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Evolutionary dynamics

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https://www.readbyqxmd.com/read/28653624/parallel-evolution-of-influenza-across-multiple-spatiotemporal-scales
#1
Katherine S Xue, Terry Stevens-Ayers, Angela P Campbell, Janet A Englund, Steven A Pergam, Michael Boeckh, Jesse D Bloom
Viral variants that arise in the global influenza population begin as de novo mutations in single infected hosts, but the evolutionary dynamics that transform within-host variation to global genetic diversity are poorly understood. Here, we demonstrate that influenza evolution within infected humans recapitulates many evolutionary dynamics observed at the global scale. We deep-sequence longitudinal samples from four immunocompromised patients with long-term H3N2 influenza infections. We find parallel evolution across three scales: within individual patients, in different patients in our study, and in the global influenza population...
June 27, 2017: ELife
https://www.readbyqxmd.com/read/28652352/insect-outbreak-shifts-the-direction-of-selection-from-fast-to-slow-growth-rates-in-the-long-lived-conifer-pinus-ponderosa
#2
Raul de la Mata, Sharon Hood, Anna Sala
Long generation times limit species' rapid evolution to changing environments. Trees provide critical global ecosystem services, but are under increasing risk of mortality because of climate change-mediated disturbances, such as insect outbreaks. The extent to which disturbance changes the dynamics and strength of selection is unknown, but has important implications on the evolutionary potential of tree populations. Using a 40-y-old Pinus ponderosa genetic experiment, we provide rare evidence of context-dependent fluctuating selection on growth rates over time in a long-lived species...
June 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28652129/evolutionary-dynamics-and-significance-of-multiple-subclonal-mutations-in-cancer
#3
REVIEW
Robert A Beckman, Lawrence A Loeb
For the last 40 years the authors have collaborated on trying to understand the complexities of human cancer by formulating testable mathematical models that are based on mutation accumulation in human malignancies. We summarize the concepts encompassed by multiple mutations in human cancers in the context of source, accumulation during carcinogenesis and tumor progression, and therapeutic consequences. We conclude that the efficacious treatment of human cancer by targeted therapy will involve individualized, uniquely directed specific agents singly and in simultaneous combinations, and take into account the importance of targeting resistant subclonal mutations, particularly those subclones with alterations in DNA repair genes, DNA polymerase, and other genes required to maintain genetic stability...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28651535/molecular-phylogeny-reveals-food-plasticity-in-the-evolution-of-true-ladybird-beetles-coleoptera-coccinellidae-coccinellini
#4
Hermes E Escalona, Andreas Zwick, Hao-Sen Li, Jiahui Li, Xingmin Wang, Hong Pang, Diana Hartley, Lars S Jermiin, Oldřich Nedvěd, Bernhard Misof, Oliver Niehuis, Adam Ślipiński, Wioletta Tomaszewska
BACKGROUND: The tribe Coccinellini is a group of relatively large ladybird beetles that exhibits remarkable morphological and biological diversity. Many species are aphidophagous, feeding as larvae and adults on aphids, but some species also feed on other hemipterous insects (i.e., heteropterans, psyllids, whiteflies), beetle and moth larvae, pollen, fungal spores, and even plant tissue. Several species are biological control agents or widespread invasive species (e.g., Harmonia axyridis (Pallas))...
June 26, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28651357/using-viral-gene-sequences-to-compare-and-explain-the-heterogeneous-spatial-dynamics-of-virus-epidemics
#5
Simon Dellicour, Rebecca Rose, Nuno Rodrigues Faria, Luiz Fernando Pereira Vieira, Hervé Bourhy, Marius Gilbert, Philippe Lemey, Oliver G Pybus
Rabies is an important zoonotic disease distributed worldwide. A key question in rabies epidemiology is the identification of factors that impact virus dispersion. Here we apply new analytical methods, based on phylogeographic reconstructions of viral lineage movement, to undertake a comparative evolutionary-epidemiological study of the spatial dynamics of rabies virus (RABV) epidemics in different hosts and habitats. We have compiled RABV data sets from skunk, raccoon, bat and domestic dog populations in order to investigate the viral diffusivity of different RABV epidemics, and detect and compare those environmental factors that impact the velocity of viral spread in continuous spatial landscapes...
June 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28648561/exact-results-for-the-probability-and-stochastic-dynamics-of-fixation-in-the-wright-fisher-model
#6
Hassan Shafiey, David Waxman
In this work we consider fixation of an allele in a population. Fixation is key to understanding the way long-term evolutionary change occurs at the gene and molecular levels. Two basic aspects of fixation are: (i) the chance it occurs and (ii) the way the gene frequency progresses to fixation. We present exact results for both aspects of fixation for the Wright-Fisher model. We give the exact fixation probability for some different schemes of frequency-dependent selection. We also give the corresponding exact stochastic equation that generates frequency trajectories which ultimately fix...
