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Coevolution

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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
#1
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 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28220840/coupling-effect-of-nodes-popularity-and-similarity-on-social-network-persistence
#2
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
https://www.readbyqxmd.com/read/28212440/emergent-inequality-and-self-organized-social-classes-in-a-network-of-power-and-frustration
#3
Benoit Mahault, Avadh Saxena, Cristiano Nisoli
We propose a simple agent-based model on a network to conceptualize the allocation of limited wealth among more abundant expectations at the interplay of power, frustration, and initiative. Concepts imported from the statistical physics of frustrated systems in and out of equilibrium allow us to compare subjective measures of frustration and satisfaction to collective measures of fairness in wealth distribution, such as the Lorenz curve and the Gini index. We find that a completely libertarian, law-of-the-jungle setting, where every agent can acquire wealth from or lose wealth to anybody else invariably leads to a complete polarization of the distribution of wealth vs...
2017: PloS One
https://www.readbyqxmd.com/read/28207490/how-hiv-1-entry-mechanism-and-broadly-neutralizing-antibodies-guide-structure-based-vaccine-design
#4
Marie Pancera, Anita Changela, Peter D Kwong
PURPOSE OF REVIEW: An HIV-1 vaccine that elicits broadly neutralizing antibodies (bNAbs) remains to be developed. Here, we review how knowledge of bNAbs and HIV-1 entry mechanism is guiding the structure-based design of vaccine immunogens and immunization regimens. RECENT FINDINGS: Isolation of bNAbs from HIV-1-infected donors has led to an unprecedented understanding of the sites of vulnerability that these antibodies target on the HIV-1 envelope (Env) as well as of the immunological pathways that these antibody lineages follow to develop broad and potent neutralization...
February 15, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28202591/non-classical-phase-diagram-for-virus-bacterial-coevolution-mediated-by-clustered-regularly-interspaced-short-palindromic-repeats
#5
Pu Han, Michael W Deem
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28186629/evolutionary-asymmetry-in-the-arbuscular-mycorrhizal-symbiosis-conservatism-in-fungal-morphology-does-not-predict-host-plant-growth
#6
Alexander M Koch, Pedro M Antunes, Hafiz Maherali, Miranda M Hart, John N Klironomos
Although arbuscular mycorrhizal (AM) fungi are obligate symbionts that can influence plant growth, the magnitude and direction of these effects are highly variable within fungal genera and even among isolates within species, as well as among plant taxa. To determine whether variability in AM fungal morphology and growth is correlated with AM fungal effects on plant growth, we established a common garden experiment with 56 AM fungal isolates comprising 17 genera and six families growing with three plant host species...
February 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/28173765/selection-on-the-mitochondrial-atp-synthase-6-and-the-nadh-dehydrogenase-2-genes-in-hares-lepus-capensis-l-1758-from-a-steep-ecological-gradient-in-north-africa
#7
Hichem Ben Slimen, Helmut Schaschl, Felix Knauer, Franz Suchentrunk
BACKGROUND: Recent studies of selection on mitochondrial (mt) OXPHOS genes suggest adaptation due mainly to environmental variation. In this context, Tunisian hares that display several external phenotypes with phylogenetically rather homogenous gene pool and shallow population structure provide a good precondition to detect positive selection on mt genes related to environmental/climatic variation, specifically ambient temperature and precipitation. RESULTS: We used codon-based methods along with population genetic data to test for positive selection on ATPase synthase 6 (ATP6) and NADH dehydrogenase 2 (ND2) of cape hares (Lepus capensis) collected along a steep ecological gradient in Tunisia...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28173760/grandparental-immune-priming-in-the-pipefish-syngnathus-typhle
#8
Anne Beemelmanns, Olivia Roth
BACKGROUND: Phenotypic changes in response to environmental influences can persist from one generation into the next. In many systems parental parasite experience influences offspring immune responses, known as transgenerational immune priming (TGIP). TGIP in vertebrates is mainly maternal and short-term, supporting the adaptive immune system of the offspring during its maturation. However, if fathers and offspring have a close physical connection, evolution of additional paternal immune priming can be adaptive...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28150358/diversity-and-evolution-of-paramoeba-spp-and-their-kinetoplastid-endosymbionts
#9
Shannon J Sibbald, Ugo Cenci, Morgan Colp, Yana Eglit, Charles J O'Kelly, John M Archibald
Members of the genus Paramoeba (including Neoparamoeba) (Amoebozoa) are single-celled eukaryotes of economic and ecological importance due to their association with disease in a variety of marine animals including fish, sea urchins, and lobster. Interestingly, they harbor a eukaryotic endosymbiont of kinetoplastid ancestry, Perkinsela sp. To investigate the complex relationship between Paramoeba spp. and Perkinsela sp., as well as the relationships between different Paramoeba species, molecular data was obtained for four novel isolates...
