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Landscape structure

David J Wales
Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations...
April 20, 2018: Annual Review of Physical Chemistry
Peter J Mahoney, Julie K Young, Kent R Hersey, Randy T Larsen, Brock R McMillan, David C Stoner
Predator control is often implemented with the intent of disrupting top-down regulation in sensitive prey populations. However, ambiguity surrounding the efficacy of predator management, as well as the strength of top-down effects of predators in general, is often exacerbated by the spatially implicit analytical approaches used in assessing data with explicit spatial structure. Here, we highlight the importance of considering spatial context in the case of a predator control study in south-central Utah. We assessed the spatial match between aerial removal risk in coyotes (Canis latrans) and mule deer (Odocoileus hemionus) resource selection during parturition using a spatially explicit, multi-level Bayesian model...
April 2018: Ecological Applications: a Publication of the Ecological Society of America
Courtney G Collins, Jason E Stajich, Sören E Weber, Nuttapon Pombubpa, Jeffrey M Diez
Global climate and land use change are altering plant and soil microbial communities worldwide, particularly in arctic and alpine biomes where warming is accelerated. The widespread expansion of woody shrubs into historically herbaceous alpine plant zones is likely to interact with climate to affect soil microbial community structure and function, however our understanding of alpine soil ecology remains limited. This study aimed to 1) determine whether the diversity and community composition of soil fungi vary across elevation gradients and to 2) assess the impact of woody shrub expansion on these patterns...
April 19, 2018: Molecular Ecology
Ingemar André, Sinisa Bjelic
The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs-into-holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of two monomers, can assemble into a wide range of states. They can form canonical as well as noncanonical coiled coils, be parallel or antiparallel, where helices associate with different degrees of shift, tilt, and rotation...
April 20, 2018: Proteins
Luis Ruiz Pestana, Natalie Minnetian, Laura Nielsen Lammers, Teresa Head-Gordon
When driven out of equilibrium, many diverse systems can form complex spatial and dynamical patterns, even in the absence of attractive interactions. Using kinetic Monte Carlo simulations, we investigate the phase behavior of a binary system of particles of dissimilar size confined between semiflexible planar surfaces, in which the nanoconfinement introduces a non-local coupling between particles, which we model as an activation energy barrier to diffusion that decreases with the local fraction of the larger particle...
February 14, 2018: Chemical Science
Félix Musil, Sandip De, Jack Yang, Joshua E Campbell, Graeme M Day, Michele Ceriotti
Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules...
February 7, 2018: Chemical Science
Michael L Barta, Shoichi Tachiyama, Meenakumari Muthuramalingam, Olivia Arizmendi, Cecilia E Villanueva, Kasra X Ramyar, Brian V Geisbrecht, Scott Lovell, Kevin P Battaile, Wendy L Picking, William D Picking
Bacterial type III secretion systems (T3SS) are used to inject proteins into mammalian cells to subvert cellular functions. The Shigella T3SS apparatus (T3SA) is comprised of a basal body, cytoplasmic sorting platform and exposed needle with needle "tip complex" (TC). TC maturation occurs when the translocator protein IpaB is recruited to the needle tip where both IpaD and IpaB control secretion induction. IpaB insertion into the host membrane is the first step of translocon pore formation and secretion induction...
April 19, 2018: Protein Science: a Publication of the Protein Society
Corinne A Lutomski, Nicholas A Lyktey, Elizabeth E Pierson, Zhongchao Zhao, Adam Zlotnick, Martin F Jarrold
For a three-dimensional structure to spontaneously self-assemble from many identical components, the steps on the pathway must be kinetically accessible. Many virus capsids are icosahedral and assembled from hundreds of identical proteins, but how they navigate the assembly process is poorly understood. Capsid assembly is thought to involve stepwise addition of subunits to a growing capsid fragment. Coarse-grained models suggest that the reaction occurs on a downhill energy landscape, so intermediates are expected to be fleeting...
April 19, 2018: Journal of the American Chemical Society
Timothy P Moneypenny, Anna Yang, Nathan P Walter, Toby J Woods, Danielle L Gray, Yang Zhang, Jeffrey S Moore
In the dynamic synthesis of covalent organic frameworks and molecular cages, the typical synthetic approach involves heuristic methods of discovery. While this approach has yielded many remarkable products, the ability to predict the structural outcome of subjecting a multitopic precursor to dynamic covalent chemistry (DCC) remains a challenge in the field. The synthesis of covalent organic cages is a prime example of this phenomenon, where precursors designed with the intention of affording a specific product may deviate dramatically when the DCC synthesis is attempted...
April 19, 2018: Journal of the American Chemical Society
Jessica R Kohn, Sarah L Heath, Rudy Behnia
Confronted with an ever-changing visual landscape, animals must be able to detect relevant stimuli and translate this information into behavioral output. A visual scene contains an abundance of information: to interpret the entirety of it would be uneconomical. To optimally perform this task, neural mechanisms exist to enhance the detection of important features of the sensory environment while simultaneously filtering out irrelevant information. This can be accomplished by using a circuit design that implements specific "matched filters" that are tuned to relevant stimuli...
2018: Frontiers in Neural Circuits
Ahmed I Marwan, Uladzimir Shabeka, Julie A Reisz, Connie Zheng, Natalie J Serkova, Evgenia Dobrinskikh
INTRODUCTION: Fetal tracheal occlusion (TO) is currently an experimental approach to drive accelerated lung growth. It is stimulated by mechanotransduction that results in increased cellular proliferation and growth. However, it is currently unknown how TO affects the metabolic landscape of fetal lungs. MATERIALS AND METHODS: TO or sham was performed on fetal rabbits at 26 days followed by lung harvest on day 30. Mass spectrometry was performed to evaluate global metabolic changes...
