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https://www.readbyqxmd.com/read/28926153/comparative-and-population-genomics-landscape-of-phellinus-noxius-a-hypervariable-fungus-causing-root-rot-in-trees
#1
Chia-Lin Chung, Tracy J Lee, Mitsuteru Akiba, Hsin-Han Lee, Tzu-Hao Kuo, Dang Liu, Huei-Mien Ke, Toshiro Yokoi, Marylette B Roa, Meiyeh J Lu, Ya-Yun Chang, Pao-Jen Ann, Jyh-Nong Tsai, Chien-Yu Chen, Shean-Shong Tzean, Yuko Ota, Tsutomu Hattori, Norio Sahashi, Ruey-Fen Liou, Taisei Kikuchi, Isheng J Tsai
The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomics analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens, and trunk pathogen Porodaedalea pini...
September 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28900644/properties-of-kinetic-transition-networks-for-atomic-clusters-and-glassy-solids
#2
John W R Morgan, Dhagash Mehta, David J Wales
A database of minima and transition states corresponds to a network where the minima represent nodes and the transition states correspond to edges between the pairs of minima they connect via steepest-descent paths. Here we construct networks for small clusters bound by the Morse potential for a selection of physically relevant parameters, in two and three dimensions. The properties of these unweighted and undirected networks are analysed to examine two features: whether they are small-world, where the shortest path between nodes involves only a small number or edges; and whether they are scale-free, having a degree distribution that follows a power law...
September 13, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28893328/plasticity-in-host-utilization-by-two-host-associated-populations-of-aphis-gossypii-glover
#3
A K Barman, K R Gadhave, B Dutta, R Srinivasan
Biological and morphological plasticity in polyphagous insect herbivores allow them to exploit diverse host plant species. Geographical differences in resource availability can lead to preferential host exploitation and result in inconsistent host specialization. Biological and molecular data provide insights into specialization and plasticity of such herbivore populations. In agricultural landscapes, Aphis gossypii encounters several crop and non-crop hosts, which exist in temporal and spatial proximity. We investigated the host-specialization of two A...
September 12, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28892078/detection-of-dysregulated-protein-association-networks-by-high-throughput-proteomics-predicts-cancer-vulnerabilities
#4
John D Lapek, Patricia Greninger, Robert Morris, Arnaud Amzallag, Iulian Pruteanu-Malinici, Cyril H Benes, Wilhelm Haas
The formation of protein complexes and the co-regulation of the cellular concentrations of proteins are essential mechanisms for cellular signaling and for maintaining homeostasis. Here we use isobaric-labeling multiplexed proteomics to analyze protein co-regulation and show that this allows the identification of protein-protein associations with high accuracy. We apply this 'interactome mapping by high-throughput quantitative proteome analysis' (IMAHP) method to a panel of 41 breast cancer cell lines and show that deviations of the observed protein co-regulations in specific cell lines from the consensus network affects cellular fitness...
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28884406/similarities-and-differences-in-barriers-and-opportunities-affecting-climate-change-adaptation-action-in-four-north-american-landscapes
#5
Whitney R Lonsdale, Heidi E Kretser, Cheryl-Lesley B Chetkiewicz, Molly S Cross
Climate change presents a complex set of challenges for natural resource managers across North America. Despite recognition that climate change poses serious threats to species, ecosystems, and human communities, implementation of adaptation measures is not yet happening on a broad scale. Among different regions, a range of climate change trajectories, varying political contexts, and diverse social and ecological systems generate a myriad of factors that can affect progress on climate change adaptation implementation...
September 7, 2017: Environmental Management
https://www.readbyqxmd.com/read/28882564/searching-for-synergy-identifying-optimal-antiviral-combination-therapy-using-hepatitis-c-virus-hcv-agents-in-a-replicon-system
#6
Justin J Pomeroy, George L Drusano, Jaime L Rodriquez, Ashley N Brown
Direct acting antiviral agents (DAAs) are potent inhibitors of Hepatitis C virus (HCV) that have revolutionized the treatment landscape for this important viral disease. There are currently four classes of DAAs that inhibit HCV replication via distinct mechanisms of action: nonstructural protein (NS) 3/4a protease inhibitors, NS5A inhibitors, NS5B nucleoside polymerase inhibitors, and NS5B non-nucleoside polymerase inhibitors. Combination therapy with two or more DAAs has great potential to further enhance antiviral potency...
September 4, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28857974/the-strategic-value-of-affiliation-partnerships-in-securing-future-relevance
#7
Ninfa M Saunders
Finding the best route to navigate the changing landscape of healthcare has become an obsession for many organizations. Their quest to stay competitive, significant, and ultimately relevant is a continuous discovery process. Many hospitals and health systems have considered affiliations and partnerships as important tactical options. Partnerships can range from loose arrangements, such as nonequity collaborations and management agreements, to total affiliation, as in a merger and acquisition. Whichever option an organization decides to pursue, a comprehensive assessment is necessary to find the best partner-the right fit...
