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Landscape structure

L Chasmer, C Hopkinson
This study demonstrates linkages between the 1997/98 El Niño/Southern Oscillation index and a threshold shift to increased permafrost loss within a southern Taiga Plains watershed, Northwest Territories, Canada. Three-dimensional contraction of permafrost plateaus and changes in vegetation structural characteristics are determined from multi-temporal airborne Light Detection And Ranging (LiDAR) surveys in 2008, 2011 and 2015. Morphological changes in permafrost cover are compared with optical image analogues from 1970, 1977, 2000, and 2008 and time-series hydro-climate data...
October 22, 2016: Global Change Biology
Jamel Meslamani, Steven G Smith, Roberto Sanchez, Ming-Ming Zhou
Bromodomains are conserved structural modules responsible for recognizing acetylated-lysine residues on histone tails and other transcription-associated proteins, such as transcription factors and co-factors. Owing to their important functions in the regulation of ordered gene transcription in chromatin, bromodomains of the BET family proteins have recently been shown as druggable targets for a wide array of human diseases, including cancer and inflammation. Here we review the structural and functional features of the bromodomains and their small-molecule inhibitors...
March 2016: Drug Discovery Today. Technologies
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiri Sponer
G-quadruplexes are the most important non-canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradicting models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach the thermodynamics equilibrium...
October 21, 2016: Journal of Chemical Theory and Computation
Iain A Sawyer, David Sturgill, Myong-Hee Sung, Gordon L Hager, Miroslav Dundr
Nuclear bodies contribute to non-random organization of the human genome and nuclear function. Using a major prototypical nuclear body, the Cajal body, as an example, we suggest that these structures assemble at specific gene loci located across the genome as a result of high transcriptional activity. Subsequently, target genes are physically clustered in close proximity in Cajal body-containing cells. However, Cajal bodies are observed in only a limited number of human cell types, including neuronal and cancer cells...
October 21, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
R Kelman Wieder, Melanie A Vile, Kimberli D Scott, Cara M Albright, Kelly McMillen, Dale H Vitt, Mark Fenn
Oil extraction and development activities in the Athabasca Oil Sands Region of northern Alberta, Canada release NOx, SOx, and NHx to the atmosphere, ultimately resulting in increasing N and S inputs to surrounding ecosystems through atmospheric deposition. Peatlands are a major feature of the northern Alberta landscape, with bogs covering 6-10% of the land area, and fens covering 21-53%. Bulk deposition of NH4+-N, NO3--N, total inorganic N (TIN), and SO42--S, was quantified using ion exchange resin collectors deployed at 23 locations, over 1-6 years, reveal maximum N and S deposition of 9...
October 21, 2016: Environmental Science & Technology
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
David Samuel Johnson, R Scott Warren, Linda A Deegan, Thomas J Mozdzer
In saltmarsh plant communities, bottom-up pressure from nutrient enrichment is predicted to increase productivity, alter community structure, decrease biodiversity, and alter ecosystem functioning. Previous work supporting these predictions has been based largely on short-term, plot-level (e.g., 1-300 m(2) ) studies, which may miss landscape-level phenomena that drive ecosystem-level responses. We implemented an ecosystem-scale, nine-year nutrient experiment to examine how saltmarsh plants respond to simulated conditions of coastal eutrophication...
July 27, 2016: Ecological Applications: a Publication of the Ecological Society of America
Laura M Cisneros, Matthew E Fagan, Michael R Willig
BACKGROUND: Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms...
2016: PeerJ
Guillaume Van der Rest, Human Rezaei, Frédéric Halgand
Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry...
October 18, 2016: Journal of the American Society for Mass Spectrometry
Fernando Racimo, Davide Marnetto, Emilia Huerta-Sánchez
Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process - adaptive introgression - may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection...