February 1, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28141806/coevolutionary-dynamics-of-phenotypic-diversity-and-contingent-cooperation
#10
Te Wu, Long Wang, Feng Fu
Phenotypic diversity is considered beneficial to the evolution of contingent cooperation, in which cooperators channel their help preferentially towards others of similar phenotypes. However, it remains largely unclear how phenotypic variation arises in the first place and thus leads to the construction of phenotypic complexity. Here we propose a mathematical model to study the coevolutionary dynamics of phenotypic diversity and contingent cooperation. Unlike previous models, our model does not assume any prescribed level of phenotypic diversity, but rather lets it be an evolvable trait...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28122948/de-novo-transcriptome-characterization-of-a-sterilizing-trematode-parasite-microphallus-sp-from-two-species-of-new-zealand-snails
#11
Laura Bankers, Maurine Neiman
Snail-borne trematodes represent a large, diverse, and evolutionarily, ecologically, and medically important group of parasites, often imposing strong selection on their hosts and causing host morbidity and mortality. Even so, there are very few genomic and transcriptomic resources available for this important animal group. We help to fill this gap by providing transcriptome resources from trematode metacercariae infecting two congeneric snail species, Potamopyrgus antipodarum and P. estuarinus This genus of New Zealand snails has gained prominence in large part through the development of P...
January 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28120799/demonstration-of-immune-responses-against-devil-facial-tumour-disease-in-wild-tasmanian-devils
#12
Ruth Pye, Rodrigo Hamede, Hannah V Siddle, Alison Caldwell, Graeme W Knowles, Kate Swift, Alexandre Kreiss, Menna E Jones, A Bruce Lyons, Gregory M Woods
Devil facial tumour disease (DFTD) is a recently emerged fatal transmissible cancer decimating the wild population of Tasmanian devils (Sarcophilus harrisii). Biting transmits the cancer cells and the tumour develops in the new host as an allograft. The literature reports that immune escape mechanisms employed by DFTD inevitably result in host death. Here we present the first evidence that DFTD regression can occur and that wild devils can mount an immune response against the disease. Of the 52 devils tested, six had serum antibodies against DFTD cells and, in one case, prominent T lymphocyte infiltration in its tumour...
October 2016: Biology Letters
https://www.readbyqxmd.com/read/28117504/experimental-tests-of-host-virus-coevolution-in-natural-killer-yeast-strains
#13
Magdalena D Pieczynska, Ryszard Korona, J Arjan G M de Visser
Fungi may carry cytoplasmic viruses that encode anticompetitor toxins. These so called killer viruses may provide competitive benefits to their host, but also incur metabolic costs associated with viral replication, toxin production and immunity. Mechanisms responsible for the stable maintenance of these endosymbionts are insufficiently understood. Here, we test whether co-adaptation of host and killer virus underlies their stable maintenance in seven natural and one laboratory strain of the genus Saccharomyces...
January 24, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28112828/ecological-associations-of-autopodial-osteology-in-neotropical-geckos
#14
Priscila S Rothier, Renata Brandt, Tiana Kohlsdorf
Coevolution of form and function inspires investigation of associations between morphological variation and the exploitation of specific ecological settings. Such relationships, based mostly on traits of external morphology, have been extensively described for vertebrates, and especially so for squamates. External features are, however, composed by both soft tissues and bones, and these likely play different biomechanical roles during locomotion, such as in the autopodia. Therefore, ecological trends identified on the basis of external morphological measurements may not be directly correlated with equivalent variation in osteology...
