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Neutral evolution

Elena Sugrue, Paul D Carr, Colin Scott, Colin J Jackson
The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little is known regarding how enzymes can naturally evolve active sites with highly reactive and desolvated charges. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated from different bacterial strains: TrzN from Nocardioides sp. strain MTD22 contains a catalytic glutamate residue (Glu241) that is surrounded by hydrophobic and aromatic second-shell residues (Pro214, Tyr215), whereas TrzN from Nocardioides sp...
October 21, 2016: Biochemistry
Yong Yang, Mei Wang, Peili Zhang, Weihan Wang, Hongxian Han, Licheng Sun
Modification of p-type Si surface by active and stable earth abundant electrocatalysts is an effective strategy to improve the sluggish kinetics for the hydrogen evolution reaction (HER) at p-Si/electrolyte interface and to develop highly efficient and low-cost photocathodes for hydrogen production from water. To this end, Si nanowire (Si-NW) array has been loaded with highly efficient electrocatalysts, M-B (M = Ni, Co), by facile and quick electroless plating to build M-B catalyst-modified Si nanowire-array-textured photocathodes for water reduction to H2...
October 20, 2016: ACS Applied Materials & Interfaces
Zhanna Kobalava
The burden of cardiovascular diseases (CVD) in general and heart failure (HF) in particular continues to increase worldwide. CVD are major contributors to death and morbidity and recognized as important drivers of healthcare expenditure. Chronic overactivity of the renin-angiotensin-aldosterone system (RAAS) plays a key role in human hypertension and HF pathophysiology. RAAS is fundamental in the overall regulation of cardiovascular homeostasis through the actions of hormones, which regulate vascular tone, and specifically blood pressure through vasoconstriction and renal sodium and water retention...
September 2016: Journal of Hypertension
Jialei Du, Jianying Wang, Lvlv Ji, Xiaoxiang Xu, Zuofeng Chen
Although significant progress has been made recently, copper-based materials had long been considered to be ineffective catalysts toward hydrogen evolution reaction (HER), in most cases, requiring high overpotentials more than 300 mV. We report here that a Cu(0)-based nanoparticle film electrodeposited in situ from a Cu(II) oxime complex can act as a highly active and robust HER electrocatalyst in neutral phosphate buffer solution. The as-prepared nanoparticle film is of poor crystallization, which incorporates significant amounts of oxime ligand residues and buffer anions PO43-...
October 17, 2016: ACS Applied Materials & Interfaces
Trevor A Graham, Andrea Sottoriva
The temporal dynamics of cancer evolution remain elusive because it is impractical to longitudinally observe cancers unperturbed by treatment. Consequently, our knowledge of how cancers grow largely derives from inferences made from a single point in time - the end point in the cancer's evolution when it is removed from the body and studied in the lab. Fortuitously however, the cancer genome, by virtue of on-going mutations that uniquely mark clonal lineages within the tumour, provides a rich yet surreptitious record of cancer development...
October 14, 2016: Journal of Pathology
Soohyung Park, Junkyeong Jeong, Gyeongho Hyun, Minju Kim, Hyunbok Lee, Yeonjin Yi
The energy level alignments at donor/acceptor interfaces in organic photovoltaics (OPVs) play a decisive role in device performance. However, little is known about the interfacial energetics in polymer OPVs due to technical issues of the solution process. Here, the frontier ortbial line-ups at the donor/acceptor interface in high performance polymer OPVs, PTB7/PC71BM, were investigated using in situ UPS, XPS and IPES. The evolution of energy levels during PTB7/PC71BM interface formation was investigated using vacuum electrospray deposition, and was compared with that of P3HT/PC61BM...
October 13, 2016: Scientific Reports
Evgeni Bolotin, Ruth Hershberg
Gene loss is a major contributor to the evolution of bacterial gene content. Gene loss may occur as a result of shifts in environment leading to changes in the intensity and/or directionality of selection applied for the maintenance of specific genes. Gene loss may also occur in a more neutral manner, when gene functions are lost that were not subject to strong selection to be maintained, irrespective of changes to environment. Here, we used a pangenome-based approach to investigate patterns of gene loss across 15 bacterial species...
