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Landscape structure

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https://www.readbyqxmd.com/read/28097736/restoration-and-management-for-plant-diversity-enhances-the-rate-of-belowground-ecosystem-recovery
#1
Ryan P Klopf, Sara G Baer, Elizabeth M Bach, J Six
The positive relationship between plant diversity and ecosystem functioning has been criticized for its applicability at large scales and in less controlled environments that are relevant to land management. To inform this gap between ecological theory and application, we compared recovery rates of belowground properties using two chronosequences consisting of continuously cultivated and independently restored fields with contrasting diversity management strategies: grasslands restored with high plant richness and managed for diversity with frequent burning (n=20) and grasslands restored with fewer species that were infrequently burned (n=15)...
January 17, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28097712/force-generation-by-titin-folding
#2
Zsolt Mártonfalvi, Pasquale Bianco, Katalin Naftz, György G Ferenczy, Miklós Kellermayer
Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (<10 pN), extension fluctuated without resolvable discrete events...
January 18, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28095770/the-unique-genomic-landscape-surrounding-the-epsps-gene-in-glyphosate-resistant-amaranthus-palmeri-a-repetitive-path-to-resistance
#3
William T Molin, Alice A Wright, Amy Lawton-Rauh, Christopher A Saski
BACKGROUND: The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28094063/a-change-in-landscape-lessons-learned-from-abandonment-of-ancient-wari-agricultural-terraces-in-southern-peru
#4
Ana C Londoño, Patrick Ryan Williams, Megan L Hart
Ancient agricultural terrace practices have survived for millennia, sustaining populations through extreme climatic shifts and political regime changes. In arid regions with abrupt relief such as Southern Peru, agricultural terracing is undergoing a resurgence, as has seen revitalization of once abandoned terrace and hydraulic systems. Wari terraces at Cerro Baul provide clues to past cultural practices. They also document sustainable farming practices by using resilient land management techniques which can help combat desertification and degradation of arable lands...
January 13, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28093763/where-east-meets-west-in-the-house-of-individuation
#5
Murray Stein
The psychological process of individuation as experienced in Jungian work may lead to states of consciousness that resemble advanced spiritual developments across religious traditions and cultures. This is where Westerners may reach a common ground with the East. In the essentials and with respect to the final goal there is little difference among the many ways to the self, even if the cultural features in the landscape are disparate. In late stage Jungian analysis and individuation and in what Erich Neumann calls 'centroversion', the personal and the impersonal aspects of the personality accumulate around the ego-self axis to form a composite identity...
February 2017: Journal of Analytical Psychology
https://www.readbyqxmd.com/read/28093097/present-day-central-african-forest-is-a-legacy-of-the-19th-century-human-history
#6
Julie Morin-Rivat, Adeline Fayolle, Charly Favier, Laurent Bremond, Sylvie Gourlet-Fleury, Nicolas Bayol, Philippe Lejeune, Hans Beeckman, Jean-Louis Doucet
The populations of light-demanding trees that dominate the canopy of central African forests are now aging. Here, we show that the lack of regeneration of these populations began ca. 165 ya (around 1850) after major anthropogenic disturbances ceased. Since 1885, less itinerancy and disturbance in the forest has occurred because the colonial administrations concentrated people and villages along the primary communication axes. Local populations formerly gardened the forest by creating scattered openings, which were sufficiently large for the establishment of light-demanding trees...
January 17, 2017: ELife
https://www.readbyqxmd.com/read/28091741/chemical-physical-and-biological-factors-shape-littoral-invertebrate-community-structure-in-coal-mining-end-pit-lakes
#7
Andreas Luek, Joseph B Rasmussen
Aquatic invertebrates form the base of the consumer food web in lakes. In coal-mining end-pit lakes, invertebrates are exposed to an environment with potentially challenging physical and chemical features. We hypothesized that the physical and chemical features of end-pit lakes reduce critical littoral habitat and thus reduce invertebrate diversity, thereby limiting the potential for these lakes to be naturalized. We used a multivariate approach using principle component analysis and redundancy analysis to study relationships between invertebrate community structure, habitat features, and water quality in five end-pit lakes and five natural lakes in the Rocky Mountain foothills of west-central Alberta, Canada...