October 18, 2016: Molecular Biology and Evolution
Jeffrey D Kline, Mark E Harmon, Thomas A Spies, Anita T Morzillo, Robert J Pabst, Brenda C McComb, Frank Schnekenburger, Keith A Olsen, Blair Csuti, Jody C Vogeler
Forest policymakers and managers have long sought ways to evaluate the capability of forest landscapes to jointly produce timber, habitat, and other ecosystem services in response to forest management. Currently, carbon is of particular interest as policies for increasing carbon storage on federal lands are being proposed. However, a challenge in joint production analysis of forest management is adequately representing ecological conditions and processes that influence joint production relationships. We used simulation models of vegetation structure, forest sector carbon, and potential wildlife habitat to characterize landscape-level joint production possibilities for carbon storage, timber harvest, and habitat for seven wildlife species across a range of forest management regimes...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
Bérenger Bourgeois, Eduardo González, Anne Vanasse, Isabelle Aubin, Monique Poulin
The disruption of hydrological connectivity by human activities such as flood regulation or land-use changes strongly impacts riparian plant communities. However, landscape-scale processes have generally been neglected in riparian restoration projects as opposed to local conditions, even though such processes might largely influence community recovery. We surveyed plant composition of field edges and riverbanks in 51 riparian zones restored by tree planting (565 1-m(2) plots) within two agricultural watersheds in southeastern Québec, Canada...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
Jonathan A Mee, John R Post, Hillary Ward, Kyle L Wilson, Eric Newton, Ariane Cantin
Effective management of socioecological systems requires an understanding of the complex interactions between people and the environment. In recreational fisheries, which are prime examples of socioecological systems, anglers are analogous to mobile predators in natural predator-prey systems, and individual fisheries in lakes across a region are analogous to a spatially structured landscape of prey patches. Hence, effective management of recreational fisheries across large spatial scales requires an understanding of the dynamic interactions among ecological density dependent processes, landscape-level characteristics, and angler behaviors...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Renata L Muylaert, Richard D Stevens, Milton C Ribeiro
Understanding how animal groups respond to contemporary habitat loss and fragmentation is essential for development of strategies for species conservation. Until now, there has been no consensus about how landscape degradation affects the diversity and distribution of Neotropical bats. Some studies demonstrate population declines and species loss in impacted areas, although the magnitude and generality of these effects on bat community structure are unclear. Empirical fragmentation thresholds predict an accentuated drop in biodiversity, and species richness in particular, when less than 30% of the original amount of habitat in the landscape remains...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Jessica A Castillo, Clinton W Epps, Mackenzie R Jeffress, Chris Ray, Thomas J Rodhouse, Donelle Schwalm
Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Dayoung Park, Narine Arabyan, Cynthia C Williams, Ting Song, Anupam Mitra, Bart C Weimer, Emanual Maverakis, Carlito B Lebrilla
Although gut host-pathogen interactions are glycan-mediated processes, few details are known about the participating structures. Here we employ high-resolution mass spectrometric profiling to comprehensively identify and quantitatively measure the exact modifications of native intestinal epithelial cell surface N-glycans induced by S. Typhimurium infection. Sixty minutes post-infection, select sialylated structures showed decreases in terms of total number and abundances. To assess the effect of cell surface mannosylation, we selectively rerouted glycan expression on the host using the alpha-mannosidase inhibitor, kifunensine, toward overexpression of high mannose...
October 17, 2016: Molecular & Cellular Proteomics: MCP
Maria Zhivagui, Michael Korenjak, Jiri Zavadil
Mutation spectra in cancer genomes provide information on the disease aetiology and the causality underlying the evolution and progression of cancer. Genome-wide mutation patterns reflect the effects of mutagenic insults and can thus reveal past carcinogen-specific exposures and inform hypotheses on the causative factors for specific cancer types. In order to identify mutation profiles in human cancers, single genes studies were first employed, focusing mainly on the tumour suppressor gene TP53. Furthermore, experimental studies had been developed in model organisms...
October 18, 2016: Basic & Clinical Pharmacology & Toxicology
Daniel Nava Rodrigues, Gunther Boysen, Semini Sumanasuriya, George Seed, Angelo M De Marzo, Johann de Bono
Prostate cancer (PCa) is a clinically heterogeneous disease and current treatment strategies are based largely on anatomical and pathological parameters. In the recent past, several DNA sequencing studies of primary and advanced PCa have revealed recurrent patterns of genomic aberrations that expose mechanisms of resistance to available therapies and potential new drug targets. Suppression of androgen receptor (AR) signalling is the cornerstone of advanced prostate cancer treatment. Genomic aberrations of the androgen receptor or alternative splicing of its mRNA are increasingly recognized as biomarkers of resistance to AR-targeted therapy such as abiraterone or enzalutamide...
October 18, 2016: Journal of Pathology
Koning Shen, Barbara Calamini, Jonathan A Fauerbach, Boxue Ma, Sarah H Shahmoradian, Ivana L Serrano Lachapel, Wah Chiu, Donald C Lo, Judith Frydman
Many neurodegenerative diseases are linked to amyloid aggregation. In Huntington's disease (HD), neurotoxicity correlates with increased aggregation propensity of a polyglutamine (polyQ) expansion in exon 1 of mutant huntingtin protein (mHtt). Here we establish how the domains flanking the polyQ tract shape the mHtt conformational landscape in vitro and in neurons. In vitro, the flanking domains have opposing effects on the conformation and stabilities of oligomers and amyloid fibrils. The N-terminal N17 promotes amyloid fibril formation, while the C-terminal Proline Rich Domain destabilizes fibrils and enhances oligomer formation...
October 18, 2016: ELife
Keping Sun, Rebecca T Kimball, Tong Liu, Xuewen Wei, Longru Jin, Tinglei Jiang, Aiqing Lin, Jiang Feng
Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry...
October 17, 2016: Scientific Reports
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