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Neutral evolution

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https://www.readbyqxmd.com/read/29220511/unbiased-estimate-of-synonymous-and-non-synonymous-substitution-rates-with-non-stationary-base-composition
#1
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
https://www.readbyqxmd.com/read/29220487/ancestral-genome-estimation-reveals-the-history-of-ecological-diversification-in-agrobacterium
#2
Florent Lassalle, Rémi Planel, Simon Penel, David Chapulliot, Valérie Barbe, Audrey Dubost, Alexandra Calteau, David Vallenet, Damien Mornico, Thomas Bigot, Laurent Guéguen, Ludovic Vial, Daniel Muller, Vincent Daubin, Xavier Nesme
Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29218863/population-structure-and-migration-of-the-tobacco-blue-mold-pathogen-peronospora-tabacina-into-north-america-and-europe
#3
Monica Blanco-Meneses, Ignazio Carbone, Jean B Ristaino
Tobacco blue mold, caused by Peronospora tabacina, is an oomycete plant pathogen that causes yearly epidemics in tobacco (Nicotiana tabacum) in the U.S. and Europe. The genetic structure of P. tabacina was examined in order to understand genetic diversity, population structure and patterns of migration. Two nuclear loci, Igs2 and Ypt1 and one mitochondrial locus, cox2, were amplified, cloned and sequenced from fifty four isolates of P. tabacina from the U.S., Central America-Caribbean-Mexico (CCAM), Europe and the Middle East (EULE)...
December 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29208413/characterization-of-ml0314c-of-mycobacterium-leprae-and-deciphering-its-role-in-the-immune-response-in-leprosy-patients
#4
Gurkamajit Kaur, Aashish Sharma, Tarun Narang, Sunil Dogra, Jagdeep Kaur
Mycobacterium leprae has a reduced genome size due to the reductive evolution over a long period of time. Lipid metabolism plays an important role in the life cycle and pathogenesis of this bacterium. In comparison to 26 lip genes (Lip A-Z) of M. tuberculosis, M. leprae retained only three orthologs indicating their importance in its life cycle. ML0314c (LipU) is one of them. It is conserved throughout the mycobacterium species. Bioinformatics analysis showed the presence of an α/β hydrolase fold and 'GXSXG' characteristic of the esterases/lipases...
December 2, 2017: Gene
https://www.readbyqxmd.com/read/29207506/longitudinal-surveillance-of-porcine-rotavirus-b-strains-from-the-united-states-and-canada-and-in-silico-identification-of-antigenically-important-sites
#5
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
https://www.readbyqxmd.com/read/29206439/redox-active-hydrogel-polymer-electrolytes-with-different-ph-values-for-enhancing-the-energy-density-of-the-hybrid-solid-state-supercapacitor
#6
Xiaohui Tang, Yu Hui Lui, Abdul Rahman Merhi, Bolin Chen, Shaowei Ding, Bowei Zhang, Shan Hu
To enhance the energy density of solid-state supercapacitors, a novel solid-state cell, made of redox-active polyvinyl alcohol (PVA) hydrogel electrolytes and functionalized carbon nanotube coated cellulose paper electrodes, was investigated in this work. Briefly, acidic PVA-[BMIM]Cl-Lactic acid-LiBr and neutral PVA-[BMIM]Cl-Sodium acetate-LiBr hydrogel polymer electrolytes are used as catholyte and anolyte, respectively. The acidic condition of the catholyte contributes to suppress the undesired irreversible reaction of 〖Br〗^-and to extend the oxygen evolution reaction potential to a higher value than the redox potential of 〖Br〗^-/〖Br〗_3^- reaction...
December 5, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29201432/tube-construction-by-a-tanaidacean-crustacean-using-a-novel-mucus-secretion-system-involving-the-anal-opening
#7
Keiichi Kakui, Chizue Hiruta
Background: Animals in diverse aquatic groups construct tubes using mucus and filaments, and the acquisition of this capability has likely played an important role in the evolution and diversification of small benthic animals. Tanaidacea is a crustacean order that includes tube-constructing species, most of which belong to Tanaidoidea and Paratanaoidea, with a few in Kalliapseudidae (Apseudoidea). Two previously reported systems used in tube construction are the thoracic-gland system, with secretory glands in thoracic segments (pereonites), and the pereopodal-gland system, with glands in pereopods...
2017: Zoological Letters
https://www.readbyqxmd.com/read/29197792/new-insight-into-pm2-5-pollution-patterns-in-beijing-based-on-one-year-measurement-of-chemical-compositions
#8
Tianyi Tan, Min Hu, Mengren Li, Qingfeng Guo, Yusheng Wu, Xin Fang, Fangting Gu, Yu Wang, Zhijun Wu
In recent years, air pollution has become a major concern in China, especially in the capital city of Beijing. Haze events occur in Beijing over all four seasons, exhibiting distinct characteristics. In this study, the typical evolution patterns of atmospheric particulate matter with a diameter of less than 2.5μm (PM2.5) in each season were illustrated by episode-based analysis. In addition, a novel method was developed to elucidate the driving species of pollution, which is the largest contributor to the incremental PM2...