June 22, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28647644/from-quantum-measurement-to-biology-via-retrocausality
#7
REVIEW
Koichiro Matsuno
A reaction cycle in general or a metabolic cycle in particular owes its evolutionary emergence to the covering reaction environment acting as a measurement apparatus of a natural origin. The quantum measurement of the environmental origin underlying the molecular processes observed in the biological realm is operative cohesively between the measuring and the measured. The measuring part comes to pull in a quantum as an indivisible lump available from an arbitrary material body to be measured. The inevitable difference between the impinging quantum upon the receiving end on the part of the environment and the actual quantum pulled into the receiving end comes to effectively be nullified through the retrocausative propagation of the corresponding wave function proceeding backwards in time...
June 21, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28646625/fluctuating-effects-of-genetic-and-plastic-changes-in-body-mass-on-population-dynamics-in-a-large-herbivore
#8
Gabriel Pigeon, Thomas H G Ezard, Marco Festa-Bianchet, David W Coltman, Fanie Pelletier
Recent studies suggest that evolutionary changes can occur on a contemporary time scale. Hence, evolution can influence ecology and vice-versa. To understand the importance of eco-evolutionary dynamics in population dynamics, we must quantify the relative contribution of ecological and evolutionary changes to population growth and other ecological processes. To date, however, most eco-evolutionary dynamics studies have not partitioned the relative contribution of plastic and evolutionary changes in traits on population, community and ecosystem processes...
June 24, 2017: Ecology
https://www.readbyqxmd.com/read/28645146/analysis-of-in-vitro-evolution-reveals-the-underlying-distribution-of-catalytic-activity-among-random-sequences
#9
Abe Pressman, Janina E Moretti, Gregory W Campbell, Ulrich F Müller, Irene A Chen
The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequences would emerge. Here, we analyze the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute estimates of catalytic activity for hundreds of ribozyme families. The analysis efficiently identified highly active ribozymes and estimated catalytic activity with good accuracy...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28644986/designing-novel-inhibitors-against-histone-acetyltransferase-hat-%C3%A2-gcn5-of-plasmodium-falciparum
#10
Amarjeet Kumar, Krishanu Bhowmick, Kunwar Somesh Vikramdeo, Neelima Mondal, Naidu Subbarao, Suman Kumar Dhar
During active proliferation phase of intra-erythrocytic cycle, the genome of P. falciparum is regulated epigenetically and evolutionary conserved parasite-specific histone proteins are extensively acetylated. The reversible process of lysine acetylation, causing transcriptional activation and its deacetylation, causing transcriptional repression is regulated by balanced activities of HATs and HDACs. They are also known to regulate antigenic variations and gametocytic conversion in P. falciparum. These histone modifying enzymes have been identified as potential targets for development of anitmalarials in literature...
June 10, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28644542/the-conservation-significance-of-natural-hybridisation-in-mediterranean-plants-from-a-case-study-on-cyclamen-primulaceae-to-a-general-perspective
#11
John D Thompson, Perrine Gauthier, Guillaume Papuga, Virginie Pons, Max Debussche, Emmanuele Farris
Hybridisation plays a prominent role in plant evolution due to its influence on genetic diversity, fitness and adaptive potential We identify a case of on-going hybrid evolution of floral phenotypes in disjunct populations of Cyclamen balearicum and C. repandum subsp. repandum on Corsica and Sardinia. Hybrid populations on the two islands contain similar patterns of variation in flower colour and size but are probably at different stages in the evolutionary process of hybridisation and differences in the frequency of floral types and flower size suggest hybrid vigour that may contribute to the dynamics and maintenance of hybrid forms...
June 23, 2017: Plant Biology
https://www.readbyqxmd.com/read/28642863/friends-enemies-endogenous-retroviruses-are-major-transcriptional-regulators-of-human-dna
#12
REVIEW
Anton A Buzdin, Vladimir Prassolov, Andrew V Garazha
Endogenous retroviruses are mobile genetic elements hardly distinguishable from infectious, or "exogenous," retroviruses at the time of insertion in the host DNA. Human endogenous retroviruses (HERVs) are not rare. They gave rise to multiple families of closely related mobile elements that occupy ~8% of the human genome. Together, they shape genomic regulatory landscape by providing at least ~320,000 human transcription factor binding sites (TFBS) located on ~110,000 individual HERV elements. The HERVs host as many as 155,000 mapped DNaseI hypersensitivity sites, which denote loci active in the regulation of gene expression or chromatin structure...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28642229/evolutionary-dynamics-of-the-kinetochore-network-in-eukaryotes-as-revealed-by-comparative-genomics
#13
Jolien Je van Hooff, Eelco Tromer, Leny M van Wijk, Berend Snel, Geert Jpl Kops
During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule-mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes...