October 2017: Frontiers of Health Services Management
https://www.readbyqxmd.com/read/28852911/compositional-changes-in-foliage-phenolics-with-plant-age-a-natural-experiment-in-boreal-forests
#8
Hilde Karine Wam, Caroline Stolter, Line Nybakken
The composition of plant secondary metabolites (PSMs) extensively impacts ecosystem functioning. It is vital that we understand temporal patterns in the plants' allocation of resources to PSMs, particularly those influenced by human activity. Existing data are insufficient in the long-term perspective of perennial plants (age or ontogeny). We analysed phenolic concentrations in foliage from birch (Betula pubescens Ehr.) considered to be undamaged and growing on 5, 10 and 15 years old clear-cuts in two boreal forest landscapes in Norway, sampled at the peak of the growing season...
August 29, 2017: Journal of Chemical Ecology
https://www.readbyqxmd.com/read/28841079/lifitegrast-for-the-treatment-of-dry-eye-disease-in-adults
#9
Eric D Donnenfeld, Henry D Perry, Alanna S Nattis, Eric D Rosenberg
Dry eye disease (DED) is a common ocular disorder that can have a substantial burden on quality of life and daily activities. Lifitegrast ophthalmic solution 5.0% is the first medication approved in the US for the treatment of the signs and symptoms of DED. The aim of this article is to summarize the preclinical and clinical data on lifitegrast and discuss how lifitegrast may fit into the current treatment landscape for DED. Areas covered: A literature search of published preclinical and clinical data was conducted to review the chemistry, pharmacodynamics, pharmacokinetics, and clinical efficacy/safety of lifitegrast...
October 2017: Expert Opinion on Pharmacotherapy
https://www.readbyqxmd.com/read/28822493/interactions-between-bee-foraging-and-floral-resource-phenology-shape-bee-populations-and-communities
#10
REVIEW
Jane E Ogilvie, Jessica Rk Forrest
Flowers are ephemeral, yet bees rely on them for food throughout their lives. Floral resource phenology - which can be altered by changes in climate and land-use - is therefore key to bee fitness and community composition. Here, we discuss the interactions between floral resource phenology, bee foraging behaviour, and traits such as diet breadth, sociality, and body size. Recent research on bumble bees has examined behavioural responses to local floral turnover and effects of landscape-scale floral resource phenology on fitness, abundance, and foraging distances...
June 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28822491/role-of-dispersal-in-resistance-evolution-and-spread
#11
REVIEW
Nicholas J Miller, Thomas W Sappington
Gene flow via immigration affects rate of evolution of resistance to a pest management tactic, while emigration from a resistant population can spread resistance alleles spatially. Whether resistance detected across the landscape reflects ongoing de novo evolution in different hotspots or spread from a single focal population can determine the most effective mitigation strategy. Pest dispersal dynamics determine the spatio-temporal scale at which mitigation tactics must be applied to contain or reverse resistance in an area...
June 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28815237/induced-polarization-restricts-the-conformational-distribution-of-a-light-harvesting-molecular-triad-in-the-ground-state
#12
Oleg N Starovoytov, Pengzhi Zhang, Piotr Cieplak, Margaret S Cheung
The light-harvesting molecular triad consisting of carotenoid polyene (C), diaryl-porphyrin (P) and pyrrole-fullerene (C60) is a donor-acceptor molecule capable of absorbing incident light in the visible range. Its ability to convert solar energy to electrical excitation and charge separation energy suggests a great potential in real-world applications. The ensemble of its conformations under ambient conditions varies widely according to its electronic state. In previous work, we applied a non-polarizable model to study the conformational distribution of the molecular triad in the ground and charge separated states...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28814780/adaptive-simulations-towards-interactive-protein-ligand-modeling
#13
Daniel Lecina, Joan F Gilabert, Victor Guallar
Modeling the dynamic nature of protein-ligand binding with atomistic simulations is one of the main challenges in computational biophysics, with important implications in the drug design process. Although in the past few years hardware and software advances have significantly revamped the use of molecular simulations, we still lack a fast and accurate ab initio description of the binding mechanism in complex systems, available only for up-to-date techniques and requiring several hours or days of heavy computation...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28812634/optimization-of-lag-phase-shapes-the-evolution-of-a-bacterial-enzyme
#14
Bharat V Adkar, Michael Manhart, Sanchari Bhattacharyya, Jian Tian, Michael Musharbash, Eugene I Shakhnovich
Mutations provide the variation that drives evolution, yet their effects on fitness remain poorly understood. Here we explore how mutations in the essential enzyme adenylate kinase (Adk) of Escherichia coli affect multiple phases of population growth. We introduce a biophysical fitness landscape for these phases, showing how they depend on molecular and cellular properties of Adk. We find that Adk catalytic capacity in the cell (the product of activity and abundance) is the major determinant of mutational fitness effects...
