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https://www.readbyqxmd.com/read/27913358/conformational-sampling-of-a-biomolecular-rugged-energy-landscape
#1
Jakub Rydzewski, Rafal Jakubowski, Giuseppe Nicosia, Wieslaw Nowak
The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field...
December 1, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27913354/a-novel-elastic-force-field-to-influence-mediolateral-foot-placement-during-walking
#2
Elizabeth Nyberg, Jordan Broadway, Christian Finetto, Jesse Dean
Bipedal gait can be stabilized through mechanically-appropriate mediolateral foot placement, although this strategy is disrupted in a subset of neurologically injured individuals with balance deficits. The goal of the present work was to develop a device to influence mediolateral foot placement during treadmill walking. We created a novel force-field using a combination of passive elasticity and active control; wires in series with extension springs run parallel to the treadmill belts and can be rapidly repositioned to exert mediolateral forces on the legs of users...
December 1, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/27912134/uncertainties-in-mapping-forest-carbon-in-urban-ecosystems
#3
Gang Chen, Emre Ozelkan, Kunwar K Singh, Jun Zhou, Marilyn R Brown, Ross K Meentemeyer
Spatially explicit urban forest carbon estimation provides a baseline map for understanding the variation in forest vertical structure, informing sustainable forest management and urban planning. While high-resolution remote sensing has proven promising for carbon mapping in highly fragmented urban landscapes, data cost and availability are the major obstacle prohibiting accurate, consistent, and repeated measurement of forest carbon pools in cities. This study aims to evaluate the uncertainties of forest carbon estimation in response to the combined impacts of remote sensing data resolution and neighborhood spatial patterns in Charlotte, North Carolina...
November 29, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27912064/modular-assembly-of-the-bacterial-large-ribosomal-subunit
#4
Joseph H Davis, Yong Zi Tan, Bridget Carragher, Clinton S Potter, Dmitry Lyumkis, James R Williamson
The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ∼4-5 Å resolution and could be placed in an assembly pathway...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27912024/functional-diversity-of-non-lethal-effects-chemical-camouflage-and%C3%A2-variation-in-fish-avoidance-in-colonizing-beetles
#5
William J Resetarits, Matthew R Pintar
Predators play an extremely important role in natural communities. In freshwater systems, fish can dominate sorting both at the colonization and post-colonization stage. Specifically, for many colonizing species, fish can have non-lethal, direct effects that exceed the lethal direct effects of predation. Functionally diverse fish species with a range of predatory capabilities have previously been observed to elicit functionally equivalent responses on oviposition in tree frogs. We tested this hypothesis of functional equivalence of non-lethal effects for four predatory fish species, using naturally colonizing populations of aquatic beetles...
December 2016: Ecology
https://www.readbyqxmd.com/read/27912015/invasion-in-patchy-landscapes-is-affected-by-dispersal-mortality-and-mate-finding-failure
#6
Jonathan A Walter, Ariel L Firebaugh, Patrick C Tobin, Kyle J Haynes
Range expansions are a function of population growth and dispersal, and nascent populations often must overcome demographic Allee effects (positive density dependence at low population densities) driven by factors such as mate-finding failure. Given the importance of individual movement to mate finding, links between landscape structure and movement may be critical to range expansion; however, landscape effects on other factors including mortality may be equally or more important. In one of the most comprehensive investigations of the interactions of these processes to date, we combined field experiments, simulation modeling, and analysis of empirical spread patterns to investigate how landscape structure affected the spread of the gypsy moth in Virginia and West Virginia...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911998/tropical-forest-loss-and-its-multitrophic-effects-on-insect-herbivory
#7
José Carlos Morante-Filho, Víctor Arroyo-Rodríguez, Madelon Lohbeck, Teja Tscharntke, Deborah Faria
Forest loss threatens biodiversity, but its potential effects on multitrophic ecological interactions are poorly understood. Insect herbivory depends on complex bottom-up (e.g., resource availability and plant antiherbivore defenses) and top-down forces (e.g., abundance of predators and herbivorous), but its determinants in human-altered tropical landscapes are largely unknown. Using structural equation models, we assessed the direct and indirect effects of forest loss on insect herbivory in 40 landscapes (115 ha each) from two regions with contrasting land-use change trajectories in the Brazilian Atlantic rainforest...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911722/dawn-of-the-in-vivo-rna-structurome-and-interactome
#8
REVIEW
Chun Kit Kwok
RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure-function relationship on a transcriptomic scale...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911230/bromodomain-inhibitors-and-cancer-therapy-from-structures-to-applications
#9
Montserrat Pérez-Salvia, Manel Esteller
Aberrations in the epigenetic landscape are a hallmark of cancer. Alterations in enzymes that are "writers", "erasers", or "readers" of histone modification marks are common. Bromodomains are "readers" that bind acetylated lysines in histone tails. Their most important function is the regulation of gene transcription by the recruitment of different molecular partners. Moreover, proteins containing bromodomains are also epigenetic regulators, although little is known about the specific function of these domains...
