Transition from connected to fragmented vegetation across an environmental gradient: scaling laws in ecotone geometry

A change in the environmental conditions across space—for example, altitude or latitude—can cause significant changes in the density of a vegetation type and, consequently, in spatial connectivity. We use spatially explicit simulations to study the transition from connected to fragmented vegetation. A static (gradient percolation) model is compared to dynamic (gradient contact process) models. Connectivity is characterized from the perspective of various species that use this vegetation type for habitat and differ in dispersal or migration range, that is, “step length” across the landscape. The boundary of connected vegetation delineated by a particular step length is termed the “ hull edge.” We found that for every step length and for every gradient, the hull edge is a fractal with dimension 7/4. The result is the same for different spatial models, suggesting that there are universal laws in ecotone geometry. To demonstrate that the model is applicable to real data, a hull edge of fractal dimension 7/4 is shown on a satellite image of a piñon‐juniper woodland on a hillside. We propose to use the hull edge to define the boundary of a vegetation type unambiguously. This offers a new tool for detecting a shift of the boundary due to a climate change

Structural Origins of Misfolding Propensity in the Platelet Adhesive Von Willebrand Factor A1 Domain

AbstractThe von Willebrand factor (VWF) A1 and A3 domains are structurally isomorphic yet exhibit distinct mechanisms of unfolding. The A1 domain, responsible for platelet adhesion to VWF in hemostasis, unfolds through a molten globule intermediate in an apparent three-state mechanism, while A3 unfolds by a classical two-state mechanism. Inspection of the sequences or structures alone does not elucidate the source of this thermodynamic conundrum; however, the three-state character of the A1 domain suggests that it has more than one cooperative substructure yielding two separate unfolding transitions not present in A3. We investigate the extent to which structural elements contributing to intermediate conformations can be identified using a residue-specific implementation of the structure-energy-equivalence-of-domains algorithm (SEED), which parses proteins of known structure into their constituent thermodynamically cooperative components using protein-group-specific, transfer free energies. The structural elements computed to contribute to the non-two-state character coincide with regions where Von Willebrand disease mutations induce misfolded molten globule conformations of the A1 domain. This suggests a mechanism for the regulation of rheological platelet adhesion to A1 based on cooperative flexibility of the α2 and α3 helices flanking the platelet GPIbα receptor binding interface

A domain ontology for the non-coding RNA field

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology

The Non-Coding RNA Ontology : a comprehensive resource for the unification of non-coding RNA biology

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users

Turnover of grassland roots in mountain ecosystems revealed by their radiocarbon signature: role of temperature and management

Root turnover is an important carbon flux component in grassland ecosystems because it replenishes substantial parts of carbon lost from soil via heterotrophic respiration and leaching. Among the various methods to estimate root turnover, the root’s radiocarbon signature has rarely been applied to grassland soils previously, although the value of this approach is known from studies in forest soils. In this paper, we utilize the root’s radiocarbon signatures, at 25 plots, in mountain grasslands of the montane to alpine zone of Europe.We place the results in context of a global data base on root turnover and discuss driving factors. Root turnover rates were similar to those of a subsample of the global data, comprising a similar temperature range, but measured with different approaches, indicating that the radiocarbon method gives reliable, plausible and comparable results. Root turnover rates (0.06–1.0 y-1) scaled significantly and exponentially with mean annual temperatures. Root turnover rates indicated no trend with soil depth. The temperature sensitivity was significantly higher in mountain grassland, compared to the global data set, suggesting additional factors influencing root turnover. Information on management intensity from the 25 plots reveals that root turnover may be accelerated under intensive and moderate management compared to low intensity or semi-natural conditions. Because management intensity, in the studied ecosystems, co-varied with temperature, estimates on root turnover, based on mean annual temperature alone, may be biased. A greater recognition of management as a driver for root dynamics is warranted when effects of climatic change on belowground carbon dynamics are studied in mountain grasslands.KB received support from the Swiss National Science Foundation, project 200021-115891 (www.snf.ch). SM received support from the Swiss State Secretariat for Education and Research, project C07.0031 (www.sbfi.admin.ch). MTS received support from the Spanish Ministry of Science and Innovation, (project CAPAS, CGL2010-22378-C03- 01) (www.idi.mineco.gob.es)

