A coupled vegetation/sediment transport model for dryland environments

Dryland regions are characterised by patchy vegetation, erodible surfaces and erosive aeolian processes. Understanding how these constituent factors interact and shape landscape evolution is critical for managing potential environmental and anthropogenic impacts in drylands. However, modelling wind erosion on partially vegetated surfaces is a complex problem that has remained challenging for researchers. We present the new, coupled cellular automaton Vegetation and Sediment TrAnsport model (ViSTA), which is designed to address fundamental questions about the development of arid and semi-arid landscapes in a spatially explicit way. The technical aspects of the ViSTA model are described, including a new method for directly imposing oblique wind and transport directions onto a cell-based domain. Verification tests for the model are reported, including stable state solutions, the impact of drought and fire stress, wake flow dynamics, temporal scaling issues and the impact of feedbacks between sediment movement and vegetation growth on landscape morphology. The model is then used to simulate an equilibrium nebkha dunefield, and the resultant bedforms are shown to have very similar size and spacing characteristics to nebkhas observed in the Skeleton Coast, Namibia. The ViSTA model is a versatile geomorphological tool that could be used to predict threshold-related transitions in a range of dryland ecogeomorphic systems

Modelling aeolian sand transport using a dynamic mass balancing approach

Knowledge of the changing rate of sediment flux in space and time is essential for quantifying surface erosion and deposition in desert landscapes. While many aeolian studies have relied on time-averaged parameters such as wind velocity (U) and wind shear velocity (u.) to determine sediment flux, there is increasing field evidence that high-frequency turbulence is an important driving force behind the entrainment and transport of sand. At this scale of analysis, inertia in the saltation system causes changes in sediment transport to lag behind de/accelerations in flow. However, saltation inertia has yet to be incorporated into a functional sand transport model that can be used for predictive purposes. In this study, we present a new transport model that dynamically balances the sand mass being transported in the wind flow. The ‘dynamic mass balance’ (DMB) model we present accounts for high- frequency variations in the horizontal (u) component of wind flow, as saltation is most strongly associated with the positive component of the wind. The performance of the DMB model is tested by fitting it to two field-derived (Namibia’s Skeleton Coast) datasets of wind velocity and sediment transport: (i) a 10-minute (10 Hz measurement resolution) dataset; (ii) a 2-hour (1 Hz measurement resolution) dataset. The DMB model is shown to outperform two existing models that rely on time-averaged wind velocity data (e.g. Radok, 1977; Dong et al., 2003), when predicting sand transport over the two experiments. For all measurement averaging intervals presented in this study (10 Hz–10 min), the DMB model predicted total saltation count to within at least 0.48%, whereas the Radok and Dong models over- or underestimated total count by up to 5.50% and 20.53% respectively. The DMB model also produced more realistic (less ‘peaky’) time series of sand flux than the other two models, and a more accurate distribution of sand flux data. The best predictions of total sand transport are achieved using our DMB model at a temporal resolution of 4 s in cases where the temporal scale of investigation is relatively short (on the order of minutes), and at a resolution of 1 min for longer wind and transport datasets (on the order of hours). The proposed new sand transport model could prove to be significant for integrating turbulence-scale transport processes into longer-term, macro-scale landscape modelling of drylands

Frequent Fires in Ancient Shrub Tundra: Implications of Paleorecords for Arctic Environmental Change

Understanding feedbacks between terrestrial and atmospheric systems is vital for predicting the consequences of global change, particularly in the rapidly changing Arctic. Fire is a key process in this context, but the consequences of altered fire regimes in tundra ecosystems are rarely considered, largely because tundra fires occur infrequently on the modern landscape. We present paleoecological data that indicate frequent tundra fires in northcentral Alaska between 14,000 and 10,000 years ago. Charcoal and pollen from lake sediments reveal that ancient birch-dominated shrub tundra burned as often as modern boreal forests in the region, every 144 years on average (+/− 90 s.d.; n = 44). Although paleoclimate interpretations and data from modern tundra fires suggest that increased burning was aided by low effective moisture, vegetation cover clearly played a critical role in facilitating the paleofires by creating an abundance of fine fuels. These records suggest that greater fire activity will likely accompany temperature-related increases in shrub-dominated tundra predicted for the 21st century and beyond. Increased tundra burning will have broad impacts on physical and biological systems as well as on land-atmosphere interactions in the Arctic, including the potential to release stored organic carbon to the atmosphere

