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Neutral evolution

Jens Klockgether, Nina Cramer, Sebastian Fischer, Lutz Wiehlmann, Burkhard Tümmler
RATIONALE: The chronic airway infections with Pseudomonas aeruginosa determine morbidity in most individuals with cystic fibrosis (CF). P. aeruginosa may persist for decades in CF lungs which provides the rare opportunity to study the long-term within-host evolution of a bacterial airway pathogen. OBJECTIVES: To resolve the genetic adaptation of P. aeruginosa in CF lungs from the onset of colonization until the patient's death or permanent replacement by another P...
February 22, 2018: American Journal of Respiratory Cell and Molecular Biology
Minsoo Kim, Brooke R Druliner, Nikolaos Vasmatzis, Taejeong Bae, Nicholas Chia, Alexej Abyzov, Lisa A Boardman
Besides the classical evolutionary model of colorectal cancer (CRC) defined by the stepwise accumulation of mutations in which normal epithelium transforms through an intermediary polyp stage to cancer, a few studies have proposed alternative modes of evolution (MOE): early eruptive subclonal expansion, branching of the subclones in parallel evolution, and neutral evolution. However, frequencies of MOEs and their connection to mutational characteristics of cancer remain elusive. In this study, we analyzed patterns of somatic single nucleotide variations (SNVs) and copy number aberrations (CNAs) in CRC with residual polyp of origin from 13 patients in order to determine this relationship...
January 23, 2018: Oncotarget
Jiyun M Moon, David M Aronoff, John A Capra, Patrick Abbot, Antonis Rokas
Sialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activation to recycling and degradation, are involved in sialic acid biology. Because of their role in immunity, sialic acid biology genes have been hypothesized to exhibit elevated rates of evolutionary change. Consistent with this hypothesis, several genes involved in sialic acid biology have experienced higher rates of non-synonymous substitutions in the human lineage than their counterparts in other great apes, perhaps in response to ancient pathogens that infected hominins millions of years ago (paleopathogens)...
February 21, 2018: G3: Genes—Genomes—Genetics
Yuchao Zhang, Hongna Zhang, Anan Liu, Chuncheng Chen, Wenjing Song, Jincai Zhao
Photoelectrochemical (PEC) water oxidation has attracted heightened interest in solar fuel production. It is well accepted that water oxidation on hematite is mediated by surface trapped holes, characterized to be the high valent -Fe═O species. However, the mechanism of the subsequent rate-limiting O-O bond formation step is still a missing piece. Herein we investigate the reaction order of interfacial hole transfer by rate law analysis based on electrochemical impedance spectroscopy (EIS) measurement and probe the reaction intermediates by operando Fourier-transform infrared (FT-IR) spectroscopy...
February 21, 2018: Journal of the American Chemical Society
Juan Li, Jin Jiang, Su-Yan Pang, Yang Zhou, Yuan Gao, Yi Yang, Shaofang Sun, Guanqi Liu, Jun Ma, Chengchun Jiang, Lihong Wang
This work investigated impacts of iodide (I- ) on the transformation of the widely used phenolic preservative methylparaben (MeP) as well as 11 other phenolic compounds by potassium permanganate (KMnO4 ). It was found that KMnO4 showed a low reactivity towards MeP in the absence of I- with apparent second-order rate constants (kapp ) ranging from 0.065 ± 0.0071 to 1.0 ± 0.1 M-1 s-1 over the pH range of 5-9. The presence of I- remarkably enhanced the transformation rates of MeP by KMnO4 via the contribution of hypoiodous acid (HOI) in situ formed, which displayed several orders of magnitude higher reactivity towards MeP than KMnO4 ...