April 28, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812552/competition-along-trajectories-governs-adaptation-rates-towards-antimicrobial-resistance
#15
C Brandon Ogbunugafor, Margaret J Eppstein
The increasing availability of genotype-phenotype maps for different combinations of mutations has empowered evolutionary biologists with the tools to interrogate the predictability of adaptive evolution, especially in the context of the evolution of antimicrobial resistance. Large microbial populations are known to generate competing beneficial mutations, but determining how these mutations contribute to the adaptive trajectories that are most likely to be followed remains a challenge. Despite a recognition that there may also be competition between successive alleles on the same trajectory, prior studies have not fully considered how this impacts adaptation rates along, or likelihood of following, individual trajectories...
November 21, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811483/the-impact-of-human-population-pressure-on-flying-fox-niches-and-the-potential-consequences-for-hendra-virus-spillover
#16
Michael G Walsh, Anke Wiethoelter, M A Haseeb
Hendra virus (HeV) is an emerging pathogen of concern in Australia given its ability to spillover from its reservoir host, pteropid bats, to horses and further on to humans, and the severe clinical presentation typical in these latter incidental hosts. Specific human pressures over recent decades, such as expanding human populations, urbanization, and forest fragmentation, may have altered the ecological niche of Pteropus species acting as natural HeV reservoirs and may modulate spillover risk. This study explored the influence of inter-decadal net human local migration between 1970 and 2000 on changes in the habitat suitability to P...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28809951/stronger-selection-can-slow-down-evolution-driven-by-recombination-on-a-smooth-fitness-landscape
#17
Masahiko Ueda, Nobuto Takeuchi, Kunihiko Kaneko
Stronger selection implies faster evolution-that is, the greater the force, the faster the change. This apparently self-evident proposition, however, is derived under the assumption that genetic variation within a population is primarily supplied by mutation (i.e. mutation-driven evolution). Here, we show that this proposition does not actually hold for recombination-driven evolution, i.e. evolution in which genetic variation is primarily created by recombination rather than mutation. By numerically investigating population genetics models of recombination, migration and selection, we demonstrate that stronger selection can slow down evolution on a perfectly smooth fitness landscape...
2017: PloS One
https://www.readbyqxmd.com/read/28807858/host-specificity-pathogen-exposure-and-superinfections-impact-the-distribution-of-anaplasma-phagocytophilum-genotypes-in-ticks-roe-deer-and-livestock-in-a-fragmented-agricultural-landscape
#18
Amélie Chastagner, Angélique Pion, Hélène Verheyden, Bruno Lourtet, Bruno Cargnelutti, Denis Picot, Valérie Poux, Émilie Bard, Olivier Plantard, Karen D McCoy, Agnes Leblond, Gwenaël Vourc'h, Xavier Bailly
Anaplasma phagocytophilum is a bacterial pathogen mainly transmitted by Ixodes ricinus ticks in Europe. It infects wild mammals, livestock, and, occasionally, humans. Roe deer are considered to be the major reservoir, but the genotypes they carry differ from those that are found in livestock and humans. Here, we investigated whether roe deer were the main source of the A. phagocytophilum genotypes circulating in questing I. ricinus nymphs in a fragmented agricultural landscape in France. First, we assessed pathogen prevalence in 1837 I...
August 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28807238/unravelling-the-complexity-of-signalling-networks-in-cancer-a-review-of-the-increasing-role-for-computational-modelling
#19
REVIEW
John Garland
Cancer induction is a highly complex process involving hundreds of different inducers but whose eventual outcome is the same. Clearly, it is essential to understand how signalling pathways and networks generated by these inducers interact to regulate cell behaviour and create the cancer phenotype. While enormous strides have been made in identifying key networking profiles, the amount of data generated far exceeds our ability to understand how it all "fits together". The number of potential interactions is astronomically large and requires novel approaches and extreme computation methods to dissect them out...
September 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28805808/constraints-and-consequences-of-the-emergence-of-amino-acid-repeats-in-eukaryotic-proteins
#20
Sreenivas Chavali, Pavithra L Chavali, Guilhem Chalancon, Natalia Sanchez de Groot, Rita Gemayel, Natasha S Latysheva, Elizabeth Ing-Simmons, Kevin J Verstrepen, Santhanam Balaji, M Madan Babu
Proteins with amino acid homorepeats have the potential to be detrimental to cells and are often associated with human diseases. Why, then, are homorepeats prevalent in eukaryotic proteomes? In yeast, homorepeats are enriched in proteins that are essential and pleiotropic and that buffer environmental insults. The presence of homorepeats increases the functional versatility of proteins by mediating protein interactions and facilitating spatial organization in a repeat-dependent manner. During evolution, homorepeats are preferentially retained in proteins with stringent proteostasis, which might minimize repeat-associated detrimental effects such as unregulated phase separation and protein aggregation...
September 2017: Nature Structural & Molecular Biology
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