June 22, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28639406/controlling-cyanobacterial-harmful-blooms-in-freshwater-ecosystems
#14
Hans W Paerl
Cyanobacteria's long evolutionary history has enabled them to adapt to geochemical and climatic changes, and more recent human and climatic modifications of aquatic ecosystems, including nutrient over-enrichment, hydrologic modifications, and global warming. Harmful (toxic, hypoxia-generating, food web altering) cyanobacterial bloom (CyanoHAB) genera are controlled by the synergistic effects of nutrient (nitrogen and phosphorus) supplies, light, temperature, water residence/flushing times, and biotic interactions...
June 21, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28639169/the-effects-of-predator-evolution-and-genetic-variation-on-predator-prey-population-level-dynamics
#15
Michael H Cortez, Swati Patel
This paper explores how predator evolution and the magnitude of predator genetic variation alter the population-level dynamics of predator-prey systems. We do this by analyzing a general eco-evolutionary predator-prey model using four methods: Method 1 identifies how eco-evolutionary feedbacks alter system stability in the fast and slow evolution limits; Method 2 identifies how the amount of standing predator genetic variation alters system stability; Method 3 identifies how the phase lags in predator-prey cycles depend on the amount of genetic variation; and Method 4 determines conditions for different cycle shapes in the fast and slow evolution limits using geometric singular perturbation theory...
June 21, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28638118/conformational-plasticity-and-evolutionary-analysis-of-the-myotilin-tandem-ig-domains
#16
Vid Puž, Miha Pavšič, Brigita Lenarčič, Kristina Djinović-Carugo
Myotilin is a component of the sarcomere where it plays an important role in organisation and maintenance of Z-disk integrity. This involves direct binding to F-actin and filamin C, a function mediated by its Ig domain pair. While the structures of these two individual domains are known, information about their relative orientation and flexibility remains limited. We set on to characterise the Ig domain pair of myotilin with emphasis on its molecular structure, dynamics and phylogeny. First, sequence conservation analysis of myotilin shed light on the molecular basis of myotilinopathies and revealed several motifs in Ig domains found also in I-band proteins...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#17
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633473/experimental-evolution-and-the-adjustment-of-metabolic-strategies-in-lactic-acid-bacteria
#18
Herwig Bachmann, Douwe Molenaar, Filipe Branco Dos Santos, Bas Teusink
Experimental evolution of microbes has gained lots of interest in recent years, mainly due to the ease of strain characterisation through next-generation sequencing. While evolutionary and systems biologists use experimental evolution to address fundamental questions in their respective fields, studies with lactic acid bacteria are often more directed by applied questions. Insight into population and genome dynamics are valuable for experimental design and data interpretation, and it is becoming increasingly apparent how different constraints limit and govern the outcome of microbial adaptation to a selective environment...
June 19, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28633194/moving-forward-in-circles-challenges-and-opportunities-in-modelling-population-cycles
#19
REVIEW
Frédéric Barraquand, Stilianos Louca, Karen C Abbott, Christina A Cobbold, Flora Cordoleani, Donald L DeAngelis, Bret D Elderd, Jeremy W Fox, Priscilla Greenwood, Frank M Hilker, Dennis L Murray, Christopher R Stieha, Rachel A Taylor, Kelsey Vitense, Gail S K Wolkowicz, Rebecca C Tyson
Population cycling is a widespread phenomenon, observed across a multitude of taxa in both laboratory and natural conditions. Historically, the theory associated with population cycles was tightly linked to pairwise consumer-resource interactions and studied via deterministic models, but current empirical and theoretical research reveals a much richer basis for ecological cycles. Stochasticity and seasonality can modulate or create cyclic behaviour in non-intuitive ways, the high-dimensionality in ecological systems can profoundly influence cycling, and so can demographic structure and eco-evolutionary dynamics...
June 20, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28632458/aquaporins-novel-targets-for-age-related-ocular-disorders
#20
Rajkumar Patil, Haishan Wang, Najam A Sharif, Alok Mitra
Aquaporins (AQPs), a large family of membrane protein channels that facilitate transport of water and other small solutes, play important roles in physiological functions and human diseases. Up till now, 13 types of AQPs, numbered 0 through 12, have been identified in various mammalian tissues. Homologous genes for AQPs in amphibians, insects, and bacteria highlight the evolutionary conservation and, thus, the importance of these membrane channels. Many members of the AQP family are expressed in the eye. AQP1, which is a water-selective channel, is expressed in the anterior chamber (cornea, ciliary body, trabecular meshwork) and posterior chamber (retina and microvessels in choroid), controlling the fluid homeostasis in the eye...
June 20, 2017: Journal of Ocular Pharmacology and Therapeutics
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