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Neutral evolution

Darren A Natale, Cecilia N Arighi, Judith A Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R Christie, Julie Cowart, Peter D'Eustachio, Alexander D Diehl, Harold J Drabkin, William D Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H Wu
The Protein Ontology (PRO; formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference...
November 28, 2016: Nucleic Acids Research
Magdalena Bonarowska, Maria Wojciechowska, Maciej Zieliński, Angelika Kiderys, Michał Zieliński, Piotr Winiarek, Zbigniew Karpiński
Pd/MgO, Pd/MgF₂ and Pd/MgO-MgF₂ catalysts were investigated in the reaction of CCl₄ hydrodechlorination. All the catalysts deactivated in time on stream, but the degree of deactivation varied from catalyst to catalyst. The MgF₂-supported palladium with relatively large metal particles appeared the best catalyst, characterized by good activity and selectivity to C₂-C₅ hydrocarbons. Investigation of post-reaction catalyst samples allowed to find several details associated with the working state of hydrodechlorination catalysts...
November 25, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Julieta M Manrique, Leandro R Jones
This work set out to shed light on the phylogeography of the SAR11 clade of Alphaproteobacteria, which is probably the most abundant group of heterotrophic bacteria on Earth. In particular, we assessed the degree to which empirical evidence (environmental DNA sequences) supports the concept that SAR11 lineages evolve faster than they are dispersed thus generating vicariant distributions, as predicted by recent simulation efforts. We generated 16S rRNA gene sequences from surface seawater collected at the South West Atlantic Ocean and combined these data with previously published sequences from similar environments from elsewhere...
November 25, 2016: Molecular Phylogenetics and Evolution
Tatiana Corrêa Ribeiro, Carla Weiblen, Maria Isabel de Azevedo, Sônia de Avila Botton, Lizandra Jaqueline Robe, Daniela Isabel Brayer Pereira, Danieli Urach Monteiro, Douglas Miotto Lorensetti, Janio Morais Santurio
Pythium insidiosum is an important oomycete due to its ability to infect humans and animals. It causes pythiosis, a disease of difficult treatment that occurs more frequently in humans in Thailand and in horses in Brazil. Since cell-wall components are frequently related to host shifts, we decided here to use sequences from the exo-1.3-β-glucanase gene (exo1), which encodes an immunodominant protein putatively involved in cell wall remodeling, to investigate the microevolutionary relationships of Brazilian and Thai isolates of P...
November 25, 2016: Infection, Genetics and Evolution
Yinze Zhang, Fan Wu, Manni Wang, Naibao Zhuang, Huayou Zhou, Hua Xu
BACKGROUND: Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. When RhD-negative individuals are exposed to RhD-positive blood, they may produce anti-D alloantibody, potentially resulting in delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn, which are difficult to treat. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases...
November 11, 2016: Blood Transfusion, Trasfusione del Sangue
Julia C Geue, Csongor I Vágási, Mona Schweizer, Péter L Pap, Henri A Thomassen
Both neutral and adaptive evolutionary processes can cause population divergence, but their relative contributions remain unclear. We investigated the roles of these processes in population divergence in house sparrows (Passer domesticus) from Romania and Bulgaria, regions characterized by high landscape heterogeneity compared to Western Europe. We asked whether morphological divergence, complemented with genetic data in this human commensal species, was best explained by environmental variation, geographic distance, or landscape resistance-the effort it takes for an individual to disperse from one location to the other-caused by either natural or anthropogenic barriers...
November 2016: Ecology and Evolution
Federico Boschi, Vanni Rizzatti, Mauro Zamboni, Andrea Sbarbati
BACKGROUND: Lipid droplets are cellular organelles that regulate the storage and hydrolysis of neutral lipids. The dynamic of lipid droplets (LDs), during the differentiation process from fibroblast-like cells into adipocyte, is strictly related to the lipid storage in cells. The number and size of the LDs depends on the lipidic or lipolytic stimulations to which the cells are exposed. METHOD: Here, we propose a computational approach to study the processes regulating the LDs' number and growth/reduction in size using Monte Carlo simulations...
