Differential DNA extraction of challenging simulated sexual assault samples: a Swiss collaborative study.

ABSTRACT: In sexual assault cases, autosomal DNA analysis of gynecological swabs is a challenge, as the presence of a large quantity of female material may prevent the detection of the male DNA. A solution to this problem is differential DNA extraction, but as there are different protocols, it was decided to test their efficiency on simulated casework samples. Four difficult samples were sent to the nine Swiss laboratories active in the forensic genetics. They used their routine protocols to separate the epithelial cell fraction, enriched with the non-sperm DNA, from the sperm fraction. DNA extracts were then sent to the organizing laboratory for analysis. Estimates of male to female DNA ratio without differential DNA extraction ranged from 1:38 to 1:339, depending on the semen used to prepare the samples. After differential DNA extraction, most of the ratios ranged from 1:12 to 9:1, allowing the detection of the male DNA. Compared to direct DNA extraction, cell separation resulted in losses of 94-98% of the male DNA. As expected, more male DNA was generally present in the sperm than in the epithelial cell fraction. However, for about 30% of the samples, the reverse trend was observed. The recovery of male and female DNA was highly variable depending on the laboratories. Experimental design similar to the one used in this study may help for local protocol testing and improvement.

Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism.

Abstract The plasmid pME6863, carrying the aiiA gene from the soil bacterium Bacillus sp. A24 that encodes a lactonase enzyme able to degrade N-acyl-homoserine lactones (AHLs), was introduced into the rhizosphere isolate Pseudomonas fluorescens P3. This strain is not an effective biological control agent against plant pathogens. The transformant P. fluorescens P3/pME6863 acquired the ability to degrade AHLs. In planta, P. fluorescens P3/pME6863 significantly reduced potato soft rot caused by Erwinia carotovora and crown gall of tomato caused by Agrobacterium tumefaciens to a similar level as Bacillus sp. A24. Little or no disease reduction was observed for the wild-type strain P3 carrying the vector plasmid without aiiA. Suppression of potato soft rot was observed even when the AHL-degrading P. fluorescens P3/pME6863 was applied to tubers 2 days after the pathogen, indicating that biocontrol was not only preventive but also curative. When antagonists were applied individually with the bacterial plant pathogens, biocontrol activity of the AHL degraders was greater than that observed with several Pseudomonas 2,4-diacetylphloroglucinol-producing strains and with Pseudomonas chlororaphis PCL1391, which relies on production of phenazine antibiotic for disease suppression. Phenazine production by this well characterized biological control strain P. chlororaphis PCL1391 is regulated by AHL-mediated quorum sensing. When P. chlororaphis PCL1391 was co-inoculated with P. fluorescens P3/pME6863 in a strain mixture, the AHL degrader interfered with the normally excellent ability of the antibiotic producer to suppress tomato vascular wilt caused by Fusarium oxysporum f. sp. lycopersici. Our results demonstrate AHL degradation as a novel biocontrol mechanism, but also demonstrate the potential for non-target interactions that can interfere with the biocontrol efficacy of other strains.

Soil and water conservation strategies and impact on sustainable livelihood in Cape Verde – Case study of Ribeira Seca watershed

Cape Verde, located off the coast of Senegal in western Africa, is a volcanic archipelago where a combination of human, climatic, geomorphologic and pedologic factors has led to extensive degradation of the soils. Like other Sahelian countries, Cape Verde has suffered the effects of desertification through the years, threatening the livelihood of the islands population and its fragile environment. In fact, the steep slopes in the ore agricultural islands, together with semi-arid and arid environments, characterized by an irregular and poorly distributed rainy season, with high intensity rainfall events, make dryland production a challenge. To survive in these fragile conditions, the stabilization of the farming systems and the maintenance of sustainable yields have become absolute priorities, making the islands an erosion control laboratory. Soil and water conservation strategies have been a centerpiece of the government0s agricultural policies for the last half century. Aiming to maintain the soil in place and the water inside the soil, the successive governments of Cape Verde have implemented a number of soil and water conservation techniques, the most common ones being terraces, half moons, live barriers, contour rock walls, contour furrows and microcatchments, check dams and reforestation with drought resistant species. The soil and water conservation techniques implemented have contributed to the improvement of the economical and environmental conditions of the treated landscape, making crop production possible, consequently, improving the livelihood of the people living on the islands. In this paper, we survey the existing soil and water conservation techniques, analyze their impact on the livelihood condition of the population through a thorough literature review and field monitoring using a semi-quantitative methodology and evaluate their effectiveness and impact on crop yield in the Ribeira Seca watershed. A brief discussion is given on the cost and effectiveness of the techniques to reduce soil erosion and to promote rainfall infiltration. Finally, we discuss the critical governance factors that lead to the successful implementation of such strategy in a country with scarce natural resources.

