated. Furthermore, the biological mechanisms determining the DFE in natural populations remain unclear. Here, we show that theoretical models emphasizing different biological factors at determining the DFE, such as protein stability, back-mutations, species complexity, and mutational robustness make distinct predictions about how the DFE will differ between species...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28400296/recombinant-expression-and-purification-of-the-rna-binding-larp6-proteins-from-fish-genetic-model-organisms
#18
José M Castro, Daniel A Horn, Karen A Lewis
The RNA-binding proteins that comprise the La-related protein (LARP) superfamily have been implicated in a wide range of cellular functions, from tRNA maturation to regulation of protein synthesis. To more expansively characterize the biological function of the LARP6 subfamily, we have recombinantly expressed the full-length LARP6 proteins from two teleost fish, platyfish (Xiphophorus maculatus) and zebrafish (Danio rerio). The yields of the recombinant proteins were enhanced to >2 mg/L using a tandem approach of an N-terminal His6-SUMO tag and an iterative solubility screening assay to identify structurally stabilizing buffer components...
April 8, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28399403/thada-regulates-the-organismal-balance-between-energy-storage-and-heat-production
#19
Alexandra Moraru, Gulcin Cakan-Akdogan, Katrin Strassburger, Matilda Males, Sandra Mueller, Markus Jabs, Michael Muelleder, Martin Frejno, Bart P Braeckman, Markus Ralser, Aurelio A Teleman
Human susceptibility to obesity is mainly genetic, yet the underlying evolutionary drivers causing variation from person to person are not clear. One theory rationalizes that populations that have adapted to warmer climates have reduced their metabolic rates, thereby increasing their propensity to store energy. We uncover here the function of a gene that supports this theory. THADA is one of the genes most strongly selected during evolution as humans settled in different climates. We report here that THADA knockout flies are obese, hyperphagic, have reduced energy production, and are sensitive to the cold...
April 10, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28398839/foundational-and-translational-research-opportunities-to-improve-plant-health
#20
Richard W Michelmore, Gitta Coaker, Rebecca Bart, Gwyn A Beattie, Andrew Bent, Toby Bruce, Duncan Cameron, Jeff Dangl, Savithramma Dinesh-Kumar, Robert Edwards, Sebastian Eves-van den Akker, Walter Gassmann, Jean Greenberg, Richard Harrison, Ping He, Jagger Harvey, Alisa Huffaker, Scot Hulbert, Roger Innes, Jonathan D Jones, Isgouhi Kaloshian, Sophien Kamoun, Fumiaki Katagiri, Jan E Leach, Wenbo Ma, John M McDowell, June Medford, Blake Meyers, Rebecca Nelson, Richard Peter Oliver, Yiping Qi, Diane Saunders, Michael Shaw, Prasanta Subudhi, Leslie Torrance, Brett M Tyler, John Walsh
This whitepaper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses...
April 11, 2017: Molecular Plant-microbe Interactions: MPMI
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