How DNA Barcodes Complement Taxonomy and Explore Species Diversity: The Case Study of a Poorly Understood Marine Fauna

BACKGROUND: The species boundaries of some venerids are difficult to define based solely on morphological features due to their indistinct intra- and interspecific phenotypic variability. An unprecedented biodiversity crisis caused by human activities has emerged. Thus, to access the biological diversity and further the conservation of this taxonomically muddling bivalve group, a fast and simple approach that can efficiently examine species boundaries and highlight areas of unrecognized diversity is urgently needed. DNA barcoding has proved its effectiveness in high-volume species identification and discovery. In the present study, Chinese fauna was chosen to examine whether this molecular biomarker is sensitive enough for species delimitation, and how it complements taxonomy and explores species diversity. METHODOLOGY/PRINCIPAL FINDINGS: A total of 315 specimens from around 60 venerid species were included, qualifying the present study as the first major analysis of DNA barcoding for marine bivalves. Nearly all individuals identified to species level based on morphological traits possessed distinct barcode clusters, except for the specimens of one species pair. Among the 26 individuals that were not assigned binomial names a priori, twelve respectively nested within a species genealogy. The remaining individuals formed five monophyletic clusters that potentially represent species new to science or at least unreported in China. Five putative hidden species were also uncovered in traditional morphospecies. CONCLUSIONS/SIGNIFICANCE: The present study shows that DNA barcoding is effective in species delimitation and can aid taxonomists by indicating useful diagnostic morphological traits, informing needful revision, and flagging unseen species. Moreover, the BOLD system, which deposits barcodes, morphological, geographical and other data, has the potential as a convenient taxonomic platform

Comparison of dissolved and particulate arsenic distributions in shallow aquifers of Chakdaha, India, and Araihazar, Bangladesh

International audienceBackground The origin of the spatial variability of dissolved As concentrations in shallow aquifers of the Bengal Basin remains poorly understood. To address this, we compare here transects of simultaneously-collected groundwater and aquifer solids perpendicular to the banks of the Hooghly River in Chakdaha, India, and the Old Brahmaputra River in Araihazar, Bangladesh. Results Variations in surface geomorphology mapped by electromagnetic conductivity indicate that permeable sandy soils are associated with underlying aquifers that are moderately reducing to a depth of 10–30 m, as indicated by acid-leachable Fe(II)/Fe ratios 5 mg L-1. More reducing aquifers are typically capped with finer-grained soils. The patterns suggest that vertical recharge through permeable soils is associated with a flux of oxidants on the banks of the Hooghly River and, further inland, in both Chakdaha and Araihazar. Moderately reducing conditions maintained by local recharge are generally associated with low As concentrations in Araihazar, but not systematically so in Chakdaha. Unlike Araihazar, there is also little correspondence in Chakdaha between dissolved As concentrations in groundwater and the P-extractable As content of aquifer particles, averaging 191 ± 122 ug As/L, 1.1 ± 1.5 mg As kg-1 (n = 43) and 108 ± 31 ug As/L, 3.1 ± 6.5 mg As kg-1 (n = 60), respectively. We tentatively attribute these differences to a combination of younger floodplain sediments, and therefore possibly more than one mechanism of As release, as well as less reducing conditions in Chakdaha compared to Araihazar. Conclusion Systematic dating of groundwater and sediment, combined with detailed mapping of the composition of aquifer solids and groundwater, will be needed to identify the various mechanisms underlying the complex distribution of As in aquifers of the Bengal Basin

Future perspectives in melanoma research. Meeting report from the "Melanoma Research: a bridge Naples-USA. Naples, December 6th-7 th2010"

Progress in understanding the molecular basis of melanoma has made possible the identification of molecular targets with important implications in clinical practice. In fact, new therapeutic approaches are emerging from basic science and it will be important to implement their rapid translation into clinical practice by active clinical investigation

Arsenic in drinking water and cerebrovascular disease, diabetes mellitus, and kidney disease in Michigan: a standardized mortality ratio analysis