October 13, 2016: Scientific Reports
Eric R Weiss, Galit Alter, Javier Gordon Ogembo, Jennifer L Henderson, Barbara Tabak, Yasin Bakiş, Mohan Somasundaran, Manuel Garber, Liisa Selin, Katherine Luzuriaga
: The Epstein Barr virus (EBV) gp350 glycoprotein interacts with the cellular receptor to mediate viral entry and is thought to be the major target for neutralizing antibodies. To better understand the role of EBV-specific antibodies in the control of viral replication and evolution of sequence diversity, we measured EBV gp350-specific antibody responses and sequenced the gp350 gene in samples obtained from individuals experiencing primary EBV infection (acute infectious mononucleosis; AIM) and again 6 months later (convalescence, CONV)...
October 12, 2016: Journal of Virology
Hui Song, Pengfei Wang, Changsheng Li, Suoyi Han, Javier Lopez-Baltazar, Xinyou Zhang, Xingjun Wang
Lipoxygenase (LOX) genes are widely distributed in plants and play crucial roles in resistance to biotic and abiotic stress. Although they have been characterized in various plants, little is known about the evolution of legume LOX genes. In this study, we identified 122 full-length LOX genes in Arachis duranensis, Arachis ipaënsis, Cajanus cajan, Cicer arietinum, Glycine max, Lotus japonicus and Medicago truncatula. In total, 64 orthologous and 36 paralogous genes were identified. The full-length, polycystin-1, lipoxygenase, alpha-toxin (PLAT) and lipoxygenase domain sequences from orthologous and paralogous genes exhibited a signature of purifying selection...
October 12, 2016: Scientific Reports
Marta Haro, Claudia Solis, Vicente M Blas-Ferrando, Olivier Margeat, Sadok Ben Dhkil, Christine Videlot-Ackermann, Jörg Ackermann, Fabio Di Fonzo, Antonio Guerrero, Sixto Gimenez
Here, we have developed an organic photocathode for water reduction to H2 , delivering more than 1 mA cm(-2) at 0 V versus RHE and above 3 mA cm(-2) at -0.5 V versus RHE with moderate stability under neutral pH conditions. The initial competitive reduction of water to H2 and ZnO to metallic Zn is responsible for the dynamic behaviour of both photocurrent and Faradaic efficiency of the device, which reaches 100 % Faradaic efficiency after 90 min operation. In any case, outstanding stable H2 flow of approximately 2 μmol h(-1) is measured over 1 h at 0 V versus RHE and at neutral pH, after equilibrium between the Zn(2+) /Zn(0) concentration in the AZO film is reached...
October 12, 2016: ChemSusChem
Yongxia Cui, Beng Kah Song, Lin-Feng Li, Ya-Ling Li, Zhongyun Huang, Ana L Caicedo, Yulin Jia, Kenneth M Olsen
Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation...
October 11, 2016: G3: Genes—Genomes—Genetics
Celia Payen, Anna B Sunshine, Giang T Ong, Jamie L Pogachar, Wei Zhao, Maitreya J Dunham
High-throughput sequencing has enabled genetic screens that can rapidly identify mutations that occur during experimental evolution. The presence of a mutation in an evolved lineage does not, however, constitute proof that the mutation is adaptive, given the well-known and widespread phenomenon of genetic hitchhiking, in which a non-adaptive or even detrimental mutation can co-occur in a genome with a beneficial mutation and the combined genotype is carried to high frequency by selection. We approximated the spectrum of possible beneficial mutations in Saccharomyces cerevisiae using sets of single-gene deletions and amplifications of almost all the genes in the S...
October 2016: PLoS Genetics
Yujun Cui, Yajun Song
This chapter summarizes researches on genome and evolution features of Yersinia pestis, the young pathogen that evolved from Y. pseudotuberculosis at least 5000 years ago. Y. pestis is a highly clonal bacterial species with closed pan-genome. Comparative genomic analysis revealed that genome of Y. pestis experienced highly frequent rearrangement and genome decay events during the evolution. The genealogy of Y. pestis includes five major branches, and four of them seemed raised from a "big bang" node that is associated with the Black Death...