December 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27910970/exploration-of-hydrogen-bond-networks-and-potential-energy-surfaces-of-methanol-clusters-using-a-two-stage-clustering-algorithm
#10
Po-Jen Hsu, Kun-Lin Ho, Sheng-Hsien Lin, Jer-Lai Kuo
The potential energy surface (PES), structures and thermal properties of methanol clusters (MeOH)n with n = 8-15 were explored by replica-exchange molecular dynamics (REMD) simulations with an empirical model and refined using density functional theory (DFT) methods. For a given size, local minima structures were sampled from REMD trajectories and archived by a newly developed molecular database via a two-stage clustering algorithm (TSCA). Our TSCA utilizes both the topology of O-HO hydrogen bonding networks and the similarity of the shapes to filter out duplicates...
December 2, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27909951/contrasting-patterns-in-solitary-and-eusocial-bees-while-responding-to-landscape-features-in-the-brazilian-cerrado-a-multiscaled-perspective
#11
D P Silva, D S Nogueira, P De Marco
Landscape structure is an important determinant of biological fluxes and species composition, but species do not respond equally to landscape features or spatial extents. Evaluating "multi-scale" responses of species to landscape structure is an important framework to be considered, allowing insights about habitat requirements for different groups. We evaluated the response of Brazilian Cerrado's bees (eusocial vs. solitary ones) to both the amount and isolation of remnant vegetation in eight nested multiple-local scales...
December 1, 2016: Neotropical Entomology
https://www.readbyqxmd.com/read/27909921/high-valent-copper-in-biomimetic-and-biological-oxidations
#12
REVIEW
William Keown, J Brannon Gary, T Daniel P Stack
A long-standing debate in the Cu-O2 field has revolved around the relevance of the Cu(III) oxidation state in biological redox processes. The proposal of Cu(III) in biology is generally challenged as no spectroscopic or structural evidence exists currently for its presence. The reaction of synthetic Cu(I) complexes with O2 at low temperature in aprotic solvents provides the opportunity to investigate and define the chemical landscape of Cu-O2 species at a small-molecule level of detail; eight different types are characterized structurally, three of which contain at least one Cu(III) center...
December 1, 2016: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/27908108/dual-hydrogen-bonding-motifs-in-complexes-formed-between-tropolone-and-formic-acid
#13
Deacon J Nemchick, Michael K Cohen, Patrick H Vaccaro
The near-ultraviolet π(*)←π absorption system of weakly bound complexes formed between tropolone (TrOH) and formic acid (FA) under cryogenic free-jet expansion conditions has been interrogated by exploiting a variety of fluorescence-based laser-spectroscopic probes, with synergistic quantum-chemical calculations built upon diverse model chemistries being enlisted to unravel the structural and dynamical properties of the pertinent ground [X̃(1)A(')] and excited [Ã(1)A(')π(*)π] electronic states. For binary TrOH ⋅ FA adducts, the presence of dual hydrogen-bond linkages gives rise to three low-lying isomers designated (in relative energy order) as INT, EXT1, and EXT2 depending on whether docking of the FA ligand to the TrOH substrate takes place internal or external to the five-membered reaction cleft of tropolone...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27907260/ten-year-responses-of-ground-dwelling-spiders-to-retention-harvest-in-the-boreal-forest
#14
Jaime Pinzon, John R Spence, David W Langor, David P Shorthouse
The Ecosystem Management Emulating Natural Disturbances (EMEND) project tests the hypothesis that varying levels of green tree retention maintain and retain forest biodiversity better than conventional clear-cutting. We studied epigaeic spiders to assess biodiversity changes 2, 5, and 10 yr following a range of partial retention harvests (clear-cut, 10-75% retention) and unharvested controls in four boreal mixedwood cover types. A total of 56 371 adult spiders representing 220 species was collected using pitfall traps...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27907255/a-hyperspectral-image-can-predict-tropical-tree-growth-rates-in-single-species-stands
#15
T Trevor Caughlin, Sarah J Graves, Gregory P Asner, Michiel van Breugel, Jefferson S Hall, Roberta E Martin, Mark S Ashton, Stephanie A Bohlman
Remote sensing is increasingly needed to meet the critical demand for estimates of forest structure and composition at landscape to continental scales. Hyperspectral images can detect tree canopy properties, including species identity, leaf chemistry and disease. Tree growth rates are related to these measurable canopy properties but whether growth can be directly predicted from hyperspectral data remains unknown. We used a single hyperspectral image and light detection and ranging-derived elevation to predict growth rates for 20 tropical tree species planted in experimental plots...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27906486/the-fractional-occupation-number-weighted-density-as-a-versatile-analysis-tool-for-molecules-with-a-complicated-electronic-structure
