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https://www.readbyqxmd.com/read/28729483/epigenetic-plasticity-and-the-hallmarks-of-cancer
#1
REVIEW
William A Flavahan, Elizabeth Gaskell, Bradley E Bernstein
Chromatin and associated epigenetic mechanisms stabilize gene expression and cellular states while also facilitating appropriate responses to developmental or environmental cues. Genetic, environmental, or metabolic insults can induce overly restrictive or overly permissive epigenetic landscapes that contribute to pathogenesis of cancer and other diseases. Restrictive chromatin states may prevent appropriate induction of tumor suppressor programs or block differentiation. By contrast, permissive or "plastic" states may allow stochastic oncogene activation or nonphysiologic cell fate transitions...
July 21, 2017: Science
https://www.readbyqxmd.com/read/28721211/microbial-metal-resistance-and-metabolism-across-dynamic-landscapes-high-throughput-environmental-microbiology
#2
REVIEW
Hans Carlson, Adam Deutschbauer, John Coates
Multidimensional gradients of inorganic compounds influence microbial activity in diverse pristine and anthropogenically perturbed environments. Here, we suggest that high-throughput cultivation and genetics can be systematically applied to generate quantitative models linking gene function, microbial community activity, and geochemical parameters. Metal resistance determinants represent a uniquely universal set of parameters around which to study and evaluate microbial fitness because they represent a record of the environment in which all microbial life evolved...
2017: F1000Research
https://www.readbyqxmd.com/read/28718764/crispr-mediated-genetic-interaction-profiling-identifies-rna-binding-proteins-controlling-metazoan-fitness
#3
Adam D Norris, Xicotencatl Gracida, John Calarco
Genetic interaction screens have aided our understanding of complex genetic traits, diseases, and biological pathways. However, approaches for synthetic genetic analysis with null-alleles in metazoans have not been feasible. Here, we present a CRISPR/Cas9-based Synthetic Genetic Interaction (CRISPR-SGI) approach enabling systematic double-mutant generation. Applying this technique in Caenorhabditis elegans, we comprehensively screened interactions within a set of 14 conserved RNA binding protein genes, generating all possible single and double mutants...
July 18, 2017: ELife
https://www.readbyqxmd.com/read/28714571/domestication-and-fitness-in-the-wild-a-multivariate-view
#4
Jarle Tufto
Domesticated species continually escaping and interbreeding with wild relatives impose a migration load on wild populations. As domesticated stocks become increasingly different as a result of artificial and natural selection in captivity, fitness of escapees in the wild is expected to decline, reducing the effective rate of migration into wild populations. Recent theory suggest that this may alleviate and eventually eliminate the resulting migration load. I develop a multivariate model of trait and wild fitness evolution resulting from the joint effects of artificial and natural selection in the captive environment...
July 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28709354/crossing-fitness-canyons-by-a-finite-population
#5
David B Saakian, Alexander S Bratus, Chin-Kun Hu
We consider the Wright-Fisher model of the finite population evolution on a fitness landscape defined in the sequence space by a path of nearly neutral mutations. We study a specific structure of the fitness landscape: One of the intermediate mutations on the mutation path results in either a large fitness value (climbing up a fitness hill) or a low fitness value (crossing a fitness canyon), the rest of the mutations besides the last one are neutral, and the last sequence has much higher fitness than any intermediate sequence...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28709207/population-annealing-simulations-of-a-binary-hard-sphere-mixture
#6
Jared Callaham, Jonathan Machta
Population annealing is a sequential Monte Carlo scheme well suited to simulating equilibrium states of systems with rough free energy landscapes. Here we use population annealing to study a binary mixture of hard spheres. Population annealing is a parallel version of simulated annealing with an extra resampling step that ensures that a population of replicas of the system represents the equilibrium ensemble at every packing fraction in an annealing schedule. The algorithm and its equilibration properties are described, and results are presented for a glass-forming fluid composed of a 50/50 mixture of hard spheres with diameter ratio of 1...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28707221/modelling-the-evolution-of-traits-in-a-two-sex-population-with-an-application-to-grandmothering
#7
Matthew H Chan, Kristen Hawkes, Peter S Kim
We present a mathematical simplification for the evolutionary dynamics of a heritable trait within a two-sex population. This trait is assumed to control the timing of sex-specific life-history events, such as the age of sexual maturity and end of female fertility, and each sex has a distinct fitness trade-off associated with the trait. We provide a formula for the fitness landscape of the population and show a natural extension of the result to an arbitrary number of heritable traits. Our method can be viewed as a dynamical systems generalisation of the Price equation to include two sexes, age structure and multiple traits...
