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https://www.readbyqxmd.com/read/29785521/spatial-stochastic-intracellular-kinetics-a-review-of-modelling-approaches
#1
Stephen Smith, Ramon Grima
Models of chemical kinetics that incorporate both stochasticity and diffusion are an increasingly common tool for studying biology. The variety of competing models is vast, but two stand out by virtue of their popularity: the reaction-diffusion master equation and Brownian dynamics. In this review, we critically address a number of open questions surrounding these models: How can they be justified physically? How do they relate to each other? How do they fit into the wider landscape of chemical models, ranging from the rate equations to molecular dynamics? This review assumes no prior knowledge of modelling chemical kinetics and should be accessible to a wide range of readers...
May 21, 2018: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/29775634/the-direction-of-protein-evolution-is-destined-by-the-stability
#2
Natsuko Ota, Ryo Kurahashi, Satoshi Sano, Kazufumi Takano
Protein evolution is potentially governed by protein stability. Here, we investigated the relationship between protein evolution and stability through the random mutational drift of a thermophilic bacterial protein, an esterase of Alicyclobacillus acidocaldarius (Aac-Est), at high and low temperatures. In the first random mutation of Aac-Est, few proteins exhibit increased activity at 65°C, indicating that the wild-type (WT) Aac-Est is located on the peak of a mountain in a fitness landscape for activity at high temperature...
May 15, 2018: Biochimie
https://www.readbyqxmd.com/read/29754783/therapeutic-spaces-of-care-farming-transformative-or-ameliorating
#3
Alexandra Kaley, Chris Hatton, Christine Milligan
Since Wil Gesler's earliest articulation (Gesler, 1992; Gesler, 1996) key thinkers in the field of therapeutic landscapes have sought to emphasise the embodied, contextual and wholly relational nature of the relationship that exists between people and place. However, the extant research has tended to focus on the relational healing experience as this occurs 'in the moment' and with reference to a specific location or site of healing, with less attention being paid to what happens to people when they return to their ordinary or everyday places...
May 4, 2018: Social Science & Medicine
https://www.readbyqxmd.com/read/29745136/-spatial-heterogeneity-of-soil-salinization-and-its-influencing-factors-in-the-typical-region-of-the-mu-us-desert-loess-plateau-transitional-zone-northwest-china
#4
Xuan Zhao, Qi Li Hao, Ying Ying Sun
Studies on the spatial heterogeneity of saline soil in the Mu Us Desert-Loess Plateau transition zone are meaningful for understanding the mechanisms of land desertification. Taking the Mu Us Desert-Loess Plateau transition zone as the study subject, its spatial heterogeneity of pH, electrical conductivity (EC) and total salt content were analyzed by using on-site sampling followed with indoor analysis, classical statistical and geostatistical analysis. The results indicated that: 1) The average values of pH, EC and total salt content were 8...
June 18, 2017: Ying Yong Sheng Tai Xue Bao, the Journal of Applied Ecology
https://www.readbyqxmd.com/read/29742475/valuing-the-visual-impact-of-wind-farms-a-calculus-method-for-synthesizing-choice-experiments-studies
#5
REVIEW
Cheng Wen, Martin Dallimer, Steve Carver, Guy Ziv
Despite the great potential of mitigating carbon emission, development of wind farms is often opposed by local communities due to the visual impact on landscape. A growing number of studies have applied nonmarket valuation methods like Choice Experiments (CE) to value the visual impact by eliciting respondents' willingness to pay (WTP) or willingness to accept (WTA) for hypothetical wind farms through survey questions. Several meta-analyses have been found in the literature to synthesize results from different valuation studies, but they have various limitations related to the use of the prevailing multivariate meta-regression analysis...
May 6, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29736242/association-with-humans-and-seasonality-interact-to-reverse-predictions-for-animal-space-use
#6
Peter N Laver, Kathleen A Alexander
Background: Variation in animal space use reflects fitness trade-offs associated with ecological constraints. Associated theories such as the metabolic theory of ecology and the resource dispersion hypothesis generate predictions about what drives variation in animal space use. But, metabolic theory is usually tested in macro-ecological studies and is seldom invoked explicitly in within-species studies. Full evaluation of the resource dispersion hypothesis requires testing in more species...
2018: Movement Ecology
https://www.readbyqxmd.com/read/29710633/endocrine-disruptors-in-breeding-ponds-and-reproductive-health-of-toads-in-agricultural-urban-and-natural-landscapes
#7
Veronika Bókony, Bálint Üveges, Nikolett Ujhegyi, Viktória Verebélyi, Edina Nemesházi, Olivér Csíkvári, Attila Hettyey
Many chemical pollutants have endocrine disrupting effects which can cause lifelong reproductive abnormalities in animals. Amphibians are the most threatened group of vertebrates, but there is little information on the nature and quantity of pollutants occurring in typical amphibian breeding habitats and on the reproductive capacities of amphibian populations inhabiting polluted areas. In this study we investigated the occurrence and concentrations of endocrine disrupting chemicals in the water and sediment of under-studied amphibian breeding habitats in natural, agricultural and urbanized landscapes...
