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https://www.readbyqxmd.com/read/28326980/gene-sequence-analyses-of-the-healthy-oral-microbiome-in-humans-and-companion-animals
#1
Eric M Davis
It has long been accepted that certain oral bacterial species are responsible for the development of periodontal disease. However, the focus of microbial and immunological research is shifting from studying the organisms associated with disease to examining the indigenous microbial inhabitants that are present in health. Microbiome refers to the aggregate genetic material of all microorganisms living in, or on, a defined habitat. Recent developments in gene sequence analysis have enabled detection and identification of bacteria from polymicrobial samples, including subgingival plaque...
June 2016: Journal of Veterinary Dentistry
https://www.readbyqxmd.com/read/28318651/postmating-female-control-20-years-of-cryptic-female-choice
#2
REVIEW
Renée C Firman, Clelia Gasparini, Mollie K Manier, Tommaso Pizzari
Cryptic female choice (CFC) represents postmating intersexual selection arising from female-driven mechanisms at or after mating that bias sperm use and impact male paternity share. Although biologists began to study CFC relatively late, largely spurred by Eberhard's book published 20 years ago, the field has grown rapidly since then. Here, we review empirical progress to show that numerous female processes offer potential for CFC, from mating through to fertilization, although seldom has CFC been clearly demonstrated...
March 16, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28298420/staged-induction-of-hiv-1-glycan-dependent-broadly-neutralizing-antibodies
#3
Mattia Bonsignori, Edward F Kreider, Daniela Fera, R Ryan Meyerhoff, Todd Bradley, Kevin Wiehe, S Munir Alam, Baptiste Aussedat, William E Walkowicz, Kwan-Ki Hwang, Kevin O Saunders, Ruijun Zhang, Morgan A Gladden, Anthony Monroe, Amit Kumar, Shi-Mao Xia, Melissa Cooper, Mark K Louder, Krisha McKee, Robert T Bailer, Brendan W Pier, Claudia A Jette, Garnett Kelsoe, Wilton B Williams, Lynn Morris, John Kappes, Kshitij Wagh, Gift Kamanga, Myron S Cohen, Peter T Hraber, David C Montefiori, Ashley Trama, Hua-Xin Liao, Thomas B Kepler, M Anthony Moody, Feng Gao, Samuel J Danishefsky, John R Mascola, George M Shaw, Beatrice H Hahn, Stephen C Harrison, Bette T Korber, Barton F Haynes
A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb...
March 15, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28298352/the-interactions-of-ants-with-their-biotic-environment
#4
EDITORIAL
Guillaume Chomicki, Susanne S Renner
This special feature results from the symposium 'Ants 2016: ant interactions with their biotic environments' held in Munich in May 2016 and deals with the interactions between ants and other insects, plants, microbes and fungi, studied at micro- and macroevolutionary levels with a wide range of approaches, from field ecology to next-generation sequencing, chemical ecology and molecular genetics. In this paper, we review key aspects of these biotic interactions to provide background information for the papers of this special feature After listing the major types of biotic interactions that ants engage in, we present a brief overview of ant/ant communication, ant/plant interactions, ant/fungus symbioses, and recent insights about ants and their endosymbionts...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28295769/hill-robertson-interference-maintained-by-red-queen-dynamics-favours-the-evolution-of-sex
#5
Jack da Silva, James D Galbraith
Although it is well established theoretically that selective interference among mutations (Hill-Robertson interference) favours meiotic recombination, genome-wide mean rates of mutation and strengths of selection appear too low to support this as the mechanism favouring recombination in nature. A possible solution to this discrepancy between theory and observation is that selection is at least intermittently very strong due to the antagonistic coevolution between a host and its parasites. The Red Queen theory posits that such coevolution generates fitness epistasis among loci, which generates negative linkage disequilibrium among beneficial mutations, which in turn favours recombination...
March 15, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28289198/large-scale-identification-of-coevolution-signals-across-homo-oligomeric-protein-interfaces-by-direct-coupling-analysis
#6
Guido Uguzzoni, Shalini John Lovis, Francesco Oteri, Alexander Schug, Hendrik Szurmant, Martin Weigt
Proteins have evolved to perform diverse cellular functions, from serving as reaction catalysts to coordinating cellular propagation and development. Frequently, proteins do not exert their full potential as monomers but rather undergo concerted interactions as either homo-oligomers or with other proteins as hetero-oligomers. The experimental study of such protein complexes and interactions has been arduous. Theoretical structure prediction methods are an attractive alternative. Here, we investigate homo-oligomeric interfaces by tracing residue coevolution via the global statistical direct coupling analysis (DCA)...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28288943/cophylogenetics-and-biogeography-reveal-a-coevolved-relationship-between-sloths-and-their-symbiont-algae
#7
Emily D Fountain, Jonathan N Pauli, Jorge E Mendoza, Jenna Carlson, M Zachariah Peery
Specialized species, like arboreal folivores, often develop beneficial relationships with symbionts to exploit ecologically constrained lifestyles. Although coevolution can drive speciation by specialization of a symbiont to a host, a symbiotic relationship is not indicative of coevolution between host and symbiont. We tested for coevolved relationships between highly specialized two- and three-toed sloths (Choloepus spp. and Bradypus spp., respectively) and their symbiotic algae using cophylogenies and phylogeography...