Electronic Shell Structure and Relative Abundances of Cesium-Coated C60

URL:http://link.aps.org/doi/10.1103/PhysRevLett.77.1127 DOI:10.1103/PhysRevLett.77.1127The relative abundances of C60Cs(N), N≤500, determined from mass spectra measurements, are presented and explained in terms of the successive filling of the electronic shells by the cesium valence electrons. The motion of the Cs valence electrons, confined to a metal layer surrounding the C60 molecule, is described within the jellium model, with Cs spread into a uniform positive background. The electronic shell structure is calculated with the local approximation to density-functional theory and is shown to correspond to measured abundances. Strong Friedel oscillations in the electronic density are found and closed forms for them are given for jellium spheres both with and without the void.M. S. and S. S. would like to thank the Research Board of the University of Missouri for partial financial assistance

Age-related differences in human skin proteoglycans

Previous work has shown that versican, decorin and a catabolic fragment of decorin, termed decorunt, are the most abundant proteoglycans in human skin. Further analysis of versican indicates that four major core protein species are present in human skin at all ages examined from fetal to adult. Two of these are identified as the V0 and V1 isoforms, with the latter predominating. The other two species are catabolic fragments of V0 and V1, which have the amino acid sequence DPEAAE as their carboxyl terminus. Although the core proteins of human skin versican show no major age-related differences, the glycosaminoglycans (GAGs) of adult skin versican are smaller in size and show differences in their sulfation pattern relative to those in fetal skin versican. In contrast to human skin versican, human skin decorin shows minimal age-related differences in its sulfation pattern, although, like versican, the GAGs of adult skin decorin are smaller than those of fetal skin decorin. Analysis of the catabolic fragments of decorin from adult skin reveals the presence of other fragments in addition to decorunt, although the core proteins of these additional decorin catabolic fragments have not been identified. Thus, versican and decorin of human skin show age-related differences, versican primarily in the size and the sulfation pattern of its GAGs and decorin in the size of its GAGs. The catabolic fragments of versican are detected at all ages examined, but appear to be in lower abundance in adult skin compared with fetal skin. In contrast, the catabolic fragments of decorin are present in adult skin, but are virtually absent from fetal skin. Taken together, these data suggest that there are age-related differences in the catabolism of proteoglycans in human skin. These age-related differences in proteoglycan patterns and catabolism may play a role in the age-related changes in the physical properties and injury response of human ski

Plasma medicine: an introductory review

This introductory review on plasma health care is intended to provide the interested reader with a summary of the current status of this emerging field, its scope, and its broad interdisciplinary approach, ranging from plasma physics, chemistry and technology, to microbiology, biochemistry, biophysics, medicine and hygiene. Apart from the basic plasma processes and the restrictions and requirements set by international health standards, the review focuses on plasma interaction with prokaryotic cells (bacteria), eukaryotic cells (mammalian cells), cell membranes, DNA etc. In so doing, some of the unfamiliar terminology—an unavoidable by-product of interdisciplinary research—is covered and explained. Plasma health care may provide a fast and efficient new path for effective hospital (and other public buildings) hygiene— helping to prevent and contain diseases that are continuously gaining ground as resistance of pathogens to antibiotics grows. The delivery of medically active ‘substances’ at the molecular or ionic level is another exciting topic of research through effects on cell walls (permeabilization), cell excitation (paracrine action) and the introduction of reactive species into cell cytoplasm. Electric fields, charging of surfaces, current flows etc can also affect tissue in a controlled way. The field is young and hopes are high. It is fitting to cover the beginnings in New Journal of Physics, since it is the physics (and nonequilibrium chemistry) of room temperature atmospheric pressure plasmas that have made this development of plasma health care possible