April 13, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29705127/genomic-methylation-and-transcriptomic-profiling-provides-insights-into-heading-depression-in-inbred-brassica-rapa-l-ssp-pekinensis
#8
Yan Liu, Cui Xu, Xuebing Tang, Surui Pei, Di Jin, Minghao Guo, Meng Yang, Yaowei Zhang
Inbreeding depression is the reduction in fitness observed in inbred populations. In plants, it leads to disease, weaker resistance to adverse environmental conditions, inhibition of growth, and decrease of yield. To elucidate molecular mechanisms behind inbreeding depression, we compared global DNA methylation and transcriptome profiles of a normal and a highly inbred heading degenerated variety of the Chinese cabbage (Brassica rapa L. ssp. pekinensis). DNA methylation was reduced in inbred plants, suggesting a change in the epigenetic landscape...
April 26, 2018: Gene
https://www.readbyqxmd.com/read/29698417/the-response-to-selection-in-glycoside-hydrolase-family-13-structures-a-comparative-quantitative-genetics-approach
#9
Jose Sergio Hleap, Christian Blouin
The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates and members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We find that the TIM-barrel (a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone, common to all amylases) is not selectable since it is under purifying selection...
2018: PloS One
https://www.readbyqxmd.com/read/29691656/exploration-of-nucleoprotein-%C3%AE-more-and-xd-interactions-of-nipah-and-hendra-viruses
#10
Xu Shang, Wenting Chu, Xiakun Chu, Liufang Xu, Sonia Longhi, Jin Wang
Henipavirus, including Hendra virus (HeV) and Nipah virus (NiV), is a newly discovered human pathogen genus. The nucleoprotein of Henipavirus contains an α-helical molecular recognition element (α-MoRE) that folds upon binding to the X domain (XD) of the phosphoprotein (P). In order to explore the conformational dynamics of free α-MoREs and the underlying binding-folding mechanism with XD, atomic force field-based and hybrid structure-based MD simulations were carried out. In our empirical force field-based simulations, characteristic structures and helicities of α-MoREs reveal the co-existence of partially structured and disordered conformations, as in the case of the well characterized cognate measles virus (MeV) α-MoRE...
April 24, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29687344/spatiotemporal-relationships-defining-the-adaptive-gating-of-the-bacterial-mechanosensitive-channel-mscs
#11
Uğur Çetiner, Andriy Anishkin, Sergei Sukharev
Adaptive desensitization and inactivation are common properties of most ion channels and receptors. The mechanosensitive channel of small conductance MscS, which serves as a low-threshold osmolyte release valve in most bacteria, inactivates not from the open, but from the resting state under moderate tensions. This mechanism enables the channel to respond differently to slow tension ramps versus abruptly applied stimuli. In this work, we present a reconstruction of the energy landscape for MscS transitions based on patch current kinetics recorded under special pressure protocols...
April 23, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29686238/multi-environment-fitness-landscapes-of-a-trna-gene
#12
Chuan Li, Jianzhi Zhang
A fitness landscape (FL) describes the genotype-fitness relationship in a given environment. To explain and predict evolution, it is imperative to measure the FL in multiple environments because the natural environment changes frequently. Using a high-throughput method that combines precise gene replacement with next-generation sequencing, we determine the in vivo FL of a yeast tRNA gene comprising over 23,000 genotypes in four environments. Although genotype-by-environment interaction is abundantly detected, its pattern is so simple that we can transform an existing FL to that in a new environment with fitness measures of only a few genotypes in the new environment...
April 23, 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29665847/tensions-in-ethics-and-policy-created-by-national-precision-medicine-programs
#13
Jusaku Minari, Kyle B Brothers, Michael Morrison
Precision medicine promises to use genomics and other data-intensive approaches to improve diagnosis and develop new treatments for major diseases, but also raises a range of ethical and governance challenges. Implementation of precision medicine in "real world" healthcare systems blurs the boundary between research and care. This has implications for the meaning and validity of consent, and increased potential for discrimination, among other challenges. Increased sharing of personal information raises concerns about privacy, commercialization, and public trust...