February 10, 2018: Water Research
Brian T Graham, Axel C Moore, David L Burris, Christopher Price
The interstitial fluid within articular cartilage shields the matrix from mechanical stresses, reduces friction and wear, enables biochemical processes, and transports solutes into and out of the avascular extracellular matrix. The balanced competition between fluid exudation and recovery under load is thus critical to the mechanical and biological functions of the tissue. We recently discovered that sliding alone can induce rapid solute transport into buried cartilage contact areas via a phenomenon termed tribological rehydration...
February 8, 2018: Journal of Biomechanics
Lacey L Westphal, Jasmine Lau, Zuly Negro, Ivan J Moreno, Wazim Ismail Mohammed, Heewook Lee, Haixu Tang, Steven E Finkel, Karin E Kram
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms...
February 14, 2018: Research in Microbiology
Arjun K Mishra, Roy A Mariuzza
Affinity maturation is the process whereby the immune system generates antibodies of higher affinities during a response to antigen. It is unique in being the only evolutionary mechanism known to operate on a molecule in an organism's own body. Deciphering the structural mechanisms through which somatic mutations in antibody genes increase affinity is critical to understanding the evolution of immune repertoires. Next-generation sequencing (NGS) has allowed the reconstruction of antibody clonal lineages in response to viral pathogens, such as HIV-1, which was not possible in earlier studies of affinity maturation...
2018: Frontiers in Immunology
David B Saakian
We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness)...
January 2018: Physical Review. E
Jing Shaw, Jaume Jorba, Kun Zhao, Jane Iber, Qi Chen, Festus Adu, Adekunle Adeniji, David Bukbuk, Marycelin Baba, Elizabeth Henderson, Naomi Dybdahl-Sissoko, Sharla Macdonald, William C Weldon, Nicksy Gumede, M Steven Oberste, Olen M Kew, Cara C Burns
We followed the dynamics of capsid amino acid replacement among 403 Nigerian outbreak isolates of type 2 circulating vaccine-derived poliovirus (cVDPV2) from 2005 through 2011. Four different functional domains were analyzed: 1) neutralizing antigenic (NAg) sites, 2) residues binding the poliovirus receptor (PVR), 3) VP1 residues 1-32, and 4) the capsid structural core. Amino acid replacements mapped to 37 of 43 positions across all 4 NAg sites; the most variable and polymorphic residues were in NAg sites 2 and 3b...
February 14, 2018: Journal of Virology
Darren E Irwin
Theory and empirical patterns suggest a disproportionate role for sex chromosomes in evolution and speciation. Focusing on ZW sex determination (females ZW, males ZZ; the system in birds, many snakes, and lepidopterans), I review how evolutionary dynamics are expected to differ between the Z, W, and the autosomes, discuss how these differences may lead to a greater role of the sex chromosomes in speciation, and use data from birds to compare relative evolutionary rates of sex chromosomes and autosomes. Neutral mutations, partially or completely recessive beneficial mutations, and deleterious mutations under many conditions are expected to accumulate faster on the Z than on autosomes...
February 14, 2018: Molecular Ecology
Victor Ovchinnikov, Joy E Louveau, John P Barton, Martin Karplus, Arup K Chakraborty
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest specific classes of evolutionary lineages: if germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs...
February 14, 2018: ELife
John Bryden, Shaun P Wright, Vincent A A Jansen
Language transmission, the passing on of language features such as words between people, is the process of inheritance that underlies linguistic evolution. To understand how language transmission works, we need a mechanistic understanding based on empirical evidence of lasting change of language usage. Here, we analysed 200 million online conversations to investigate transmission between individuals. We find that the frequency of word usage is inherited over conversations, rather than only the binary presence or absence of a word in a person's lexicon...
February 2018: Journal of the Royal Society, Interface
Mary K Wang, Yi Li, Rachel E Selekman, Thomas Gaither, Anne Arnhym, Laurence S Baskin
INTRODUCTION: Patients undergo pediatric urologic surgery as infants and young children. OBJECTIVE: The purpose of the study was to evaluate the evolution of surgical scars over several years in order to inform parents and surgeons on the true cosmetic impact of pediatric surgery and evaluate patient scar satisfaction. STUDY DESIGN: This was a cross-sectional study where patients who have undergone urologic surgery at a young age are evaluated years later for scar satisfaction via an abbreviated validated questionnaire...