November 30, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29195856/codon-usage-and-expression-level-of-human-mitochondrial-13-protein-coding-genes-across-six-continents
#9
Supriyo Chakraborty, Arif Uddin, Tarikul Huda Mazumder, Monisha Nath Choudhury, Arup Kumar Malakar, Prosenjit Paul, Binata Halder, Himangshu Deka, Gulshana Akthar Mazumder, Riazul Ahmed Barbhuiya, Masuk Ahmed Barbhuiya, Warepam Jesmi Devi
The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes...
November 28, 2017: Mitochondrion
https://www.readbyqxmd.com/read/29195094/increases-in-the-competitive-fitness-of-west-nile-virus-isolates-after-introduction-into-california
#10
Gabriella Worwa, Andra A Hutton, Michèle Frey, Nisha K Duggal, Aaron C Brault, William K Reisen
To investigate the phenotypic evolution of West Nile virus (WNV) in California, we competed sixteen isolates made during 2007-08 against COAV997-5nt, a genetically marked clone from the founding 2003 California isolate COAV997-2003. Using in vivo fitness competitions in House Finches (HOFI) and Culex tarsalis mosquitoes, we found that the majority of WNV WN02 and SW03 genotype isolates exhibited elevated replicative fitness in both hosts compared to COAV997-5nt. Increased replicative capacity in HOFIs was not associated with increased mortality, indicating that these isolates had not gained avian virulence...
November 28, 2017: Virology
https://www.readbyqxmd.com/read/29194863/associations-of-stream-geomorphic-conditions-and-prevalence-of-alternative-reproductive-tactics-among-sockeye-salmon-populations
#11
Lukas B DeFilippo, Daniel E Schindler, Jackie L Carter, Timothy E Walsworth, Timothy J Cline, Wesley A Larson, Thomas Buehrens
In many species, males may exhibit alternative life histories to circumvent the costs of intrasexual competition and female courtship. While the evolution and underlying genetic and physiological mechanisms behind alternative reproductive tactics are well studied, there has been less consideration of the ecological factors that regulate their prevalence. Here, we examine six decades of age composition records from thirty-six populations of sockeye salmon (Oncorhynchus nerka) to quantify associations between spawning habitat characteristics and the prevalence of precocious sneakers known as 'jacks'...
November 30, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29192296/reaction-mechanism-of-hydrogen-evolution-catalysed-by-co-and-fe-complexes-containing-a-tetra-dentate-phosphine-ligand-a-dft-study
#12
Ya-Qiong Zhang, Rong-Zhen Liao
The reaction mechanism of the electro-catalytic proton reduction in neutral phosphate buffer enabled by mononuclear cobalt and iron complexes containing a tetra-dentate phosphine ligand (MP4N2, M = Fe, Co) has been elucidated by density functional calculations. The phosphate from the buffer was found to play a crucial role by coordinating to the metal and delivering a proton to the metal hydride in the H-H bond formation. For the more efficient cobalt catalyst, the starting species is a CoII complex with a hydrogen phosphate and a water molecule ligated at the two vacant coordination sites...
December 1, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29191388/tracing-the-evolution-of-venom-phospholipases-a2-in-gloydius-strauchii-and-related-pitvipers-a-tale-of-two-acidic-isozymes
#13
Zhang-Min Yang, Ying-Zhe Xie, Su-Xian Yan, Zhen-Zhen Liu, Jian-Cheng Song, Zhe-Zhi Wang, Inn-Ho Tsai
Two acidic Asp49-PLA2s with Glu6 substitution and a neutral Lys49-PLA (designated Gst-K49) were cloned from G. strauchii venom glands, their full amino acid sequences were deduced. The predominant acidic PLA2 (designated Gst-E6a) contains 124 residues and the M18W30 substitutions, while the minor acidic PLA2 (designated Gst-E6b) contains 122 residues and the V18A30 substitutions. Their sequences are most similar to those of the respective orthologous PLA2s of G. intermedius venom. Gst-E6a and Gst-E6b appear to be paralogs and possibly have different predatory targets or functions...
November 27, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/29191215/domestication-of-self-splicing-introns-during-eukaryogenesis-the-rise-of-the-complex-spliceosomal-machinery
#14
REVIEW
Julian Vosseberg, Berend Snel
ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated...