January 13, 2017: Environmental Management
https://www.readbyqxmd.com/read/28090593/ultralm-and-minilm-locator-tools-for-smart-tracking-of-fluorescent-cells-in-correlative-light-and-electron-microscopy
#8
Elisabeth Brama, Christopher J Peddie, Gary Wilkes, Yan Gu, Lucy M Collinson, Martin L Jones
In-resin fluorescence (IRF) protocols preserve fluorescent proteins in resin-embedded cells and tissues for correlative light and electron microscopy, aiding interpretation of macromolecular function within the complex cellular landscape. Dual-contrast IRF samples can be imaged in separate fluorescence and electron microscopes, or in dual-modality integrated microscopes for high resolution correlation of fluorophore to organelle. IRF samples also offer a unique opportunity to automate correlative imaging workflows...
December 13, 2016: Wellcome Open Res
https://www.readbyqxmd.com/read/28088724/the-effect-of-urban-growth-on-landscape-scale-restoration-for-a-fire-dependent%C3%A2-songbird
#9
Bradley A Pickens, Jeffrey F Marcus, John P Carpenter, Scott Anderson, Paul J Taillie, Jaime A Collazo
A landscape-scale perspective on restoration ecology has been advocated, but few studies have informed restoration with landscape metrics or addressed broad-scale threats. Threats such as urban growth may affect restoration effectiveness in a landscape context. Here, we studied longleaf pine savanna in the rapidly urbanizing southeastern United States where a habitat-specialist bird, Bachman's sparrow (Peucaea aestivalis), is closely associated with savanna vegetation structure and frequent fire. Our objectives were to construct a species distribution model for Bachman's sparrow, determine the relationship between fire and urbanization, quantify the urban growth effect (2010-2090), identify potential restoration areas, and determine the interaction between restoration potential and urban growth by 2050...
January 12, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28087593/norovirus-mediated-modification-of-the-translational-landscape-via-virus-and-host-induced-cleavage-of-translation-initiation-factors
#10
Edward Emmott, Frederic Sorgeloos, Sarah L Caddy, Surender Vashist, Stanislav Sosnovtsev, Richard Lloyd, Kate Heesom, Nicolas Locker, Ian Goodfellow
Noroviruses produce viral RNAs lacking a 5' cap structure and instead use a virus-encoded VPg protein covalently linked to viral RNA to interact with translation initiation factors and drive viral protein synthesis. Norovirus infection results in the induction of the innate response leading to interferon stimulated gene (ISG) transcription. However the translation of the induced ISG mRNAs is suppressed. A SILAC-based mass spectrometry approach was employed to analyse changes to protein abundance in both whole cell and m7GTP-enriched samples to demonstrate that diminished host mRNA translation correlates with changes to the composition of the eukaryotic initiation factor complex...
January 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28081015/the-prospects-of-phosphorene-as-an-anode-material-for-high-performance-lithium-ion-batteries-a-fundamental-study
#11
Congyan Zhang, Ming Yu, George Anderson, Ruchira Ravinath Dharmasena, Gamini Sumanasekera
To completely understand lithium adsorption, diffusion, and capacity on the surface of phosphorene and, therefore, the prospects of phosphorene as an anode material for high-performance lithium-ion batteries (LIBs), we carried out density-functional-theory calculations and studied the lithium adsorption energy landscape, the lithium diffusion mobility, the lithium intercalation, and the lithium capacity of phosphorene. We also carried out, for the very first time, experimental measurement of the lithium capacity of phosphorene...
January 12, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28076957/collapse-precedes-folding-in-denaturant-dependent-assembly-of-ubiquitin
#12
Govardhan Reddy, Dave Thirumalai
The folding of small protein Ubiquitin (Ub), which plays an indispensable role in targeting proteins for degradation and DNA damage response is complex. A number of experiments on Ub folding have reached differing conclusions regarding the relation between collapse and folding, and whether intermediates are populated. In order to resolve these vexing issues, we elucidate the denaturant-dependent thermodynamics and kinetics of Ub folding at low and neutral pH as a function of Guanidinium chloride and Urea using coarse-grained molecular simulations...
January 11, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28076825/polar-aromatic-periphery-increases-agonist-potency-of-spirocyclic-free-fatty-acid-receptor-gpr40-agonists-inspired-by-ly2881835
#13
Mikhail Krasavin, Alexey Lukin, Daria Bagnyukova, Nikolay Zhurilo, Aleksei Golovanov, Sergey Zozulya, Ihor Zahanich, Daniel Moore, Irina G Tikhonova
A series of spirocyclic compounds inspired by Eli Lilly's phase 1 antidiabetic FFA1 receptor agonist LY2881835 was designed to include polar aromatic periphery groups and explore a possibility of building additional contacts with the target near the agonist binding site. The frontrunner compound in the series (9i) was shown to be a potent (EC50 = 260 nM) FFA1 agonist with excellent aqueous (PBS) solubility and good Caco-2 permeability. The observed structure-activity relationships were rationalized by a docking study...