BACKGROUND: Exposure to arsenic concentrations in drinking water in excess of 300 μg/L is associated with diseases of the circulatory and respiratory system, several types of cancer, and diabetes; however, little is known about the health consequences of exposure to low-to-moderate levels of arsenic (10–100 μg/L). METHODS: A standardized mortality ratio (SMR) analysis was conducted in a contiguous six county study area of southeastern Michigan to investigate the relationship between moderate arsenic levels and twenty-three selected disease outcomes. Disease outcomes included several types of cancer, diseases of the circulatory and respiratory system, diabetes mellitus, and kidney and liver diseases. Arsenic data were compiled from 9251 well water samples tested by the Michigan Department of Environmental Quality from 1983 through 2002. Michigan Resident Death Files data were amassed for 1979 through 1997 and sex-specific SMR analyses were conducted with indirect adjustment for age and race; 99% confidence intervals (CI) were reported. RESULTS: The six county study area had a population-weighted mean arsenic concentration of 11.00 μg/L and a population-weighted median of 7.58 μg/L. SMR analyses were conducted for the entire six county study area, for only Genesee County (the most populous and urban county), and for the five counties besides Genesee. Concordance of results across analyses is used to interpret the findings. Elevated mortality rates were observed for both males (M) and females (F) for all diseases of the circulatory system (M SMR, 1.11; CI, 1.09–1.13; F SMR, 1.15; CI, 1.13,-1.17), cerebrovascular diseases (M SMR, 1.19; CI, 1.14–1.25; F SMR, 1.19; CI, 1.15–1.23), diabetes mellitus (M SMR, 1.28; CI, 1.18–1.37; F SMR, 1.27; CI, 1.19–1.35), and kidney diseases (M SMR, 1.28; CI, 1.15–1.42; F SMR, 1.38; CI, 1.25–1.52). CONCLUSION: This is some of the first evidence to suggest that exposure to low-to-moderate levels of arsenic in drinking water may be associated with several of the leading causes of mortality, although further epidemiologic studies are required to confirm the results suggested by this ecologic SMR analysis

Defining the critical hurdles in cancer immunotherapy

Scientific discoveries that provide strong evidence of antitumor effects in preclinical models often encounter significant delays before being tested in patients with cancer. While some of these delays have a scientific basis, others do not. We need to do better. Innovative strategies need to move into early stage clinical trials as quickly as it is safe, and if successful, these therapies should efficiently obtain regulatory approval and widespread clinical application. In late 2009 and 2010 the Society for Immunotherapy of Cancer (SITC), convened an "Immunotherapy Summit" with representatives from immunotherapy organizations representing Europe, Japan, China and North America to discuss collaborations to improve development and delivery of cancer immunotherapy. One of the concepts raised by SITC and defined as critical by all parties was the need to identify hurdles that impede effective translation of cancer immunotherapy. With consensus on these hurdles, international working groups could be developed to make recommendations vetted by the participating organizations. These recommendations could then be considered by regulatory bodies, governmental and private funding agencies, pharmaceutical companies and academic institutions to facilitate changes necessary to accelerate clinical translation of novel immune-based cancer therapies. The critical hurdles identified by representatives of the collaborating organizations, now organized as the World Immunotherapy Council, are presented and discussed in this report. Some of the identified hurdles impede all investigators; others hinder investigators only in certain regions or institutions or are more relevant to specific types of immunotherapy or first-in-humans studies. Each of these hurdles can significantly delay clinical translation of promising advances in immunotherapy yet if overcome, have the potential to improve outcomes of patients with cancer

Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry

YesBackground. The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection. Methodology/Principal Findings. To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance. Conclusions. This is the most comprehensive description of the global T. pallidum proteome to date. These data provide valuable insights into in vivo T. pallidum protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.This work was supported by the grants from the Flanders Research Foundation, SOFI-B Grant to CRK, http://www.fwo.be/, a Public Health Service Grant from the National Institutes of Health to CEC, (grant # AI-051334), https://www.nih.gov/ and a grant from the Grant Agency of the Czech Republic to DS and MS (P302/12/0574, GP14-29596P), https:// gacr.cz/