2016: Advances in Experimental Medicine and Biology
Zonghua Pu, Ibrahim Saana Amiinu, Xiaobo Liu, Min Wang, Shichun Mu
There is a crucial demand for cost-effective hydrogen evolution reaction (HER) catalysts towards future renewable energy systems, and the development of such catalysts operating under all pH conditions still remains a challenging task. In this work, a one-step facile approach to synthesizing nitrogen-doped carbon encapsulating molybdenum phosphide nanoparticles (MoP NPs@NC) is introduced by using ammonium molybdate, ammonium dihydrogen phosphate and melamine as precursor. Benefitting from structural advantages, including ultrasmall nanoparticles, large exposed surface area and fast charge transfer, MoP NPs@NC exhibits excellent HER catalytic activities with small overpotentials at all pH values (j = 10 mA cm(-2) at η = 115, 136 and 80 mV in 0...
October 6, 2016: Nanoscale
Zhen-Tao Yu, Xiao-Le Liu, Yong-Jun Yuan, Yong-Hui Li, Guang-Hui Chen, Zhi-Gang Zou
Well-defined gold sensitizers for hydrogen production from water remain extremely rare despite decades of interest, and are currently limited to systems based on ruthenium, iridium or platinum complexes. This report details the synthesis and characterization of a series of neutral cyclometalated gold(iii) complexes of the type [(RC^N^CR)Au(C[triple bond, length as m-dash]C-R')] (R = H or tert-butyl group; R' = aryl groups) that have been found to be good candidates to function as harvesting materials in light-induced electron transfer reactions...
October 6, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Artem Rudenko, Varun Makhija, Aram Vajdi, Thorsten Ergler, Markus Schürholz, Rajesh K Kushawaha, Joachim Ullrich, Robert Moshammer, Vinod Kumarappan
Temporal evolution of electronic and nuclear wave packets created in strong-field excitation of the carbon dioxide molecule is studied employing momentum-resolved ion spectroscopy and channel-selective Fourier analysis. Combining the data obtained with two different pump-probe set-ups, we observed signatures of vibrational dynamics in both, ionic and neutral states of the molecule. We consider far-off-resonance two-photon Raman scattering to be the most likely mechanism of vibrational excitation in the electronic ground state of the neutral CO2...
September 23, 2016: Faraday Discussions
A Fuente, J Cernicharo, E Roueff, M Gerin, J Pety, N Marcelino, R Bachiller, B Lefloch, O Roncero, A Aguado
CONTEXT: Barnard B1b has revealed as one of the most interesting globules from the chemical and dynamical point of view. It presents a rich molecular chemistry characterized by large abundances of deuterated and complex molecules. Furthermore, it hosts an extremely young Class 0 object and one candidate to First Hydrostatic Core (FHSC) proving the youth of this star forming region. AIMS: Our aim is to determine the cosmic ray ionization rate, [Formula: see text], and the depletion factors in this extremely young star forming region...
September 2016: Astronomy and Astrophysics
Jan Verpooten, Siegfried Dewitte
Two major mechanisms of aesthetic evolution have been suggested. One focuses on naturally selected preferences (Evolutionary Aesthetics), while the other describes a process of evaluative coevolution whereby preferences coevolve with signals. Signaling theory suggests that expertise moderates these mechanisms. In this article we set out to verify this hypothesis in the domain of art and use it to elucidate Western modern art's deviation from naturally selected preferences. We argue that this deviation is consistent with a Coevolutionary Aesthetics mechanism driven by prestige-biased social learning among art experts...
October 4, 2016: Human Nature: An Interdisciplinary Biosocial Perspective
Sudeesh Karumathil, Vijaya R Dirisala, Uthpala Srinadh, Valaboju Nikhil, N Satya Sampath Kumar, Rahul R Nair
Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed...
2016: Bioinformatics and Biology Insights
Quanjun Hu, Huichao Peng, Hao Bi, Zhiqiang Lu, Dongshi Wan, Qian Wang, Kangshan Mao
Interspecific hybridization and introgression can lead to partial genetic homogenization at certain neutral loci between morphologically distinct species and may obscure the species delimitation using nuclear genes. In this study, we investigated this phenomenon through population genetic survey of two alpine plants (Gentiana siphonantha and G. straminea) in the Qinghai-Tibet Plateau, where the distributions of two species are partly overlapped. We identified two clusters of chloroplast DNA haplotypes which correspond to the two species, and three clusters of ITS ribotypes...
September 30, 2016: Scientific Reports
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