January 4, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28076351/ultra-fine-scale-spatially-integrated-mapping-of-habitat-and-occupancy-using-structure-from-motion
#14
Philip McDowall, Heather J Lynch
Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models at low cost...
2017: PloS One
https://www.readbyqxmd.com/read/28075012/rare-ecomorphological-convergence-on-a-complex-adaptive-landscape-body-size-and-diet-mediate-evolution-of-jaw-shape-in-squirrels-sciuridae
#15
Miriam Leah Zelditch, Ji Ye, Jonathan S Mitchell, Donald L Swiderski
Convergence is widely regarded as compelling evidence for adaptation, often being portrayed as evidence that phenotypic outcomes are predictable from ecology, overriding contingencies of history. However, repeated outcomes may be very rare unless adaptive landscapes are simple, structured by strong ecological and functional constraints. One such constraint may be a limitation on body size because performance often scales with size, allowing species to adapt to challenging functions by modifying only size. When size is constrained, species might adapt by changing shape; convergent shapes may therefore be common when size is limiting and functions are challenging...
January 11, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28074633/a-computational-interactome-for-prioritizing-genes-associated-with-complex-agronomic-traits-in-rice
#16
Shiwei Liu, Yihui Liu, Jiawei Zhao, Shitao Cai, Hongmei Qian, Kaijing Zuo, Lingxia Zhao, Lida Zhang
Rice is one of the most important staple foods for more than half of the world's population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet/) using machine-learning with structural relationship and functional information...
January 11, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28074270/tree-leaf-litter-composition-drives-temporal-variation-in-aquatic-beetle-colonization-and-assemblage-structure-in-lentic-systems
#17
Matthew R Pintar, William J Resetarits
Tree leaf litter inputs to freshwater systems are a major resource and primary drivers of ecosystem processes and structure. Spatial variation in tree species distributions and forest composition control litter inputs across landscapes, but inputs to individual lentic habitat patches are determined by adjacent plant communities. In small, ephemeral, fishless ponds, resource quality and abundance can be the most important factor affecting habitat selection preferences of colonizing animals. We used a landscape of experimental mesocosms to assess how natural populations of aquatic beetles respond over time to variation in tree leaf litter composition (pine or hardwood)...
January 10, 2017: Oecologia
https://www.readbyqxmd.com/read/28073919/trub1-is-the-predominant-pseudouridine-synthase-acting-on-mammalian-mrna-via-a-predictable-and-conserved-code
#18
Modi Safra, Ronit Nir, Daneyal Farouq, Schraga Schwartz
Following synthesis, RNA can be modified with over 100 chemically distinct modifications, which can potentially regulate RNA expression post-transcriptionally. Pseudouridine (Ψ) was recently established to be widespread and dynamically regulated on yeast mRNA, but less is known about Ψ presence, regulation and biogenesis in mammalian mRNA. Here, we sought to characterize the Ψ landscape on mammalian mRNA, to identify the main Ψ-synthases (PUSs) catalyzing Ψ formation, and to understand the factors governing their specificity towards selected targets...
January 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28073088/characterization-of-the-iberian-y-chromosome-haplogroup-r-df27-in-northern-spain
#19
Patricia Villaescusa, María José Illescas, Laura Valverde, Miriam Baeta, Carolina Nuñez, Begoña Martínez-Jarreta, Maria Teresa Zarrabeitia, Francesc Calafell, Marian M de Pancorbo
The European paternal lineage R-DF27 has been proposed as a haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28071906/single-conformation-spectroscopy-of-suberoylanilide-hydroxamic-acid-saha-a-molecule-bites-its-tail
#20
Di Zhang, Karl N Blodgett, Xiao Zhu, Timothy S Zwier
Suberoylanilide hydroxamic acid (C6H5NHCO(CH2)6CONHOH, SAHA) is a histone deacetylase inhibitor that causes growth arrest and differentiation of many tumor types and is an approved drug for the treatment of cancer. With a hydrogen-bonding amide group adjacent to its phenyl ring "head", and a hydroxamic acid group at the "tail" end of a C6 alkyl chain linker, SAHA possesses an interesting potential energy landscape to be probed by single-conformation methods. The alkyl chain's preference for extended structures is in competition with tail-to-head (T-H) or head-to-tail (H-T) hydrogen bonds between the amide and hydroxamic acid groups...
January 10, 2017: Journal of Physical Chemistry. A
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