#16
Christoph Alexander Bauer, Andreas Hansen, Stefan Grimme
The fractional occupation number weighted density (FOD) analysis is explored as a general theoretical diagnostic for complicated electronic structures. Its main feature is to provide robustly and fast the information where 'hot' (strongly correlated and chemically active) electrons are localized in a molecule. We demonstrate its usage in four different prototypical applications: (i) As a new and fast measure for the biradical character of polycyclic aromatic hydrocarbons, (ii) for the selection of active orbital spaces in multiconfigurational or complete active space self consistent field (MCSCF/CASSCF) treatments, (iii) as a possibility to consistently describe molecular energy landscapes in regions with varying biradical character as exemplified by partial double bond torsions, and (iv) as a powerful visualization method for static electron correlation effects in large biomolecules in connection with an efficient semi-empirical tight-binding molecular orbital scheme...
December 1, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27905596/spectral-pointillism-of-enhanced-raman-scattering-for-accessing-structural-and-conformational-information-on-single-protein
#17
Jean-Emmanuel Clément, Aymeric Leray, Alexandre Bouhelier, Eric Finot
In this contribution, we provide new insights on the temporal fluctuations of surface enhanced Raman spectra (SERS) of large single molecules such as proteins. Because they can only fit partly into small active volume, SERS analysis is referred to spectral pointillism where only protein subdomains are shined and the whole protein landscape is built from the dynamics of successive individual spectra. By applying our approach on bovine serum albumin, we show that single protein subdomains are mostly comprised of three distinct amino acids...
December 1, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27905592/the-conformational-landscape-of-2-4-fluoro-phenyl-ethylamine-consequences-of-fluorine-substitution-at-the-para-position
#18
Afik Shachar, Nitzan Mayorkas, Hanan Sachs, Ilana Bar
Fluorination is considered as a possible means for alteration of conformational landscapes in molecules. The effect of fluorine substitution was studied here by measuring the vibronic and vibrational spectra of gas phase 2-(4-fluoro-phenyl)-ethylamine (4-FPEA) by resonant two-photon ionization (R2PI) and by ionization-loss stimulated Raman spectroscopy (ILSRS). The measurement of survey ILSR spectra of 4-FPEA in the amino group region allowed to associate the bands in the R2PI spectrum to origin and vibronic transitions of the ground (S0) to the excited (S1) electronic states of three different conformers...
December 1, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27902757/evidence-of-facilitation-cascade-processes-as-drivers-of-successional-patterns-of-ecosystem-engineers-at-the-upper-altitudinal-limit-of-the-dry-puna
#19
Luca Malatesta, Federico Maria Tardella, Karina Piermarteri, Andrea Catorci
Facilitation processes constitute basic elements of vegetation dynamics in harsh systems. Recent studies in tropical alpine environments demonstrated how pioneer plant species defined as "ecosystem engineers" are capable of enhancing landscape-level richness by adding new species to the community through the modification of microhabitats, and also provided hints about the alternation of different ecosystem engineers over time. Nevertheless, most of the existing works analysed different ecosystem engineers separately, without considering the interaction of different ecosystem engineers...
2016: PloS One
https://www.readbyqxmd.com/read/27902726/a-landscape-view-of-agricultural-insecticide-use-across-the-conterminous-us-from-1997-through-2012
#20
Timothy D Meehan, Claudio Gratton
Simplification of agricultural landscapes is expected to have positive effects on many crop pests and negative effects on their natural enemies, potentially leading to increased pest pressure, decreased crop yield, and increased insecticide use. While many intermediate links in this causal chain have empirical support, there is mixed evidence for ultimate relationships between landscape simplification, crop yield, and insecticide use, especially at large spatial and temporal scales. We explored relationships between landscape simplification (proportion of a county in harvested cropland) and insecticide use (proportion of harvested cropland treated with insecticides), using county-level data from the US Census of Agriculture and a variety of standard and spatiotemporal regression techniques...
2016: PloS One
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