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Coevolution

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https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#1
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28429458/genomic-evidence-for-population-specific-responses-to-coevolving-parasites-in-a-new-zealand-freshwater-snail
#2
Laura A Bankers, Peter Fields, Kyle E McElroy, Jeffrey L Boore, John M Logsdon, Maurine Neiman
Reciprocal coevolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population- or genotype-specific evolutionary change. These host-parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of coevolving host-parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwater snail Potamopyrgus antipodarum and its coevolving sterilizing trematode parasite, Microphallus sp...
April 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28426286/on-the-evolution-of-lactase-persistence-in-humans
#3
Laure Ségurel, Céline Bon
Lactase persistence-the ability of adults to digest the lactose in milk-varies widely in frequency across human populations. This trait represents an adaptation to the domestication of dairying animals and the subsequent consumption of their milk. Five variants are currently known to underlie this phenotype, which is monogenic in Eurasia but mostly polygenic in Africa. Despite being a textbook example of regulatory convergent evolution and gene-culture coevolution, the story of lactase persistence is far from clear: Why are lactase persistence frequencies low in Central Asian herders but high in some African hunter-gatherers?Whywas lactase persistence strongly selected for even though milk processing can reduce the amount of lactose? Are there other factors, outside of an advantage of caloric intake, that contributed to the selective pressure for lactase persistence? It is time to revisit what we know and still do not know about lactase persistence in humans...
April 19, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28422953/great-spotted-cuckoo-nestlings-have-no-antipredatory-effect-on-magpie-or-carrion-crow-host-nests-in-southern-spain
#4
Manuel Soler, Liesbeth de Neve, María Roldán, Tomás Pérez-Contreras, Juan José Soler
Host defences against cuckoo parasitism and cuckoo trickeries to overcome them are a classic example of antagonistic coevolution. Recently it has been reported that this relationship may turn to be mutualistic in the case of the carrion crow (Corvus corone) and its brood parasite, the great spotted cuckoo (Clamator glandarius), given that experimentally and naturally parasitized nests were depredated at a lower rate than non-parasitized nests. This result was interpreted as a consequence of the antipredatory properties of a fetid cloacal secretion produced by cuckoo nestlings, which presumably deters predators from parasitized host nests...
2017: PloS One
https://www.readbyqxmd.com/read/28422787/how-hiv-1-entry-mechanism-and-broadly-neutralizing-antibodies-guide-structure-based-vaccine-design
#5
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...
May 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28416728/global-water-cycle-and-the-coevolution-of-the-earth-s-interior-and-surface-environment
#6
Jun Korenaga, Noah J Planavsky, David A D Evans
The bulk Earth composition contains probably less than 0.3% of water, but this trace amount of water can affect the long-term evolution of the Earth in a number of different ways. The foremost issue is the occurrence of plate tectonics, which governs almost all aspects of the Earth system, and the presence of water could either promote or hinder the operation of plate tectonics, depending on where water resides. The global water cycle, which circulates surface water into the deep mantle and back to the surface again, could thus have played a critical role in the Earth's history...
May 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28416654/reconstructed-ancestral-enzymes-suggest-long-term-cooling-of-earth-s-photic-zone-since-the-archean
#7
Amanda K Garcia, J William Schopf, Shin-Ichi Yokobori, Satoshi Akanuma, Akihiko Yamagishi
Paleotemperatures inferred from the isotopic compositions (δ(18)O and δ(30)Si) of marine cherts suggest that Earth's oceans cooled from 70 ± 15 °C in the Archean to the present ∼15 °C. This interpretation, however, has been subject to question due to uncertainties regarding oceanic isotopic compositions, diagenetic or metamorphic resetting of the isotopic record, and depositional environments. Analyses of the thermostability of reconstructed ancestral enzymes provide an independent method by which to assess the temperature history inferred from the isotopic evidence...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28416576/pathways-involved-in-formation-of-mammary-organoid-architecture-have-keys-to-understanding-drug-resistance-and-to-discovery-of-druggable-targets
#8
Saori Furuta, Mina J Bissell
Signals from the extracellular matrix (ECM) are received at the cell surface receptor, transmitted to the cytoskeletons, and transferred to the nucleus and chromatin for tissue- and context-specific gene expression. Cells, in return, modulate the cell shape and ECM, allowing for the maintenance of tissue homeostasis as well as for coevolution and adaptation to the environmental signals. We postulated the existence of dynamic and reciprocal interactions between the ECM and the nucleus more than three decades ago, but now these pathways have been proven experimentally thanks to the advances in imaging and cell/molecular biology techniques...