January 2017: Computer Methods and Programs in Biomedicine
Myrna Sheldon
Stephen Jay Gould was a paleontologist and scientific celebrity at the close of the twentieth century, most famous for his popular writings on evolution and his role in the American creationist controversies of that era. In the early 1980s, Gould was drawn into the "nuclear winter" episode through his friendship with Carl Sagan, an astronomer and popular science celebrity. Sagan helped develop the theory of nuclear winter and subsequently used the theory as evidence to petition the United States government to scale back its nuclear armament...
November 21, 2016: Endeavour
Moisés A Bernal, Michelle R Gaither, W Brian Simison, Luiz A Rocha
Closely related marine species with large sympatric ranges provide opportunities to study the mechanisms of speciation, particularly when there is evidence of gene flow between the lineages. Here we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via Restriction-site Associated DNA Sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister species...
November 22, 2016: Molecular Ecology
Kathleen G Ferris
Identifying the individual loci and mutations that underlie adaptation to extreme environments has long been a goal of evolutionary biology. However, finding the genes that underlie adaptive traits is difficult for several reasons. First, because many traits and genes evolve simultaneously as populations diverge, it is difficult to disentangle adaptation from neutral demographic processes. Second, finding the individual loci involved in any trait is challenging given the respective limitations of quantitative and population genetic methods...
November 2016: Molecular Ecology
Taeyong Kwon, Dong-Uk Lee, Sung J Yoo, Sang H Je, Jeong Y Shin, Young S Lyoo
Porcine circovirus type 2 (PCV2) is a causative agent of PCV2-associated disease (PCVAD), which leads to enormous economic losses in the swine industry worldwide. A high nucleotide substitution rate allows for the continuous evolution of PCV2 and the emergence of novel PCV2 strains. However, the distribution of emerging PCV2 genotypes and the co-existence of multiple genotypes in Korea have not been elucidated. The objective of this study was to determine the genetic diversity of PCV2 in Korean pig herds between 2009 and 2016...
November 17, 2016: Virus Research
Hiroyuki Kaneko, Tsutomu Minegishi, Mamiko Nakabayashi, Naoya Shibata, Kazunari Domen
A (ZnSe)0.85 (CuIn0.7 Ga0.3 Se2 )0.15 photocathode with a bilayer structure was fabricated and found to exhibit a photocurrent almost twice that of a photocathode with a monolayer structure during hydrogen evolution from water. The cathodic photocurrent reached maximum values of 12 and 4.9 mA cm(-2) at 0 and 0.6 VRHE in a neutral phosphate buffer under simulated sunlight, while the half-cell solar-to-hydrogen conversion efficiency was 3.0 % at 0.6 VRHE , with a maximum value of 3.6 % at 0.45 VRHE ...
November 9, 2016: Angewandte Chemie
Georges Khalil, Christophe Orvain, Lu Fang, Laurent Barloy, Alain Chaumont, Christian Gaiddon, Marc Henry, Nathalie Kyritsakas, Pierre Mobian
This manuscript describes the synthesis of a series of neutral titanium(iv) monomeric complexes constructed around a TiO4N2 core. The two nitrogen atoms that compose the coordination sphere of the metallic center belong to 2,2'-bipyrimidine ligands homo-disubstituted in the 4 and 4' positions by methyl (2a), phenylvinyl (2b), naphthylvinyl (2c) or anthrylvinyl (2d) groups. The crystal structures of these complexes named [Ti(1)2(2a)], [Ti(1)2(2b)], [Ti(1)2(2c)] and [Ti(1)2(2d)] (where 1 is a 2,2'-biphenolato ligand substituted in the 6 and 6' positions by phenyl groups) are reported...
November 18, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Toshihiro Takashima, Koki Ishikawa, Hiroshi Irie
The rate-determining step of the oxygen evolution reaction on hematite electrodes was switched from the sequential electron/proton transfer process to the concerted proton-coupled electron transfer (CPET) process by adding pyridine derivatives to the electrolyte. By inducing the CPET process, the overpotential for oxygen evolution at neutral pH decreased by approximately 250 mV.
