Averting biodiversity collapse in tropical forest protected areas

The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon(1-3). With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses(4-9). As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve `health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.

A drop of active matter

We study theoretically the hydrodynamics of a fluid drop containing oriented filaments endowed with active contractile or extensile stresses and placed on a solid surface. The active stresses alter qualitatively the wetting properties of the drop, leading to new spreading laws and novel static drop shapes. Candidate systems for testing our predictions include cytoskeletal extracts with motors and ATP, suspensions of bacteria or pulsatile cells, or fluids laden with artificial self-propelled colloids.

Unconventional metallicity and giant thermopower in a strongly interacting two-dimensional electron system

We present thermal and electrical transport measurements of low-density (10(14) m(-2)), mesoscopic two-dimensional electron systems (2DESs) in GaAs/AlGaAs heterostructures at sub-Kelvin temperatures. We find that even in the supposedly strongly localized regime, where the electrical resistivity of the system is two orders of magnitude greater than the quantum of resistance h/e(2), the thermopower decreases linearly with temperature indicating metallicity. Remarkably, the magnitude of the thermopower exceeds the predicted value in noninteracting metallic 2DESs at similar carrier densities by over two orders of magnitude. Our results indicate a new quantum state and possibly a novel class of itinerant quasiparticles in dilute 2DESs at low temperatures where the Coulomb interaction plays a pivotal role.

Ex Situ X-ray Diffraction, X-ray Absorption Near Edge Structure, Electron Spin Resonance, and Transmission Electron Microscopy Study of the Hydrothermal Crystallization of Vanadium Oxide Nanotubes: An Insight into the Mechanism of Formation

The nucleation and growth of vanadium oxide nanotubes (VOx-NT) have been followed by a combination of numerous ex situ techniques. long the hydrothermal process. Intermediate solid phases extracted at different reaction times have been characterized by powder X-ray diffraction, scanning and transmission electron microscopy, electron spin resonance, and V-K edge :X-ray absorption near-edge structure spectroscopy. The supernatant vanadate solutions extracted during the hydrothermal treatment have been studied by liquid V-51 NMR and flame. spectroscopy. For short durations of the hydrothermal synthesis, the initial V2O5-surfactant intercalate. is progressively transformed into VOx-NT whose crystallization starts to be detected after a hydrothermal treatment of 24 h. Upon heating from 24 h to 7 days, VOx-NT are obtained in larger amount and with an improved crystallinity. The detection of soluble amines and cyclic metavanadate V4O12](4-) in the supernatant solution along the hydrothermal process suggests that VOx-NT result from a dissolution precipitation mechanism. Metavanadate species V4O12](4-) could behave as molecular precursors in the polymerization reactions leading to VOx-NT.

Characterization and Space-Time Downscaling of the Inundation Extent over the Inner Niger Delta Using GIEMS and MODIS Data

The objective in this work is to develop downscaling methodologies to obtain a long time record of inundation extent at high spatial resolution based on the existing low spatial resolution results of the Global Inundation Extent from Multi-Satellites (GIEMS) dataset. In semiarid regions, high-spatial-resolution a priori information can be provided by visible and infrared observations from the Moderate Resolution Imaging Spectroradiometer (MODIS). The study concentrates on the Inner Niger Delta where MODIS-derived inundation extent has been estimated at a 500-m resolution. The space-time variability is first analyzed using a principal component analysis (PCA). This is particularly effective to understand the inundation variability, interpolate in time, or fill in missing values. Two innovative methods are developed (linear regression and matrix inversion) both based on the PCA representation. These GIEMS downscaling techniques have been calibrated using the 500-m MODIS data. The downscaled fields show the expected space-time behaviors from MODIS. A 20-yr dataset of the inundation extent at 500 m is derived from this analysis for the Inner Niger Delta. The methods are very general and may be applied to many basins and to other variables than inundation, provided enough a priori high-spatial-resolution information is available. The derived high-spatial-resolution dataset will be used in the framework of the Surface Water Ocean Topography (SWOT) mission to develop and test the instrument simulator as well as to select the calibration validation sites (with high space-time inundation variability). In addition, once SWOT observations are available, the downscaled methodology will be calibrated on them in order to downscale the GIEMS datasets and to extend the SWOT benefits back in time to 1993.