April 17, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28411161/a-reassessment-of-the-phylogeny-and-circumscription-of-zaluzianskya-scrophulariaceae
#9
Jenny K Archibald, Jacqueline Cook, Bruce Anderson, Steven D Johnson, Mark E Mort
The genus Zaluzianskya (Scrophulariaceae s.s.) encompasses a diversity of traits, such as flowers ranging from 4 to 60 mm in length with various patterns of color and indumentum. However, this diversity, as described by the current taxonomic circumscription of Zaluzianskya, is an underestimate. The boundaries of this genus require expansion via incorporation of species from other genera and recognition of unnamed species. This study advances prior molecular phylogenies for the southern African genus through the addition of DNA regions and an up to 70% increase in population sampling, targeting specific taxa...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28410031/the-ecological-dynamics-of-natural-selection-traits-and-the-coevolution-of-community-structure
#10
Mark A McPeek
Natural selection has both genetic and ecological dynamics. The fitnesses of individuals change with their ecological context, and so the form and strength of selective agents change with abiotic factors and the phenotypes and abundances of interacting species. I use standard models of consumer-resource interactions to explore the ecological dynamics of natural selection and how various trait types influence these dynamics and the resulting structure of a community of coevolving species. Evolutionary optima favored by natural selection depend critically on the abundances of interacting species, and the traits of species can undergo dynamic cycling in limited areas of parameter space...
May 2017: American Naturalist
https://www.readbyqxmd.com/read/28400512/convergence-of-dna-methylation-and-phosphorothioation-epigenetics-in-bacterial-genomes
#11
Chao Chen, Lianrong Wang, Si Chen, Xiaolin Wu, Meijia Gu, Xi Chen, Susu Jiang, Yunfu Wang, Zixin Deng, Peter C Dedon, Shi Chen
Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, (6m)A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(GPS(6m)A) dinucleotides in the GPS(6m)AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(GPSA) motifs per genome, with (6m)A arising from a yet-to-be-identified methyltransferase...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28392985/conserved-dna-motifs-in-the-type-ii-a-crispr-leader-region
#12
Mason J Van Orden, Peter Klein, Kesavan Babu, Fares Z Najar, Rakhi Rajan
The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3' end of the leader, are indispensable for adaptation...
2017: PeerJ
https://www.readbyqxmd.com/read/28389039/bacterial-unculturability-and-the-formation-of-intercellular-metabolic-networks
#13
REVIEW
Samay Pande, Christian Kost
The majority of known bacterial species cannot be cultivated under laboratory conditions. Here we argue that the adaptive emergence of obligate metabolic interactions in natural bacterial communities can explain this pattern. Bacteria commonly release metabolites into the external environment. Accumulating pools of extracellular metabolites create an ecological niche that benefits auxotrophic mutants, which have lost the ability to autonomously produce the corresponding metabolites. In addition to a diffusion-based metabolite transfer, auxotrophic cells can use contact-dependent means to obtain nutrients from other co-occurring cells...
April 4, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28386187/biomimicry-of-symbiotic-multi-species-coevolution-for-discrete-and-continuous-optimization-in-rfid-networks
#14
Na Lin, Hanning Chen, Shikai Jing, Fang Liu, Xiaodan Liang
In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS(2)Os, which extend the single population particle swarm optimization (PSO) algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations...