November 17, 2016: Chemical Communications: Chem Comm
S Abigail Smith, Samantha L Burton, William Kilembe, Shabir Lakhi, Etienne Karita, Matt Price, Susan Allen, Eric Hunter, Cynthia A Derdeyn
A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative (IAVI) sites reported that viral load, HLA-A*03 genotype, and subtype C infection were strongly associated with the development of neutralization breadth. Here, we refine the findings of that study by analyzing the impact of the transmitted/founder (T/F) envelope (Env), early Env diversification, and autologous neutralization on the development of plasma neutralization breadth in 21 participants identified during recent infection at two of those sites: Kigali, Rwanda (n = 9) and Lusaka, Zambia (n = 12)...
November 2016: PLoS Pathogens
S U Franssen, R Kofler, C Schlötterer
The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose 'Evolve and Resequence' as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations...
November 16, 2016: Heredity
Murray Cadzow, Tony R Merriman, James Boocock, Nicola Dalbeth, Lisa K Stamp, Michael A Black, Peter M Visscher, Phillip L Wilcox
BACKGROUND: The gene PPARGC1A, in particular the Gly482Ser variant (rs8192678), had been proposed to be subject to natural selection, particularly in recent progenitors of extant Polynesian populations. Reasons include high levels of population differentiation and increased frequencies of the derived type 2 diabetes (T2D) risk 482Ser allele, and association with body mass index (BMI) in a small Tongan population. However, no direct statistical tests for selection have been applied. METHODS: Using a range of Polynesian populations (Tongan, Māori, Samoan) we re-examined evidence for association between Gly482Ser with T2D and BMI as well as gout...
November 15, 2016: BMC Medical Genetics
Supriyo Chakraborty, Debojyoti Nag, Tarikul Huda Mazumder, Arif Uddin
Codon bias study in an organism gains significance in understanding the molecular mechanism as well as the functional conservation of gene expression during the course of evolution. The prime focus in this study is to compare the codon usage patterns among the four species belonging to the genus Bungarus (B. multicinctus, B. fasciatus, B. candidus and B. flaviceps) using several codon bias parameters. Our results suggested that relatively low codon bias exists in the coding sequences of the selected species...
November 11, 2016: Gene
Stanislaw J Gabryszewski, Satish K Dhingra, Jill M Combrinck, Ian A Lewis, Paul S Callaghan, Matthew R Hassett, Amila Siriwardana, Philipp P Henrich, Andrew H Lee, Nina F Gnädig, Lise Musset, Manuel Llinás, Timothy J Egan, Paul D Roepe, David A Fidock
Southeast Asia is an epicenter of multidrug-resistant Plasmodium falciparum strains. Selective pressures on the subcontinent have recurrently produced several allelic variants of parasite drug resistance genes, including the P. falciparum chloroquine resistance transporter (pfcrt). Despite significant reductions in the deployment of the 4-aminoquinoline drug chloroquine (CQ), which selected for the mutant pfcrt alleles that halted CQ efficacy decades ago, the parasite pfcrt locus is continuously evolving. This is highlighted by the presence of a highly mutated allele, Cam734 pfcrt, which has acquired the singular ability to confer parasite CQ resistance without an associated fitness cost...
November 2016: PLoS Pathogens
Aiti Vizzini, Maria Giovanna Parisi, Laura Cardinale, Lelia Testasecca, Matteo Cammarata
Although the Tumor necrosis factor gene superfamily seems to be very conserved in vertebrates, phylogeny, tissue expression, genomic and gene organization, protein domains and polymorphism analyses showed that a strong change has happened mostly in invertebrates in which protochordates were a constraint during the immune-molecules history and evolution. RT PCR was used to investigate differential gene expression in different tissues. The expression shown was greater in the pharynx. Single-nucleotide polymorphism has been investigated in Ciona intestinalis Tumor necrosis factor alpha (CiTNFα) mRNA isolated from the pharynx of 30 ascidians collected from Licata, Sicily (Italy), by denaturing gradient gel electrophoresis (DGGE)...
November 6, 2016: Developmental and Comparative Immunology
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