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Levels of Alpha-Toxin Correlate with Distinct Phenotypic Response Profiles of Blood Mononuclear Cells and with agr Background of Community-Associated Staphylococcus aureus Isolates

Epidemiological studies of Staphylococcus aureus have shown a relation between certain clones and the presence of specific virulence genes, but how this translates into virulence-associated functional responses is not fully elucidated. Here we addressed this issue by analyses of community-acquired S. aureus strains characterized with respect to antibiotic resistance, ST types, agr types, and virulence gene profiles. Supernatants containing exotoxins were prepared from overnight bacterial cultures, and tested in proliferation assays using human peripheral blood mononuclear cells (PBMC). The strains displayed stable phenotypic response profiles, defined by either a proliferative or cytotoxic response. Although, virtually all strains elicited superantigen-mediated proliferative responses, the strains with a cytotoxic profile induced proliferation only in cultures with the most diluted supernatants. This indicated that the superantigen-response was masked by a cytotoxic effect which was also confirmed by flow cytometry analysis. The cytotoxic supernatants contained significantly higher levels of alpha-toxin than did the proliferative supernatants. Addition of alpha-toxin to supernatants characterized as proliferative switched the response into cytotoxic profiles. In contrast, no effect of Panton Valentine Leukocidin, delta-toxin or phenol soluble modulin alpha-3 was noted in the proliferative assay. Furthermore, a significant association between agr type and phenotypic profile was found, where agrII and agrIII strains had predominantly a proliferative profile whereas agrI and IV strains had a predominantly cytotoxic profile. The differential response profiles associated with specific S. aureus strains with varying toxin production could possibly have an impact on disease manifestations, and as such may reflect specific pathotypes.

Multivariate juggling probabilities

We consider refined versions of Markov chains related to juggling introduced by Warrington. We further generalize the construction to juggling with arbitrary heights as well as infinitely many balls, which are expressed more succinctly in terms of Markov chains on integer partitions. In all cases, we give explicit product formulas for the stationary probabilities. The normalization factor in one case can be explicitly written as a homogeneous symmetric polynomial. We also refine and generalize enriched Markov chains on set partitions. Lastly, we prove that in one case, the stationary distribution is attained in bounded time.

An estimate of the number of tropical tree species

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between similar to 40,000 and similar to 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of similar to 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of similar to 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.

Modelling staphylococcal pneumonia in a human 3D lung tissue model system delineates toxin-mediated pathology

Staphylococcus aureus necrotizing pneumonia is recognized as a toxin-mediated disease, yet the tissue-destructive events remain elusive, partly as a result of lack of mechanistic studies in human lung tissue. In this study, a three-dimensional (3D) tissue model composed of human lung epithelial cells and fibroblasts was used to delineate the role of specific staphylococcal exotoxins in tissue pathology associated with severe pneumonia. To this end, the models were exposed to the mixture of exotoxins produced by S. aureus strains isolated from patients with varying severity of lung infection, namely necrotizing pneumonia or lung empyema, or to purified toxins. The necrotizing pneumonia strains secreted high levels of alpha-toxin and Panton-Valentine leukocidin (PVL), and triggered high cytotoxicity, inflammation, necrosis and loss of E-cadherin from the lung epithelium. In contrast, the lung empyema strain produced moderate levels of PVL, but negligible amounts of alpha-toxin, and triggered limited tissue damage. alpha-toxin had a direct damaging effect on the epithelium, as verified using toxin-deficient mutants and pure alpha-toxin. Moreover, PVL contributed to pathology through the lysis of neutrophils. A combination of alpha-toxin and PVL resulted in the most severe epithelial injury. In addition, toxin-induced release of pro-inflammatory mediators from lung tissue models resulted in enhanced neutrophil migration. Using a collection of 31 strains from patients with staphylococcal pneumonia revealed that strains producing high levels of alpha-toxin and PVL were cytotoxic and associated with fatal outcome. Also, the strains that produced the highest toxin levels induced significantly greater epithelial disruption. Of importance, toxin-mediated lung epithelium destruction could be inhibited by polyspecific intravenous immunoglobulin containing antibodies against alpha-toxin and PVL. This study introduces a novel model system for study of staphylococcal pneumonia in a human setting. The results reveal that the combination and levels of alpha-toxin and PVL correlate with tissue pathology and clinical outcome associated with pneumonia.