Monetary policy with signal extraction from the bond market

Monetary policy is conducted in an environment of uncertainty. This paper sets upa model where the central bank uses real-time data from the bond market togetherwith standard macroeconomic indicators to estimate the current state of theeconomy more efficiently, while taking into account that its own actions influencewhat it observes. The timeliness of bond market data allows for quicker responsesof monetary policy to disturbances compared to the case when the central bankhas to rely solely on collected aggregate data. The information content of theterm structure creates a link between the bond market and the macroeconomythat is novel to the literature. To quantify the importance of the bond market asa source of information, the model is estimated on data for the United Statesand Australia using Bayesian methods. The empirical exercise suggests that thereis some information in the US term structure that helps the Federal Reserve toidentify shocks to the economy on a timely basis. Australian bond prices seemto be less informative than their US counterparts, perhaps because Australia is arelatively small and open economy.

Audit risk and rent extraction: Evidence from a randomized evaluation in Brazil

We report results from a randomized policy experiment designed to test whether increasedaudit risk deters rent extraction in local public procurement and service delivery in Brazil. Ourestimates suggest that temporarily increasing annual audit risk by about 20 percentage pointsreduced the proportion of irregular local procurement processes by about 17 percentage points.This reduction was driven entirely by irregularities involving mismanagement or corruption. Incontrast, we find no evidence that increased audit risk affected the quality of publicly providedpreventive and primary health care services -measured based on user satisfaction surveys- orcompliance with national regulations of the conditional cash transfer program "Bolsa Família".

The Soil and Water Assessment Tool:Historical Development, Applications, and Future Research Directions, 2007

The Soil and Water Assessment Tool (SWAT) model is a continuation of nearly 30 years of modeling efforts conducted by the U.S. Department of Agriculture (USDA), Agricultural Research Service. SWAT has gained international acceptance as a robust interdisciplinary watershed modeling tool, as evidenced by international SWAT conferences, hundreds of SWAT-related papers presented at numerous scientific meetings, and dozens of articles published in peer-reviewed journals. The model has also been adopted as part of the U.S. Environmental Protection Agency’s BASINS (Better Assessment Science Integrating Point & Nonpoint Sources) software package and is being used by many U.S. federal and state agencies, including the USDA within the Conservation Effects Assessment Project. At present, over 250 peer-reviewed, published articles have been identified that report SWAT applications, reviews of SWAT components, or other research that includes SWAT. Many of these peer-reviewed articles are summarized here according to relevant application categories such as streamflow calibration and related hydrologic analyses, climate change impacts on hydrology, pollutant load assessments, comparisons with other models, and sensitivity analyses and calibration techniques. Strengths and weaknesses of the model are presented, and recommended research needs for SWAT are provided.

The role of soil in vegetated gravelly river braid plains: more than just a passive response?

This paper reviews the role of alluvial soils in vegetated gravelly river braid plains. When considering decadal time scales of river evolution, we argue that it becomes vital to consider soil development as an emergent property of the developing ecosystem. Soil processes have been relatively overlooked in accounts of the interactions between braided river processes and vegetation, although soils have been observed on vegetated fluvial landforms. We hypothesise that soil development plays a major role in the transition (speed and pathway) from a fresh sediment deposit to a vegetated soil-covered landform. Disturbance (erosion and/or deposition), vertical sediment structure (process history), vegetation succession, biological activity and water table fluctuation are seen as the main controls on early alluvial soil evolution. Erosion and deposition processes may not only act as soil disturbing agents, but also as suppliers of ecosystem resources, because of their role in delivering and changing access (e.g. through avulsion) to fluxes of water, fine sediments and organic matter. In turn, the associated initial ecosystem may influence further fluvial landform development, such as through the trapping of fine-grained sediments (e.g. sand) by the engineering action of vegetation and the deposit stabilisation by the developing above and belowground biomass. This may create a strong feedback between geomorphological processes, vegetation succession and soil evolution which we summarise in a conceptual model. We illustrate this model by an example from the Allondon River (CH) and identify the research questions that follow.