July 13, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28694838/how-animals-distribute-themselves-in-space-variable-energy-landscapes
#8
Juan F Masello, Akiko Kato, Julia Sommerfeld, Thomas Mattern, Petra Quillfeldt
BACKGROUND: Foraging efficiency determines whether animals will be able to raise healthy broods, maintain their own condition, avoid predators and ultimately increase their fitness. Using accelerometers and GPS loggers, features of the habitat and the way animals deal with variable conditions can be translated into energetic costs of movement, which, in turn, can be translated to energy landscapes.We investigated energy landscapes in Gentoo Penguins Pygoscelis papua from two colonies at New Island, Falkland/Malvinas Islands...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/28689262/behavioral-mechanisms-leading-to-improved-fitness-in-a-subsidized-predator
#9
Elena H West, M Zachariah Peery
General mechanisms underlying the distribution and fitness of synanthropic predators in human-influenced landscapes remain unclear. Under the consumer resource-matching hypothesis, synanthropes are expected to distribute themselves among habitats according to resource availability, such that densities are greater in human-subsidized habitats, but mean individual fitness is equal among habitats because of negative density dependence. However, "under-matching" to human food resources can occur, because dominant individuals exclude subordinates from subsidized habitats and realize relatively high fitness...
July 8, 2017: Oecologia
https://www.readbyqxmd.com/read/28680146/skin-parasite-landscape-determines-host-infectiousness-in-visceral-leishmaniasis
#10
Johannes S P Doehl, Zoe Bright, Shoumit Dey, Helen Davies, John Magson, Najmeeyah Brown, Audrey Romano, Jane E Dalton, Ana I Pinto, Jon W Pitchford, Paul M Kaye
Increasing evidence suggests that the infectiousness of patients for the sand fly vector of visceral leishmaniasis is linked to parasites found in the skin. Using a murine model that supports extensive skin infection with Leishmania donovani, spatial analyses at macro-(quantitative PCR) and micro-(confocal microscopy) scales indicate that parasite distribution is markedly skewed. Mathematical models accounting for this heterogeneity demonstrate that while a patchy distribution reduces the expected number of sand flies acquiring parasites, it increases the infection load for sand flies feeding on a patch, increasing their potential for onward transmission...
July 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28679731/influence-of-local-and-landscape-factors-on-distributional-dynamics-a-species-centred-fitness-based-approach
#11
Aaron D Flesch
In spatially structured populations, distributional dynamics are driven by the quantity, connectivity and quality of habitat. Because these drivers are rarely measured directly and simultaneously at relevant scales, information on their relative importance remains unclear. I assessed the influence of both direct and indirect measures of local habitat quality, and of landscape habitat amount and connectivity on long-term territory occupancy dynamics of non-migratory pygmy owls. Direct measures of local habitat quality based on territory-specific reproductive output had greater effects on distribution than landscape factors, but only when spatio-temporal fluxes in performance linked to environmental stochasticity and intraspecific competition were considered...
July 12, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28678836/epistasis-in-genomic-and-survival-data-of-cancer-patients
#12
Dariusz Matlak, Ewa Szczurek
Cancer aggressiveness and its effect on patient survival depends on mutations in the tumor genome. Epistatic interactions between the mutated genes may guide the choice of anticancer therapy and set predictive factors of its success. Inhibitors targeting synthetic lethal partners of genes mutated in tumors are already utilized for efficient and specific treatment in the clinic. The space of possible epistatic interactions, however, is overwhelming, and computational methods are needed to limit the experimental effort of validating the interactions for therapy and characterizing their biomarkers...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28678792/a-phase-transition-induces-chaos-in-a-predator-prey-ecosystem-with-a-dynamic-fitness-landscape
#13
William Gilpin, Marcus W Feldman
In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28673912/boldness-traits-not-dominance-predict-exploratory-flight-range-and-homing-behaviour-in-homing-pigeons
#14
Steven J Portugal, Rhianna L Ricketts, Jackie Chappell, Craig R White, Emily L Shepard, Dora Biro
Group living has been proposed to yield benefits that enhance fitness above the level that would be achieved through living as solitary individuals. Dominance hierarchies occur commonly in these social assemblages, and result, by definition, in resources not being evenly distributed between group members. Determinants of rank within a dominance hierarchy can be associated with morphological characteristics, previous experience of the individual, or personality traits such as exploration tendencies. The purpose of this study was to investigate whether greater exploration and positive responses to novel objects in homing pigeons (Columba livia) measured under laboratory conditions were associated with (i) greater initial exploration of the local area around the home loft during spontaneous exploration flights (SEF), (ii) faster and more efficient homing flights when released from further afield, and (iii) whether the traits of greater exploration and more positive responses to novel objects were more likely to be exhibited by the more dominant individuals within the group...