March 2017: Saudi Journal of Biological Sciences
https://www.readbyqxmd.com/read/28381207/microbial-composition-of-spiny-ants-hymenoptera-formicidae-polyrhachis-across-their-geographic-range
#15
Manuela Oliveira Ramalho, Odair Correa Bueno, Corrie Saux Moreau
BACKGROUND: Symbiotic relationships between insects and bacteria are found across almost all insect orders, including Hymenoptera. However there are still many remaining questions about these associations including what factors drive host-associated bacterial composition. To better understand the evolutionary significance of this association in nature, further studies addressing a diversity of hosts across locations and evolutionary history are necessary. Ants of the genus Polyrhachis (spiny ants) are distributed across the Old World and exhibit generalist diets and habits...
April 5, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28373695/catalyzed-synthesis-of-zinc-clays-by-prebiotic-central-metabolites
#16
Ruixin Zhou, Kaustuv Basu, Hyman Hartman, Christopher J Matocha, S Kelly Sears, Hojatollah Vali, Marcelo I Guzman
How primordial metabolic networks such as the reverse tricarboxylic acid (rTCA) cycle and clay mineral catalysts coevolved remains a mystery in the puzzle to understand the origin of life. While prebiotic reactions from the rTCA cycle were accomplished via photochemistry on semiconductor minerals, the synthesis of clays was demonstrated at low temperature and ambient pressure catalyzed by oxalate. Herein, the crystallization of clay minerals is catalyzed by succinate, an example of a photoproduced intermediate from central metabolism...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28369510/antagonistic-coevolution-of-mer-tyrosine-kinase-expression-and-function
#17
Amanda L Evans, Jack W D Blackburn, Kyle Taruc, Angela Kipp, Brennan S Dirk, Nina R Hunt, Stephen D Barr, Jimmy D Dikeakos, Bryan Heit
TYRO3, AXL, and MERTK (TAM) receptors are a family of receptor tyrosine kinases that maintain homeostasis through the clearance of apoptotic cells, and when defective, contribute to chronic inflammatory and autoimmune diseases such as atherosclerosis, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and Crohn's disease. In addition, certain enveloped viruses utilize TAM receptors for immune evasion and entry into host cells, with several viruses preferentially hijacking MERTK for these purposes...
March 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28363863/evolution-of-stinginess-and-generosity-in-finite-populations
#18
Xue Feng, Yanling Zhang, Long Wang
In iterated continuous games, the cooperative investment in a given round is determined by the initial investment and the reciprocation rate, which describe the investment in the first round and the dependence of current investment on the partner's last move, respectively. These two traits usually intertwine during evolution. However, their coevolution is not fully explored. In this paper, we thereby study their coevolution in the iterated continuous public goods games. We find that the reciprocation rate plays a dominant role during the coevolution in both finite and infinite populations...
March 29, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28361733/emerging-fungal-threats-to-plants-and-animals-challenge-agriculture-and-ecosystem-resilience
#19
Helen N Fones, Matthew C Fisher, Sarah J Gurr
While fungi can make positive contributions to ecosystems and agro-ecosystems, for example, in mycorrhizal associations, they can also have devastating impacts as pathogens of plants and animals. In undisturbed ecosystems, most such negative interactions will be limited through the coevolution of fungi with their hosts. In this article, we explore what happens when pathogenic fungi spread beyond their natural ecological range and become invasive on naïve hosts in new ecosystems. We will see that such invasive pathogens have been problematic to humans and their domesticated plant and animal species throughout history, and we will discuss some of the most pressing fungal threats of today...
March 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28350503/a-novel-enigmatic-basal-leafflower-moth-lineage-pollinating-a-derived-leafflower-host-illustrates-the-dynamics-of-host-shifts-partner-replacement-and-apparent-coadaptation-in-intimate-mutualisms
#20
Shi-Xiao Luo, Gang Yao, Ziwei Wang, Dianxiang Zhang, David H Hembry
Leafflower plant/leafflower moth brood pollination mutualisms are widespread in the Paleotropics. Leafflower moths pollinate leafflower plants, but their larvae consume a subset of the hosts' seeds. These interactions are highly phylogenetically constrained: six clades of leafflower plants are each associated with a unique clade of leafflower moths (Epicephala). Here, we report a previously unrecognized basal seventh pollinating Epicephala lineage-associated with the highly derived leafflower clade Glochidion-in Asia...
April 2017: American Naturalist
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