March 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28282411/coevolution-with-bacteria-drives-the-evolution-of-aerobic-fermentation-in-lachancea-kluyveri
#8
Nerve Zhou, Krishna B S Swamy, Jun-Yi Leu, Michael J McDonald, Silvia Galafassi, Concetta Compagno, Jure Piškur
The Crabtree positive yeasts, such as Saccharomyces cerevisiae, prefer fermentation to respiration, even under fully aerobic conditions. The selective pressures that drove the evolution of this trait remain controversial because of the low ATP yield of fermentation compared to respiration. Here we propagate experimental populations of the weak-Crabtree yeast Lachancea kluyveri, in competitive co-culture with bacteria. We find that L. kluyveri adapts by producing quantities of ethanol lethal to bacteria and evolves several of the defining characteristics of Crabtree positive yeasts...
2017: PloS One
https://www.readbyqxmd.com/read/28281575/exploring-rna-conformational-space-under-sparse-distance-restraints
#9
William R Taylor, Russell S Hamilton
We show that the application of a small number of restraints predicted by coevolution analysis can provide a powerful restriction on the conformational freedom of an RNA molecule. The greatest degree of restriction occurs when a contact is predicted between the distal ends of a pair of adjacent stemloops but even with this location additional flexibilities in the molecule can mask the contribution. Multiple cross-links, especially those including a pseudoknot provided the strongest restraint on conformational freedom with the effect being most apparent in topologically simple folds and less so if the fold is more topologically entwined...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28277703/network-behavior-dynamics-of-adolescent-friendships-alcohol-use-and-physical-activity
#10
Emily Long, Tyson S Barrett, Ginger Lockhart
OBJECTIVE: The coevolution of adolescent social networks, alcohol use, and physical activity is studied. Previous research has independently evaluated each behavior, overlooking the potential power of examining their development within a shared social context. The current study extends previous research by examining the dynamics of friendship networks, alcohol use, and physical activity in conjunction, including the concurrent engagement in both behaviors, with a nationally representative sample of U...
March 9, 2017: Health Psychology: Official Journal of the Division of Health Psychology, American Psychological Association
https://www.readbyqxmd.com/read/28275194/internal-disequilibria-and-phenotypic-diversification-during-replication-of-hepatitis-c-virus-in-a-non-coevolving-cellular-environment
#11
Elena Moreno, Isabel Gallego, Josep Gregori, Adriana Lucía-Sanz, María Eugenia Soria, Victoria Castro, Nathan M Beach, Susanna C Manrubia, Josep Quer, Juan Ignacio Esteban, Charles M Rice, Jordi Gómez, Pablo Gastaminza, Esteban Domingo, Celia Perales
Viral quasispecies evolution upon long-term virus replication in a non-coevolving cellular environment raises relevant general issues such as the attainment of population equilibrium, compliance with the molecular clock hypothesis or stability of the phenotypic profile. Here we evaluate adaptation, mutant spectrum dynamics, and phenotypic diversification of hepatitis C virus (HCV) in the course of two hundred passages in human hepatoma cells in an experimental design that precluded coevolution of the cells with the virus...
March 8, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28270093/machine-learning-classifier-for-identification-of-damaging-missense-mutations-exclusive-to-human-mitochondrial-dna-encoded-polypeptides
#12
Antonio Martín-Navarro, Andrés Gaudioso-Simón, Jorge Álvarez-Jarreta, Julio Montoya, Elvira Mayordomo, Eduardo Ruiz-Pesini
BACKGROUND: Several methods have been developed to predict the pathogenicity of missense mutations but none has been specifically designed for classification of variants in mtDNA-encoded polypeptides. Moreover, there is not available curated dataset of neutral and damaging mtDNA missense variants to test the accuracy of predictors. Because mtDNA sequencing of patients suffering mitochondrial diseases is revealing many missense mutations, it is needed to prioritize candidate substitutions for further confirmation...