August 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28657652/life-histories-and-conservation-of-long-lived-reptiles-an-illustration-with-the-american-crocodile-crocodylus-acutus
#15
Venetia Briggs-Gonzalez, Christophe Bonenfant, Mathieu Basille, Michael Cherkiss, Jeff Beauchamp, Frank Mazzotti
Successful species conservation is dependent on adequate estimates of population dynamics, but age-specific demographics are generally lacking for many long-lived iteroparous species such as large reptiles. Accurate demographic information allows estimation of population growth rate, as well as projection of future population sizes and quantitative analyses of fitness trade-offs involved in evolution of life-history strategies. Here, a long-term capture-recapture study was conducted from 1978-2014 on the American crocodile (Crocodylus acutus) in southern Florida...
June 28, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28653582/waste-management-outlook-for-mountain-regions-sources-and-solutions
#16
Larisa Semernya, Aditi Ramola, Björn Alfthan, Claudia Giacovelli
Following the release of the global waste management outlook in 2015, the United Nations Environment Programme (UN Environment), through its International Environmental Technology Centre, is elaborating a series of region-specific and thematic waste management outlooks that provide policy recommendations and solutions based on current practices in developing and developed countries. The Waste Management Outlook for Mountain Regions is the first report in this series. Mountain regions present unique challenges to waste management; while remoteness is often associated with costly and difficult transport of waste, the potential impact of waste pollutants is higher owing to the steep terrain and rivers transporting waste downstream...
June 1, 2017: Waste Management & Research
https://www.readbyqxmd.com/read/28651631/in-which-developing-countries-are-patents-on-essential-medicines-being-filed
#17
Reed F Beall, Rosanne Blanchet, Amir Attaran
BACKGROUND: This article is based upon data gathered during a study conducted in partnership with the World Intellectual Property Organization on the patent status of products appearing on the World Health Organization's 2013 Model List of Essential Medicines (MLEM). It is a statistical analysis aimed at answering: in which developing countries are patents on essential medicines being filed? METHODS: Patent data were collected by linking those listed in the United States and Canada's medicine patent registers to corresponding patents in developing countries using two international patent databases (INPADOC and Derwent) via a commerical-grade patent search platform (Thomson Innovation)...
June 26, 2017: Globalization and Health
https://www.readbyqxmd.com/read/28645891/health-app-use-among-individuals-with-symptoms-of-depression-and-anxiety-a-survey-study-with-thematic-coding
#18
Caryn Kseniya Rubanovich, David C Mohr, Stephen M Schueller
BACKGROUND: Researchers have largely turned to commercial app stores, randomized trials, and systematic reviews to make sense of the mHealth landscape. Few studies have approached understanding by collecting information from target end users. The end user perspective is critical as end user interest in and use of mHealth technologies will ultimately drive the efficacy of these tools. OBJECTIVE: The purpose of this study was to obtain information from end users of mHealth technologies to better understand the physical and mental health apps people use and for what purposes...
June 23, 2017: JMIR Mental Health
https://www.readbyqxmd.com/read/28645318/detecting-consistent-patterns-of-directional-adaptation-using-differential-selection-codon-models
#19
Sahar Parto, Nicolas Lartillot
BACKGROUND: Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors...
June 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28632944/deconstructing-the-landscape-of-fear-in-stable-multi-species-societies
#20
A E Martínez, E Parra, L F Collado, V T Vredenburg
Animal distributions are influenced by variation in predation risk in space, which has been described as the "landscape of fear." Many studies suggest animals also reduce predation risk by eavesdropping on heterospecific alarm calls, allowing them to occupy otherwise risky habitats. One unexplored area of study is understanding how different species' alarms vary in quality, and how this variation is distributed in the landscape. We tested this phenomenon in a unique system of avian mixed species flocks in Amazonian rainforests: flock mates (eavesdropping species) strongly associate with alarm-calling antshrikes (genus Thamnomanes), which act as sentinel species...
June 20, 2017: Ecology
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