January 9, 2018: Journal of Pediatric Urology
Zhi-Mei Luo, Jia-Wei Wang, Jing-Bo Tan, Zhi-Ming Zhang, Tong-Bu Lu
We develop a facile self-template synthetic method to construct hierarchical Co-Se-S-O (CoSexS2-x@Co(OH)2) nanotubes on a carbon cloth as a self-standing electrode for electrocatalytic oxygen-evolution reaction (OER). In the synthetic process, the separate selenization and sulfurization on Co(OH)F precursor in different solvents has played an important role in constructing CoSexS2-x (Co-Se-S) hierarchical nanotubes, which was further transformed into the nanotube-like Co-Se-S-O via an in situ electrochemical oxidation process...
February 13, 2018: ACS Applied Materials & Interfaces
E López, D Ascenzi, P Tosi, J M Bofill, J de Andrés, M Albertí, J M Lucas, A Aguilar
Cyclopropyl cyanide and other simple nitriles detected in Titan's atmosphere could be precursors leading to the formation of organic macromolecules in the atmosphere of Saturn's largest satellite. Proposing a thermodynamically possible mechanism that explains their formation and supports experimental results represents a difficult challenge. Experiments done in the Atomic and Molecular Physics Laboratory at the University of Trento (AMPL) have studied the ion-molecule reaction between cyclopropyl cyanide and its protonated form, with reaction products being characterized by mass spectrometry...
February 12, 2018: Physical Chemistry Chemical Physics: PCCP
Jyoti Bala, Srinivasan Chinnapaiyan, Rajib Kumar Dutta, Hoshang Unwalla
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range...
February 12, 2018: RNA Biology
Protyusha Dey, Amit Roy
Industrial applications of xylanases have made this enzyme an important subject of applied research work. Function of this particular enzyme is to degrade or hydrolyze the plentiful polysaccharide xylan, an important component of hemicellulose. It mainly cleaves the backbone of xylan that is made up of a number of xylose residues connected with β-1,4-glycosidic linkages. Fungi with mycelia are regarded as the best producer of xylanases. These varied xylanases not only differ in their sizes and shapes but also differ in their physicochemical properties...
February 2018: 3 Biotech
Breno Frederico de Carvalho Dominguez Souza, Alexander König, Andrea Rasche, Ianei de Oliveira Carneiro, Nora Stephan, Victor Max Corman, Pia Luise Roppert, Nora Goldmann, Ramona Kepper, Simon Franz Müller, Christof Völker, Alex Junior Souza de Souza, Michele Soares Gomes-Gouvêa, Andrés Moreira-Soto, Andreas Stöcker, Michael Nassal, Carlos Roberto Franke, João Renato Rebello Pinho, Manoel do Carmo Pereira Soares, Joachim Geyer, Philippe Lemey, Christian Drosten, Eduardo Martins Netto, Dieter Glebe, Jan Felix Drexler
BACKGROUND & AIMS: All known hepatitis B virus (HBV) genotypes occur in humans and hominoid Old World nonhuman primates (NHP). The divergent Woolly Monkey HBV (WMHBV) forms another orthohepadnavirus species. The evolutionary origins of HBV are unclear. METHODS: We analyzed sera from 124 Brazilian monkeys collected during 2012-2016 for hepadnaviruses using molecular and serological tools and conducted evolutionary analyses. RESULTS: We identified a novel orthohepadnavirus species in capuchin monkeys (CMHBV)...
February 8, 2018: Journal of Hepatology
Frederik Lermyte, Dirk Valkenborg, Joseph A Loo, Frank Sobott
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation...
February 9, 2018: Mass Spectrometry Reviews
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