Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide

Random Amino Acid Mutations and Protein Misfolding Lead to Shannon Limit in Sequence-Structure Communication

The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions) and in structure (structural defects) trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a) sensitive to random errors and (b) restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials

Habitat fragmentation and the future structure of tree assemblages in a fragmented Atlantic forest landscape

The biodiversity value of human-modified landscapes has become a central question in the tropical forest conservation biology, yet the degree to which plant populations and communities are restructured in response to environmental change remains unclear. Here, we address tree species density in a fragmented Atlantic forest landscape to test the hypothesis that tree assemblages inhabiting edge-dominated forest habitats approach typical conditions of early successional systems. Seedlings and adults from 141 tree species were sampled across 39 0.1-ha plots: 19 in small fragments (55 % of all tree species exhibiting higher densities in small fragments than in mature forest, particularly pioneers (>60 % of all species). Seedlings and adults of these proliferating species differed from species exhibiting population declines in terms of wood density and seed size, respectively. Additionally, pioneers were more abundant than shade-tolerant species, as were hardwood species in the case of seedlings. Tree species showing highest population increases consisted largely of long-lived, light-demanding canopy species bearing soft or hardwood and small-to-medium-sized seeds. Tree assemblage structure also differed in terms of forest habitats with small forest fragments supporting few rare species, whereas the most rapidly proliferating species were much more widespread and abundant in fragments. However, 60 % of all adult pioneer species recorded in small fragments were not recorded as seedlings in this habitat type, although both seedling and adult assemblages were dominated by pioneer species. Edge-dominated tree assemblages are likely to experience long-term shifts toward greater dominance of long-lived, pioneer canopy species

Model Structure of Human APOBEC3G

BACKGROUND: APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G) has antiretroviral activity associated with the hypermutation of viral DNA through cytosine deamination. APOBEC3G has two cytosine deaminase (CDA) domains; the catalytically inactive amino-terminal domain of APOBEC3G (N-CDA) carries the Vif interaction domain. There is no 3-D structure of APOBEC3G solved by X-ray or nuclear magnetic resonance. METHODOLOGY/PRINCIPAL FINDINGS: We predicted the structure of human APOBEC3G based on the crystal structure of APOBEC2. To assess the model structure, we evaluated 48 mutants of APOBEC3G N-CDA that identify novel variants altering ΔVif HIV-1 infectivity and packaging of APOBEC3G. Results indicated that the key residue D128 is exposed at the surface of the model, with a negative local electrostatic potential. Mutation D128K changes the sign of that local potential. In addition, two novel functionally relevant residues that result in defective APOBEC3G encapsidation, R122 and W127, cluster at the surface. CONCLUSIONS/SIGNIFICANCE: The structure model identifies a cluster of residues important for packaging of APOBEC3G into virions, and may serve to guide functional analysis of APOBEC3G

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

A novel survival model of cardioplegic arrest and cardiopulmonary bypass in rats: a methodology paper

<p>Abstract</p> <p>Background</p> <p>Given the growing population of cardiac surgery patients with impaired preoperative cardiac function and rapidly expanding surgical techniques, continued efforts to improve myocardial protection strategies are warranted. Prior research is mostly limited to either large animal models or <it>ex vivo </it>preparations. We developed a new <it>in vivo </it>survival model that combines administration of antegrade cardioplegia with endoaortic crossclamping during cardiopulmonary bypass (CPB) in the rat.</p> <p>Methods</p> <p>Sprague-Dawley rats were cannulated for CPB (n = 10). With ultrasound guidance, a 3.5 mm balloon angioplasty catheter was positioned via the right common carotid artery with its tip proximal to the aortic valve. To initiate cardioplegic arrest, the balloon was inflated and cardioplegia solution injected. After 30 min of cardioplegic arrest, the balloon was deflated, ventilation resumed, and rats were weaned from CPB and recovered. To rule out any evidence of cerebral ischemia due to right carotid artery ligation, animals were neurologically tested on postoperative day 14, and their brains histologically assessed.</p> <p>Results</p> <p>Thirty minutes of cardioplegic arrest was successfully established in all animals. Functional assessment revealed no neurologic deficits, and histology demonstrated no gross neuronal damage.</p> <p>Conclusion</p> <p>This novel small animal CPB model with cardioplegic arrest allows for both the study of myocardial ischemia-reperfusion injury as well as new cardioprotective strategies. Major advantages of this model include its overall feasibility and cost effectiveness. In future experiments long-term echocardiographic outcomes as well as enzymatic, genetic, and histologic characterization of myocardial injury can be assessed. In the field of myocardial protection, rodent models will be an important avenue of research.</p