April 17, 2018: Human Genomics
https://www.readbyqxmd.com/read/29662246/why-come-back-home-breeding-site-fidelity-varies-with-group-size-and-parasite-load-in-a-colonial-bird
#14
Charles R Brown, Erin A Roche, Mary Bomberger Brown
Fidelity to a past breeding site is widespread among animals and may confer both costs and benefits. Colonial species occur at specific sites that can accommodate multiple breeders, and the choice of whether to return to last year's site or disperse elsewhere can affect colony site use, the colony size distribution and individual fitness. For the colonial cliff swallow, Petrochelidon pyrrhonota , which occupies colonies of widely different sizes, we used a 30-year field study in western Nebraska to investigate how the extent of infestation by ectoparasites and colony size affected breeders' colony site fidelity between years...
October 2017: Animal Behaviour
https://www.readbyqxmd.com/read/29657774/a-mathematical-model-of-marine-bacteriophage-evolution
#15
Silvia Pagliarini, Andrei Korobeinikov
To explore how particularities of a host cell-virus system, and in particular host cell replication, affect viral evolution, in this paper we formulate a mathematical model of marine bacteriophage evolution. The intrinsic simplicity of real-life phage-bacteria systems, and in particular aquatic systems, for which the assumption of homogeneous mixing is well justified, allows for a reasonably simple model. The model constructed in this paper is based upon the Beretta-Kuang model of bacteria-phage interaction in an aquatic environment (Beretta & Kuang 1998 Math...
March 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29649440/mapping-the-evolutionary-potential-of-rna-viruses
#16
REVIEW
Patrick T Dolan, Zachary J Whitfield, Raul Andino
The deterministic force of natural selection and stochastic influence of drift shape RNA virus evolution. New deep-sequencing and microfluidics technologies allow us to quantify the effect of mutations and trace the evolution of viral populations with single-genome and single-nucleotide resolution. Such experiments can reveal the topography of the genotype-fitness landscapes that shape the path of viral evolution. By combining historical analyses, like phylogenetic approaches, with high-throughput and high-resolution evolutionary experiments, we can observe parallel patterns of evolution that drive important phenotypic transitions...
April 11, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29649156/using-landscape-analysis-to-test-hypotheses-about-drivers-of-tick-abundance-and-infection-prevalence-with-borrelia-burgdorferi
#17
A Michelle Ferrell, R Jory Brinkerhoff
Patterns of vector-borne disease risk are changing globally in space and time and elevated disease risk of vector-borne infection can be driven by anthropogenic modification of the environment. Incidence of Lyme disease, caused by the bacterium Borrelia burgdorferi sensu stricto, has risen in a number of locations in North America and this increase may be driven by spatially or numerically expanding populations of the primary tick vector, Ixodes scapularis . We used a model selection approach to identify habitat fragmentation and land-use/land cover variables to test the hypothesis that the amount and configuration of forest cover at spatial scales relevant to deer, the primary hosts of adult ticks, would be the predominant determinants of tick abundance...
April 12, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29643335/quantitative-characterization-of-all-single-amino-acid-variants-of-a-viral-capsid-based-drug-delivery-vehicle
#18
Emily C Hartman, Christopher M Jakobson, Andrew H Favor, Marco J Lobba, Ester Álvarez-Benedicto, Matthew B Francis, Danielle Tullman-Ercek
Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report a technique, termed SyMAPS (Systematic Mutation and Assembled Particle Selection), that can be used to characterize the assembly competency of all single amino acid variants of a self-assembling viral structural protein. SyMAPS studies on the MS2 bacteriophage coat protein revealed a high-resolution fitness landscape that challenges some conventional assumptions of protein engineering...
April 11, 2018: Nature Communications
https://www.readbyqxmd.com/read/29627956/dynamics-of-habitat-selection-in-birds-adaptive-response-to-nest-predation-depends-on-multiple-factors
#19
J H Devries, R G Clark, L M Armstrong
According to theory, habitat selection by organisms should reflect underlying habitat-specific fitness consequences and, in birds, reproductive success has a strong impact on population growth in many species. Understanding processes affecting habitat selection also is critically important for guiding conservation initiatives. Northern pintails (Anas acuta) are migratory, temperate-nesting birds that breed in greatest concentrations in the prairies of North America and their population remains below conservation goals...
April 7, 2018: Oecologia
https://www.readbyqxmd.com/read/29625416/molecular-dynamics-and-ligand-docking-of-a-hinge-region-variant-of-south-african-hiv-1-subtype-c-protease
#20
Jake Zondagh, Vijayakumar Balakrishnan, Ikechukwu Achilonu, Heini W Dirr, Yasien Sayed
HIV-1 protease is an important antiretroviral drug target due to its key role in viral maturation. Computational models have been successfully used in the past to understand the dynamics of HIV-1 protease variants. We performed molecular dynamics simulations and induced fit docking on a wild-type South African HIV-1 subtype C protease and an N37T↑V hinge region variant. The simulations were initiated in a cubic cell universe and run in explicit solvent, with the wild-type and variant proteases in the fully closed conformation and under periodic boundary conditions...
March 27, 2018: Journal of Molecular Graphics & Modelling
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