April 18, 2018: Fetal Diagnosis and Therapy
Ganesan Senthil Kumar, Michael W Clarkson, Micha B A Kunze, Daniele Granata, A Joshua Wand, Kresten Lindorff-Larsen, Rebecca Page, Wolfgang Peti
Mitogen-activated protein kinases, which include p38, are essential for cell differentiation and autophagy. The current model for p38 activation involves activation-loop phosphorylation with subsequent substrate binding leading to substrate phosphorylation. Despite extensive efforts, the molecular mechanism of activation remains unclear. Here, using NMR spectroscopy, we show how the modulation of protein dynamics across timescales activates p38. We find that activation-loop phosphorylation does not change the average conformation of p38; rather it quenches the loop ps-ns dynamics...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
G Hoddinott, S Staples, R Brown, M Simwinga, C Mubekapi-Musadaidzwa, A C Hesseling, G Hendricks, P De Koker, L McKenna
The paediatric tuberculosis (TB) prevention and treatment landscape is moving into a new and exciting era, with knowledge from clinical trials offering real benefit to children. Community engagement is key to optimising the success of these trials. However, the clinical profile, epidemiology and social perceptions for paediatric multidrug-resistant TB (MDR-TB) complicate the operationalisation of this community engagement. We reflect on a diversity of recent experiences attempting to implement this type of research and the community engagement around it...
May 1, 2018: International Journal of Tuberculosis and Lung Disease
Jenny Ceolta-Smith, Sarah Salway, Angela Mary Tod
Recent UK welfare reforms have been less successful than expected by the Government in supporting unemployed people with long-term illness into work. Frontline workers remain a core element of the new welfare-to-work machinery, but operate within a changed organisational and policy landscape. These changes raise important questions regarding whether and how claimants' health-related barriers to work are considered. This paper examines the UK welfare-to-work frontline worker's role with claimants who have long-term illness...
April 17, 2018: Health & Social Care in the Community
Jill A Hamilton, Joshua M Miller
Understanding the processes underlying speciation has long been a challenge to evolutionary biologists. This spurs from difficulties teasing apart the various mechanisms that contribute to the evolution of barriers to reproduction. The study by Rafati et al. () in this issue of Molecular Ecology combines spatially explicit whole-genome resequencing with evaluation of differential gene expression across individuals with mixed ancestry to associate the genomic architecture of reproductive barriers with expression of reproductive incompatibilities...
March 2018: Molecular Ecology
Lin Y Chen, Mina K Chung, Larry A Allen, Michael Ezekowitz, Karen L Furie, Pamela McCabe, Peter A Noseworthy, Marco V Perez, Mintu P Turakhia
Our understanding of the risk factors and complications of atrial fibrillation (AF) is based mostly on studies that have evaluated AF in a binary fashion (present or absent) and have not investigated AF burden. This scientific statement discusses the published literature and knowledge gaps related to methods of defining and measuring AF burden, the relationship of AF burden to cardiovascular and neurological outcomes, and the effect of lifestyle and risk factor modification on AF burden. Many studies examine outcomes by AF burden classified by AF type (paroxysmal versus nonparoxysmal); however, quantitatively, AF burden can be defined by longest duration, number of AF episodes during a monitoring period, and the proportion of time an individual is in AF during a monitoring period (expressed as a percentage)...
April 16, 2018: Circulation
João M Alves, David Posada
BACKGROUND: Querying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the quality of single-cell data are critically needed. Taking advantage of previously published single-cell whole-genome and whole-exome cancer datasets, we studied the impact of sequencing depth and sampling effort towards single-cell variant detection...
April 16, 2018: Genome Medicine
Xiao-Jing Yuan, Stefano Raniolo, Vittorio Limongelli, Yechun Xu
The crystal structure of P2Y1 receptor (P2Y1R), a class A GPCR, revealed a special extra-helical site for its antagonist, BPTU, which locates in between the membrane and the protein. However, due to the limitation of crystallization experiments, the membrane was mimicked by use of detergents and the information related to the binding of BPTU to the receptor in the membrane environment is rather limited. In the present work, we conducted a total of ~7.5 µs all-atom simulations in explicit solvent using conventional molecular dynamics and multiple enhanced sampling methods, with models of BPTU and a POPC bilayer, both in the absence and presence of P2Y1R...
April 16, 2018: Journal of Chemical Theory and Computation
Norman C Elliott, Michael J Brewer, Kristopher L Giles
Winter wheat is Oklahoma's most widely grown crop, and is planted during September and October, grows from fall through spring, and is harvested in June. Winter wheat fields are typically interspersed in a mosaic of habitats in other uses, and we hypothesized that the spatial and temporal composition and configuration of landscape elements, which contribute to agroecosystem diversity also influence biological control of common aphid pests. The parasitoid Lysiphlebus testaceipes (Cresson; Hymenoptera: Aphidiinae) is highly effective at reducing aphid populations in wheat in Oklahoma, and though a great deal is known about the biology and ecology of L...
April 12, 2018: Environmental Entomology
Andrea Dechner, Kevin M Flesher, Catherine Lindell, Téo Vega de Oliveira, Brian A Maurer
Understanding the factors that influence the presence and distribution of carnivores in human-dominated agricultural landscapes is one of the main challenges for biodiversity conservation, especially in landscapes where setting aside large protected areas is not feasible. Habitat use models of carnivore communities in rubber plantations are lacking despite the critical roles carnivores play in structuring ecosystems and the increasing expansion of rubber plantations. We investigated the habitat use of a mammalian carnivore community within a 4,200-ha rubber plantation/forest landscape in Bahia, Brazil...
2018: PloS One
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