Measuring walking within and outside the neighborhood in Chinese elders: reliability and validity

Background : Walking is a preferred, prevalent and recommended activity for aging populations and is influenced by the neighborhood built environment. To study this influence it is necessary to differentiate whether walking occurs within or outside of the neighborhood. The Neighborhood Physical Activity Questionnaire (NPAQ) collects information on setting-specific physical activity, including walking, inside and outside one\u27s neighborhood. While the NPAQ has shown to be a reliable measure in adults, its reliability in older adults is unknown. Additionally its validity and the influence of type of neighborhood on reliability and validity have yet to be explored. Methods : The NPAQ walking component was adapted for Chinese speaking elders (NWQ-CS). Ninety-six Chinese elders, stratified by social economic status and neighborhood walkability, wore an accelerometer and completed a log of walks for 7 days. Following the collection of valid data the NWQ-CS was interviewer-administered. Fourteen to 20 days (average of 17 days) later the NWQ-CS was re-administered. Test-retest reliability and validity of the NWQ-CS were assessed. Results : Reliability and validity estimates did not differ with type of neighborhood. NWQ-CS measures of walking showed moderate to excellent reliability. Reliability was generally higher for estimates of weekly frequency than minutes of walking. Total weekly minutes of walking were moderately related to all accelerometry measures. Moderate-to-strong associations were found between the NWQ-CS and log-of-walks variables. The NWQ-CS yielded statistically significantly lower mean values of total walking, weekly minutes of walking for transportation and weekly frequency of walking for transportation outside the neighborhood than the log-of-walks. Conclusions : The NWQ-CS showed measurement invariance across types of neighborhoods. It is a valid measure of walking for recreation and frequency of walking for transport. However, it may systematically underestimate the duration of walking for transport in samples that engage in high levels of this type of walking

Which Factors Determine Spatial Segregation in the South American Opossums (Didelphis aurita and D. albiventris)? An Ecological Niche Modelling and Geometric Morphometrics Approach

Didelphis albiventris and D. aurita are Neotropical marsupials that share a unique evolutionary history and both are largely distributed throughout South America, being primarily allopatric throughout their ranges. In the Araucaria moist forest of Southern Brazil these species are sympatric and they might potentially compete having similar ecology. For this reason, they are ideal biological models to address questions about ecological character displacement and how closely related species might share their geographic space. Little is known about how two morphologically similar species of marsupials may affect each other through competition, if by competitive exclusion and competitive release. We combined ecological niche modeling and geometric morphometrics to explore the possible effects of competition on their distributional ranges and skull morphology. Ecological niche modeling was used to predict their potential distribution and this method enabled us to identify a case of biotic exclusion where the habit generalist D. albiventris is excluded by the presence of the specialist D. aurita. The morphometric analyses show that a degree of shape discrimination occurs between the species, strengthened by allometric differences, which possibly allowed them to occupy marginally different feeding niches supplemented by behavioral shift in contact areas. Overlap in skull morphology is shown between sympatric and allopatric specimens and a significant, but weak, shift in shape occurs only in D. aurita in sympatric areas. This could be a residual evidence of a higher past competition between both species, when contact zones were possibly larger than today. Therefore, the specialist D. aurita acts a biotic barrier to D. albiventris when niche diversity is not available for coexistence. On the other hand, when there is niche diversification (e.g. habitat mosaic), both species are capable to coexist with a minimal competitive effect on the morphology of D. aurita