Judicial presence and rent extraction

We estimate the effect of state judiciary presence on rent extraction in Brazilian local governments.We measure rents as irregularities related to waste or corruption uncovered by auditors.Our unique dataset at the level of individual inspections allows us to separately examine extensiveand intensive margins of rent extraction. The identification strategy is based on an institutionalrule of state judiciary branches according to which prosecutors and judges tend to be assigned tothe most populous among contiguous counties forming a judiciary district. Our research designexploits this rule by comparing counties that are largest in their district to counties with identicalpopulation size from other districts in the same state, where they are not the most populous. IVestimates suggest that state judiciary presence reduces the share of inspections with irregularitiesrelated to waste or corruption by about 10 percent or 0.3 standard deviations. In contrast, we findno effect on the intensive margin of rent extraction. Finally, our estimates suggest that judicialpresence reduces rent extraction only for first-term mayors.

Identification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments

The oxalate-carbonate pathway (OCP) leads to a potential carbon sink in terrestrial environments. This process is linked to the activity of oxalotrophic bacteria. Although isolation and molecular characterizations are used to study oxalotrophic bacteria, these approaches do not give information on the active oxalotrophs present in soil undergoing the OCP. The aim of this study was to assess the diversity of active oxalotrophic bacteria in soil microcosms using the Bromodeoxyuridine (BrdU) DNA labeling technique. Soil was collected near an oxalogenic tree (Milicia excelsa). Different concentrations of calcium oxalate (0.5%, 1%, and 4% w/w) were added to the soil microcosms and compared with an untreated control. After 12days of incubation, a maximal pH of 7.7 was measured for microcosms with oxalate (initial pH 6.4). At this time point, a DGGE profile of the frc gene was performed from BrdU-labeled soil DNA and unlabeled soil DNA. Actinobacteria (Streptomyces- and Kribbella-like sequences), Gammaproteobacteria and Betaproteobacteria were found as the main active oxalotrophic bacterial groups. This study highlights the relevance of Actinobacteria as members of the active bacterial community and the identification of novel uncultured oxalotrophic groups (i.e. Kribbella) active in soils.

Soil and Water Conservation Quality Review, 2007

A newsletter produced by Iowa Department of Agriculture and Land Stewardship. The DSC is responsible for state leadership in the protection and management of soil, water and mineral resources, assisting soil and water conservation districts and private landowners to meet their agricultural and environmental protection needs.

Soil and Water Conservation Strategies in Cape Verde (Cabo Verde in Portuguese) and Their Impacts on Livelihoods - An Overview from the Ribeira Seca Watershed

Severe land degradation has strongly affected both people’s livelihood and the environment in Cape Verde (Cabo Verde in Portuguese), a natural resource poor country. Despite the enormous investment in soil and water conservation measures (SWC or SLM), which are visible throughout the landscape, and the recognition of their benefits, their biophysical and socioeconomic impacts have been poorly assessed and scientifically documented. This paper contributes to filling this gap, by bringing together insights from literature and policy review, field survey and participatory assessment in the Ribeira Seca Watershed through a concerted approach devised by the DESIRE project (the “Desire approach”). Specifically, we analyze government strategies towards building resilience against the harsh conditions, analyze the state of land degradation and its drivers, survey and map the existing SWC measures, and assess their effectiveness against land degradation, on crop yield and people’s livelihood. We infer that the relative success of Cape Verde in tackling desertification and rural poverty owes to an integrated governance strategy that comprises raising awareness, institutional framework development, financial resource allocation, capacity building, and active participation of rural communities. We recommend that specific, scientific-based monitoring and assessment studies be carried out on the biophysical and socioeconomic impact of SLM and that the “Desire approach” be scaled-up to other watersheds in the country.

Evaluating leaf litter beetle data sampled by Winkler extraction from Atlantic forest sites in southern Brazil

Evaluating leaf litter beetle data sampled by Winkler extraction from Atlantic forest sites in southern Brazil. To evaluate the reliability of data obtained by Winkler extraction in Atlantic forest sites in southern Brazil, we studied litter beetle assemblages in secondary forests (5 to 55 years after abandonment) and old-growth forests at two seasonally different points in time. For all regeneration stages, species density and abundance were lower in April compared to August; but, assemblage composition of the corresponding forest stages was similar in both months. We suggest that sampling of small litter inhabiting beetles at different points in time using the Winkler technique reveals identical ecological patterns, which are more likely to be influenced by sample incompleteness than by differences in their assemblage composition. A strong relationship between litter quantity and beetle occurrences indicates the importance of this variable for the temporal species density pattern. Additionally, the sampled beetle material was compared with beetle data obtained with pitfall traps in one old-growth forest. Over 60% of the focal species captured with pitfall traps were also sampled by Winkler extraction in different forest stages. Few beetles with a body size too large to be sampled by Winkler extraction were only sampled with pitfall traps. This indicates that the local litter beetle fauna is dominated by small species. Hence, being aware of the exclusion of large beetles and beetle species occurring during the wet season, the Winkler method reveals a reliable picture of the local leaf litter beetle community.