March 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28257300/guiding-the-long-way-to-broad-hiv-neutralization
#13
David Peterhoff, Ralf Wagner
PURPOSE OF REVIEW: It has been demonstrated that extensive virus diversification and antibody coevolution are necessary to give rise to broadly neutralizing antibodies targeting the envelope protein of HIV-1. Here, we discuss recent progress of vaccine design approaches aiming on strategies to initiate and guide B-cell development toward this outcome, as well as their evaluation in mouse models engineered to express human antibodies. RECENT FINDINGS: Several specially tailored transgenic mouse strains have been developed to test the concept of engaging and guiding B-cell development by sequential immunizations...
March 2, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28252804/genotype-specificity-among-hosts-pathogens-and-beneficial-microbes-influences-the-strength-of-symbiont-mediated-protection
#14
Benjamin J Parker, Jan Hrček, Ailsa H C McLean, H Charles J Godfray
The microbial symbionts of eukaryotes influence disease resistance in many host-parasite systems. Symbionts show substantial variation in both genotype and phenotype, but it is unclear how natural selection maintains this variation. It is also unknown whether variable symbiont genotypes show specificity with the genotypes of hosts or parasites in natural populations. Genotype by genotype interactions are a necessary condition for coevolution between interacting species. Uncovering the patterns of genetic specificity among hosts, symbionts, and parasites is therefore critical for determining the role that symbionts play in host-parasite coevolution...
March 2, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28252663/dueling-biological-and-social-contagions
#15
Feng Fu, Nicholas A Christakis, James H Fowler
Numerous models explore how a wide variety of biological and social phenomena spread in social networks. However, these models implicitly assume that the spread of one phenomenon is not affected by the spread of another. Here, we develop a model of "dueling contagions", with a particular illustration of a situation where one is biological (influenza) and the other is social (flu vaccination). We apply the model to unique time series data collected during the 2009 H1N1 epidemic that includes information about vaccination, flu, and face-to-face social networks...
March 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28251870/genomic-exaptation-enables-lasius-niger-adaptation-to-urban-environments
#16
Evgenii A Konorov, Mikhail A Nikitin, Kirill V Mikhailov, Sergey N Lysenkov, Mikhail Belenky, Peter L Chang, Sergey V Nuzhdin, Victoria A Scobeyeva
BACKGROUND: The world is rapidly urbanizing, and only a subset of species are able to succeed in stressful city environments. Efficient genome-enabled stress response appears to be a likely prerequisite for urban adaptation. Despite the important role ants play in the ecosytem, only the genomes of ~13 have been sequenced so far. Here, we present the draft genome assembly of the black garden ant Lasius niger - the most successful urban inhabitant of all ants - and we compare it with the genomes of other ant species, including the closely related Camponotus floridanus...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28229287/role-of-neurochemicals-in-the-interaction-between-the-microbiota-and-the-immune-and-the-nervous-system-of-the-host-organism
#17
Alexander V Oleskin, Boris A Shenderov, Vladimir S Rogovsky
This work is concerned with the role of evolutionary conserved substances, neurotransmitters, and neurohormones, within the complex framework of the microbial consortium-immune system-nervous system axis in the human or animal organism. Although the operation of each of these systems per se is relatively well understood, their combined effects on the host organism still await further research. Drawing on recent research on host-produced and microbial low-molecular-weight neurochemicals such as biogenic amines, amino acids, and short-chain fatty acids (SCFAs), we suggest that these mediators form a part of a universal neurochemical "language...
February 22, 2017: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/28223497/architecture-and-coevolution-of-allosteric-materials
#18
Le Yan, Riccardo Ravasio, Carolina Brito, Matthieu Wyart
We introduce a numerical scheme to evolve functional elastic materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures, and the correlations among them can be computed. As an example, we consider an "allosteric" task, which requires the material to respond specifically to a stimulus at a distant active site. We find that functioning materials evolve a less-constrained trumpet-shaped region connecting the stimulus and active sites, and that the amplitude of the elastic response varies nonmonotonically along the trumpet...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28222092/the-genetic-basis-of-resistance-and-matching-allele-interactions-of-a-host-parasite-system-the-daphnia-magna-pasteuria-ramosa-model
#19
Gilberto Bento, Jarkko Routtu, Peter D Fields, Yann Bourgeois, Louis Du Pasquier, Dieter Ebert
Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28220840/coupling-effect-of-nodes-popularity-and-similarity-on-social-network-persistence
#20
Xiaogang Jin, Cheng Jin, Jiaxuan Huang, Yong Min
Network robustness represents the ability of networks to withstand failures and perturbations. In social networks, maintenance of individual activities, also called persistence, is significant towards understanding robustness. Previous works usually consider persistence on pre-generated network structures; while in social networks, the network structure is growing with the cascading inactivity of existed individuals. Here, we address this challenge through analysis for nodes under a coevolution model, which characterizes individual activity changes under three network growth modes: following the descending order of nodes' popularity, similarity or uniform random...
February 21, 2017: Scientific Reports
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