December 1, 2017: Biology Direct
https://www.readbyqxmd.com/read/29190110/ruthenium-ii-catalyzed-redox-neutral-oxidative-cyclization-of-benzimidates-with-alkenes-with-hydrogen-evolution
#15
Rajendran Manikandan, Masilamani Tamizmani, Masilamani Jeganmohan
1H-Isoindoles and 2H-isoindoles are synthesized via a ruthenium-catalyzed oxidant-free cyclization of benzimidates with alkenes at room temperature with the liberation of H2. Later, 1H-isoindoles were converted into nitrogen-containing heterocycles. The proposed reaction mechanism was strongly supported by experimental evidence and DFT calculations.
November 30, 2017: Organic Letters
https://www.readbyqxmd.com/read/29188140/forelimb-muscle-and-joint-actions-in-archosauria-insights-from-crocodylus-johnstoni-pseudosuchia-and-mussaurus-patagonicus-sauropodomorpha
#16
Alejandro Otero, Vivian Allen, Diego Pol, John R Hutchinson
Many of the major locomotor transitions during the evolution of Archosauria, the lineage including crocodiles and birds as well as extinct Dinosauria, were shifts from quadrupedalism to bipedalism (and vice versa). Those occurred within a continuum between more sprawling and erect modes of locomotion and involved drastic changes of limb anatomy and function in several lineages, including sauropodomorph dinosaurs. We present biomechanical computer models of two locomotor extremes within Archosauria in an analysis of joint ranges of motion and the moment arms of the major forelimb muscles in order to quantify biomechanical differences between more sprawling, pseudosuchian (represented the crocodile Crocodylus johnstoni) and more erect, dinosaurian (represented by the sauropodomorph Mussaurus patagonicus) modes of forelimb function...
2017: PeerJ
https://www.readbyqxmd.com/read/29187995/neutral-lipid-fatty-acid-composition-as-trait-and-constraint-in-collembola-evolution
#17
Ting-Wen Chen, Philipp Sandmann, Ina Schaefer, Stefan Scheu
Functional traits determine the occurrence of species along environmental gradients and their coexistence with other species. Understanding how traits evolved among coexisting species helps to infer community assembly processes. We propose fatty acid composition in consumer tissue as a functional trait related to both food resources and physiological functions of species. We measured phylogenetic signal in fatty acid profiles of 13 field-sampled Collembola (springtail) species and then combined the data with published fatty acid profiles of another 24 species...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29186833/terpenoids-and-phenylpropanoids-in-ligularia-duciformis-l-kongkalingensis-l-nelumbifolia-and-l-limprichtii
#18
Chiaki Kuroda, Ryohei Kobayashi, Ayumi Nagata, Yumi Nakadozono, Taketo Itoh, Yasuko Okamoto, Motoo Tori, Ryo Hanai, Xun Gong
The diversity in root chemicals and evolutionally neutral DNA regions in the complex of Ligularia duciformis, L. kongkalingensis, and L. nelumbifolia (the d/k/n complex) was studied using eight samples collected in central and northern Sichuan Province of China. Cacalol (14) and epicacalone (15), rearranged eremophilanes, were isolated from the complex for the first time. Two new phenylpropanoids were also obtained. Seven of the eight samples produced phenylpropanoids and the other produced lupeol alone. Two of the seven samples also produced furanoeremophilanes or their derivatives and one produced oplopanes...
November 25, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29186343/relative-contributions-of-neutral-and-non-neutral-processes-to-clinal-variation-in-calyx-lobe-length-in-the-series-sakawanum-asarum-aristolochiaceae
#19
Daiki Takahashi, Tsutomu Teramine, Shota Sakaguchi, Hiroaki Setoguchi
Background and Aims: Clines, the gradual variation in measurable traits along a geographical axis, play a major role in evolution and can contribute to our understanding of the relative roles of selective and neutral process in trait variation. Using genetic and morphological analyses, the relative contributions of neutral and non-neutral processes were explored to infer the evolutionary history of species of the series Sakawanum (genus Asarum), which shows significant clinal variation in calyx lobe length...
November 27, 2017: Annals of Botany
https://www.readbyqxmd.com/read/29185996/electrical-conductivity-of-in-sub-2-sub-o-sub-3-sub-and-ga-sub-2-sub-o-sub-3-sub-after-low-temperature-ion-irradiation-implications-for-instrinsic-defect-formation-and-charge-neutrality-level
#20
Lasse Vines, Chidanand Bhoodoo, Holger von Wenckstern, Marius Grundmann
The evolution of sheet resistance of n-type In2O3 and Ga2O3 exposed to bombardment with MeV 12C and 28Si ions at 35 K is studied in situ. While the sheet resistance of Ga2O3 increased by more than 8 orders of magnitude as a result of ion irradiation, In2O3 showed a more complex defect evolution and became more conductive when irradiated at the highest doses. Heating up to room temperature reduced the sheet resistivity somewhat, but Ga2O3 remained highly resistive, while In2O3 showed a lower resistance than as deposited samples...
November 29, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
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