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https://www.readbyqxmd.com/read/28815237/induced-polarization-restricts-the-conformational-distribution-of-a-light-harvesting-molecular-triad-in-the-ground-state
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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 11, 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
#8
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
#9
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...
August 14, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28805250/peer-review-the-future-is-here
#10
Maria Papatriantafyllou
Several divergent standpoints are hosted under the umbrella of Peer Review. Authors, who wish to see the results of scrupulous work published, in the anticipation of career promotion or secure funding. Editors, who are under pressure to identify sound and novel research. Reviewers, who try to fit a thoughtful and time-consuming process within busy schedules, often receiving no credit for it. And Publishers competing in a transforming landscape of fast and abundant science publishing. This article is protected by copyright...
August 14, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28799352/free-energy-landscape-and-molecular-pathways-of-gas-hydrate-nucleation
#11
Yuanfei Bi, Anna Porras, Tianshu Li
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), pB histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation...
December 7, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28793206/a-model-for-viral-assembly-around-an-explicit-rna-sequence-generates-an-implicit-fitness-landscape
#12
Eric Charles Dykeman
Previously, a stochastic model of single-stranded RNA virus assembly was created to model the cooperative effects between capsid proteins and genomic RNA that would occur in a packaging signal-mediated assembly process. In such an assembly scenario, multiple secondary structural elements from within the RNA, termed "packaging signals" (PS), contact coat proteins and facilitate efficient capsid assembly. In this work, the assembly model is extended to incorporate explicit nucleotide sequence information as well as simple aspects of RNA folding that would be occurring during the RNA/capsid coassembly process...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28791144/machine-learning-landscapes-and-predictions-for-patient-outcomes
#13
Ritankar Das, David J Wales
The theory and computational tools developed to interpret and explore energy landscapes in molecular science are applied to the landscapes defined by local minima for neural networks. These machine learning landscapes correspond to fits of training data, where the inputs are vital signs and laboratory measurements for a database of patients, and the objective is to predict a clinical outcome. In this contribution, we test the predictions obtained by fitting to single measurements, and then to combinations of between 2 and 10 different patient medical data items...
July 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28790313/evolution-of-new-regulatory-functions-on-biophysically-realistic-fitness-landscapes
#14
Tamar Friedlander, Roshan Prizak, Nicholas H Barton, Gašper Tkačik
Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28776688/mosaics-often-outperform-pyramids-insights-from-a-model-comparing-strategies-for-the-deployment-of-plant-resistance-genes-against-viruses-in-agricultural-landscapes
#15
Ramses Djidjou-Demasse, Benoît Moury, Frédéric Fabre
The breakdown of plant virus resistance genes is a major issue in agriculture. We investigated whether a set of resistance genes would last longer when stacked into a single plant cultivar (pyramiding) or when deployed individually in regional mosaics (mosaic strategy). We modeled the genetic and epidemiological processes shaping the demogenetic dynamics of viruses under a multilocus gene-for-gene system, from the plant to landscape scales. The landscape consisted of many fields, was subject to seasonality, and of a reservoir hosting viruses year-round...
August 4, 2017: New Phytologist
https://www.readbyqxmd.com/read/28750009/mrna-protein-sequence-complementarity-and-its-determinants-the-impact-of-affinity-scales
#16
Lukas Bartonek, Bojan Zagrovic
It has recently been demonstrated that the nucleobase-density profiles of mRNA coding sequences are related in a complementary manner to the nucleobase-affinity profiles of their cognate protein sequences. Based on this, it has been proposed that cognate mRNA/protein pairs may bind in a co-aligned manner, especially if unstructured. Here, we study the dependence of mRNA/protein sequence complementarity on the properties of the nucleobase/amino-acid affinity scales used. Specifically, we sample the space of randomly generated scales by employing a Monte Carlo strategy with a fitness function that depends directly on the level of complementarity...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28740638/nutritional-physiology-and-ecology-of-wildlife-in-a-changing-world
#17
Kim Birnie-Gauvin, Kathryn S Peiman, David Raubenheimer, Steven J Cooke
Over the last century, humans have modified landscapes, generated pollution and provided opportunities for exotic species to invade areas where they did not evolve. In addition, humans now interact with animals in a growing number of ways (e.g. ecotourism). As a result, the quality (i.e. nutrient composition) and quantity (i.e. food abundance) of dietary items consumed by wildlife have, in many cases, changed. We present representative examples of the extent to which vertebrate foraging behaviour, food availability (quantity and quality) and digestive physiology have been modified due to human-induced environmental changes and human activities...
2017: Conservation Physiology
https://www.readbyqxmd.com/read/28738072/monitoring-protected-areas-from-space-a-multi-temporal%C3%A2-assessment-using-raptors-as-biodiversity-surrogates
#18
Adrián Regos, Luis Tapia, Alberto Gil-Carrera, Jesús Domínguez
Monitoring protected areas (PAs) is essential for systematic evaluation of their effectiveness in terms of habitat protection, preservation and representativeness. This study illustrates how the use of species distribution models that combine remote sensing data and information about biodiversity surrogates can contribute to develop a systematic protocol for monitoring PAs. In particular, we assessed the effectiveness of the Natura 2000 (N2000) network, for conserving and preserving the representativeness of seven raptor species in a highly-dynamic landscape in northwest Spain between 2001 and 2014...
2017: PloS One
https://www.readbyqxmd.com/read/28736626/molecular-landscape-and-sub-classification-of-gastrointestinal-cancers-a-review-of-literature
#19
REVIEW
Bita Fakhri, Kian-Huat Lim
The historical approach of diagnosing cancer types based entirely on anatomic origin and histologic features, and the "one-size-fit-all" therapeutic approach, are inadequate in modern cancer treatment. From decades of research we now know that cancer is a highly heterogeneous disease driven by complex genetic or epigenetic alterations. The advent of various high throughput molecular tools has now enabled us to view and sub-classify each cancer type based on their distinct molecular features, in addition to histologic classification, with the promise of individualized treatment strategies tailored towards each specific subtype to improve patient outcomes...
June 2017: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28734110/when-can-refuges-mediate-the-genetic-effects-of-fire-regimes-a-simulation-study-of-the-effects-of-topography-and-weather-on-neutral-and-adaptive-genetic-diversity-in-fire-prone-landscapes
#20
Sam C Banks, Ian D Davies, Geoffrey J Cary
Understanding how landscape heterogeneity mediates the effects of fire on biodiversity is increasingly important under global changes in fire regimes. We used a simulation experiment to investigate how fire regimes interact with topography and weather to shape neutral and selection-driven genetic diversity under alternative dispersal scenarios, and to explore the conditions under which micro-refuges can maintain genetic diversity of populations exposed to recurrent fire. Spatial heterogeneity in simulated fire frequency occurred in topographically-complex landscapes, with fire refuges and fire-prone 'hotspots' apparent...
July 22, 2017: Molecular Ecology
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