Dispersion of natural arsenic in the Malcantone watershed, Southern Switzerland: field evidence for repeated sorption-desorption and oxidation-reduction processes

In recent years, elevated arsenic concentrations have been found in waters and soils of many, countries, often resulting in a health threat for the local population. Switzerland is not an exception and this paper deals with the release and subsequent fate of arsenic in a 200-km(2) mountainous watershed, characterized by crystalline silicate rocks (gneisses, schists, amphibolites) that contain abundant As-bearing sulfide ore deposits, some of which have been mined for iron and gold in the past. Using analytical methods common for mineralogical, ground water and soil studies (XRD, XRF, XAS-XANES and -EXAFS, electron microprobe, extraction, ICP, AAS with hydride generator, ion chromatography), seven different field situations and related dispersion processes of natural arsenic have been studied: (1) release by rock weathering, (2) transport and deposition by water and ice; (3) release of As to the ground and surface water due to increasing pH; (4) accumulation in humic soil horizons; (5) remobilization by reduction in water-saturated soils and stagnant ground waters; (6) remobilization by using P-rich fertilizers or dung and (7) oxidation, precipitation and dilution in surface waters. Comparison of the results with experimental adsorption studies and speciation diagrams from the literature allows us to reconstruct and identify the typical behavior of arsenic in a natural environment under temperate climatic conditions. The main parameters identified are: (a) once liberated from the primary minerals, sorption processes on Fe-oxy-hydroxides dominate over Al-phases, such as Al-hydroxides or clay minerals and limit the As concentrations in the spring and well waters between 20 and 300 mug/l. (b) Precipitation as secondary minerals is limited to the weathering domain, where the As concentrations are still high and not yet too diluted by rain and soils waters. (c) Although neutral and alkaline pH conditions clearly increase the mobility of As, the main factor to mobilize As is a low redox potential (Eh close or below 0 mV), which favors the dissolution of the Fe-oxy-hydroxides on which the As is sorbed. (d) X-ray absorption spectroscopy (XAS) of As in water-logged humic forest soils indicates that the reduction to As III only occurs at the solid-water interface and that the solid contains As as As V (e) A and Bh horizons of humic cambisols can effectively capture As when As-rich waters flow through them. Complex spatial and temporal variation of the various parameters in a watershed results in repeated mobilization and immobilization of As, which continuously transports As from the upper to the lower part of a watershed and ultimately to the ocean. (C) 2004 Elsevier B.V. All rights reserved.

Uranium-enrichment in soils and plants in the vicinity of a pitchblende vein at La Creusaz-Les Marecottes (W of Martigny, Valais, Switzerland)

In the NE part of the Aiguilles Rouges Massif near Martigny, at the eastern contact of the Variscan Vallorcine granite to adjacent gneisses, a series of pitchblende (UO2)-veins occur. This paper determines the level of enrichment and mobility of uranium in soils situated in the vicinity of such a UO2-vein 7 km west of Martigny. Within an area of 50 x 100 m, situated on a relatively steep slope and characterized by a strong gramma-ray anomaly, six soil profiles including their plant cover and a reference soil profile outside the influence of the UO2-vein have been examined. The soil shows pH-values between 4 and 5 and is colluvial. The applied analytical methods for the metal contents include extraction methods, common for soil studies, and bulk analysis performed with X-ray fluorescence and ICP-MS. Uranium contents found in the uppermost 20 cm of the soil profiles vary from 2,500 ppm close to the vein to 15 ppm at the lowermost point of the study area. The reference soil has around 3 ppm uranium. At greater depth (20 to 40 cm) the U-content decreases to about half of the surface values, indicating a vertical transport of uranium within the soil profile. No systematic dependance of uranium-contents to grain size (amount of clay) nor to the amount of organic matter has been found. However, the good correlation between uranium and free iron oxide concentration suggests adsorption of uranium on iron oxy-hydroxides. The ashes of grass and mosses contain up to 90 ppm U, the blueberry and redwood only up to 3 ppm. Our observations suggest that at the surface the uranium is transported by downhill creep (solifluxion) of uranium-rich rock fragments. Liberated by oxidation of the uppermost fragments in a given soil column, the uranium migrates vertically until the conditions are favourable to adsorption onto Fe-oxy-hydroxides. However, as high U-contents of local surface water show, this adsorption does not lead to a significant retention of the uranium.