January 23, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28110499/dynamic-predictions-using-flexible-joint-models-of-longitudinal-and-time-to-event-data
#15
Jessica Barretta, Li Sub
Joint models for longitudinal and time-to-event data are particularly relevant to many clinical studies where longitudinal biomarkers could be highly associated with a time-to-event outcome. A cutting-edge research direction in this area is dynamic predictions of patient prognosis (e.g., survival probabilities) given all available biomarker information, recently boosted by the stratified/personalized medicine initiative. As these dynamic predictions are individualized, flexible models are desirable in order to appropriately characterize each individual longitudinal trajectory...
January 22, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28110272/mitonuclear-interactions-mediate-transcriptional-responses-to-hypoxia-in-drosophila
#16
Jim A Mossman, Jennifer G Tross, Nick A Jourjine, Nan Li, Zhijin Wu, David M Rand
Among the major challenges in quantitative genetics and personalized medicine is to understand how gene × gene interactions (G × G: epistasis) and gene × environment interactions (G × E) underlie phenotypic variation. Here, we use the intimate relationship between mitochondria and oxygen availability to dissect the roles of nuclear DNA (nDNA) variation, mitochondrial DNA (mtDNA) variation, hypoxia, and their interactions on gene expression in Drosophila melanogaster Mitochondria provide an important evolutionary and medical context for understanding G × G and G × E given their central role in integrating cellular signals...
November 14, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28109041/endemic-cyanophages-and-the-puzzle-of-phage-bacteria-coevolution
#17
Otto X Cordero
A recent genomic analysis of Synechococcus cyanophages sampled for over 15 years reveals a remarkable pattern of stable phage population structure, highly reminiscent of the ecotype structure observed in bacteria and archaeal ecotypes. In this highlight I discuss the importance of this finding and the questions and opportunities it opens to learn more about the nature of phage-bacterial coevolution in the environment.
January 20, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28108601/phylogenomics-using-target-restricted-assembly-resolves-intra-generic-relationships-of-parasitic-lice-phthiraptera-columbicola
#18
Bret M Boyd, Julie M Allen, Nam Nguyen, Andrew D Sweet, Tandy Warnow, Michael D Shapiro, Scott M Villa, Sarah E Bush, Dale H Clayton, Kevin P Johnson
Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species...
January 19, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28103497/host-microbiota-interactions-epigenomic-regulation
#19
REVIEW
Vivienne Woo, Theresa Alenghat
The coevolution of mammalian hosts and their commensal microbiota has led to the development of complex symbiotic relationships between resident microbes and mammalian cells. Epigenomic modifications enable host cells to alter gene expression without modifying the genetic code, and therefore represent potent mechanisms by which mammalian cells can transcriptionally respond, transiently or stably, to environmental cues. Advances in genome-wide approaches are accelerating our appreciation of microbial influences on host physiology, and increasing evidence highlights that epigenomics represent a level of regulation by which the host integrates and responds to microbial signals...
January 16, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28098555/nematophagous-fungus-arthrobotrys-oligospora-mimics-olfactory-cues-of-sex-and-food-to-lure-its-nematode-prey
#20
Yen-Ping Hsueh, Matthew R Gronquist, Erich M Schwarz, Ravi David Nath, Ching-Han Lee, Shalha Gharib, Frank C Schroeder, Paul W Sternberg
To study the molecular basis for predator-prey coevolution, we investigated how Caenorhabditis elegans responds to the predatory fungus Arthrobotrys oligospora. C. elegans and other nematodes were attracted to volatile compounds produced by A. oligospora. Gas-chromatographic mass-spectral analyses of A. oligospora-derived volatile metabolites identified several odors mimicking food cues attractive to nematodes. One compound, methyl 3-methyl-2-butenoate (MMB) additionally triggered strong sex- and stage-specific attraction in several Caenorhabditis species...
January 18, 2017: ELife
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