Improved traceability of Shiga-toxin-producing <Emphasis Type="Italic">Escherichia coli</Emphasis> using CRISPRs for detection and typing

Among strains of Shiga-toxin-producing Escherichia coli (STEC), seven serogroups (O26, O45, O103, O111, O121, O145, and O157) are frequently associated with severe clinical illness in humans. The development of methods for their reliable detection from complex samples such as food has been challenging thus far, and is currently based on the PCR detection of the major virulence genes stx1, stx2, and eae, and O-serogroup-specific genes. However, this approach lacks resolution. Moreover, new STEC serotypes are continuously emerging worldwide. For example, in May 2011, strains belonging to the hitherto rarely detected STEC serotype O104:H4 were identified as causative agents of one of the world’s largest outbreak of disease with a high incidence of hemorrhagic colitis and hemolytic uremic syndrome in the infected patients. Discriminant typing of pathogens is crucial for epidemiological surveillance and investigations of outbreaks, and especially for tracking and tracing in case of accidental and deliberate contamination of food and water samples. Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of short, highly conserved DNA repeats separated by unique sequences of similar length. This distinctive sequence signature of CRISPRs can be used for strain typing in several bacterial species including STEC. This review discusses how CRISPRs have recently been used for STEC identification and typing.     

Depth-dependence and monthly variability of charophyte biomass production: consequences for the precipitation of calcium carbonate in a shallow <Emphasis Type="Italic">Chara</Emphasis>-lake

The month-to-month variability of biomass and CaCO₃ precipitation by dense charophyte beds was studied in a shallow Chara-lake at two depths, 1 and 3 m. Charophyte dry weights (d.w.), the percentage contribution of calcium carbonate to the dry weight and the precipitation of CaCO₃ per 1 m² were analysed from May to October 2011. Physical-chemical parameters of water were also measured for the same sample locations. The mean dry weight and calcium carbonate precipitation were significantly higher at 1 m than at 3 m. The highest measured charophyte dry weight (exceeding 2000 g m^?2) was noted at 1 m depth in September, and the highest CaCO₃ content in the d.w. (exceeding 80 % of d.w.) was observed at 3 m depth in August. The highest CaCO₃ precipitation per 1 m² exceeded 1695 g at 1 m depth in August. Significant differences in photosynthetically active radiation (PAR) were found between 1 and 3 m depths; there were no significant differences between depths for other water properties. At both sampling depths, there were distinct correlations between the d.w., CaCO₃ content and precipitation and water properties. In addition to PAR, the water temperature and magnesium and calcium ion concentrations were among the most significant determinants of CaCO₃ content and d.w. The results show that light availability seems to be the major factor in determining charophyte biomass in a typical, undisturbed Chara-lake. The study results are discussed in light of the role of charophyte vegetation in whole ecosystem functioning, with a particular focus on sedimentary processes and the biogeochemical cycle within the littoral zone.     

Increasing CACNA1C expression in placenta containing high Cd level: an implication of Cd toxicity

Cadmium (Cd) has known to produce many adverse effects on organs including placenta. Many essential transporters are involved in Cd transport pathways such as DMT-1, ZIP as well as L-VDCC. Fourteen pregnant women participated and were divided into two groups: high and low Cd-exposed (H-Cd, L-Cd) groups on the basis of their residential areas, Cd concentrations in the blood (B-Cd), urine (U-Cd), and placenta (P-Cd). The results showed that the B-Cd and U-Cd were significantly increased in H-Cd group (p < 0.05). Interestingly, the P-Cd in H-Cd group was elevated (p < 0.05) and positively related to their B-Cd and U-Cd values (p < 0.05). However, the mean cord blood Cd (C-Cd) concentration in H-Cd group was not significantly increased about 2.5-fold when comparing to L-Cd group. To determine the Cd accumulation in placental tissues, metallothionein-1A (MT-1A) and metallothionein-2A (MT-2A) expressions were used as biomarkers. The results revealed that mean MT-1A and MT-2A mRNAs and MT-1/2 proteins were up-regulated in H-Cd group (p < 0.05). In addition, the Ca channel alpha 1C (CACNA1C) mRNA and protein expressions were noticeably elevated in H-Cd group (p < 0.05). From these findings, we suggested that CACNA1C might be implicated in Cd transport in human placenta.     

Energy policy evaluation in practice: the case of production subsidies and DEN-B in the Netherlands

This paper describes how energy policy can be evaluated in practice. The goal is to make policy makers aware of how an evaluation can be based on scientific principles and to help economists appreciate how an evaluation can be performed if strong empirical evidence is lacking. We have built a basic evaluation framework and have applied this to a selection of Dutch energy policy instruments, namely production subsidies and their complementary non-financial instrument, DEN-B. Our evaluation criterion was effectiveness, defined as the extent to which policy instruments contribute to achieving policy goals. The evaluation was based on existing ex post evaluations complemented by interviews and other available data. We conclude that production subsidies and DEN-B were (partly) effective. Furthermore, the Dutch government increased effectiveness by reconsidering the design of production subsidies. We also formulate lessons for future policy evaluations and energy markets policies.     

A review of vulnerability indicators for deltaic social–ecological systems

The sustainability of deltas worldwide is under threat due to the consequences of global environmental change (including climate change) and human interventions in deltaic landscapes. Understanding these systems is becoming increasingly important to assess threats to and opportunities for long-term sustainable development. Here, we propose a simplified, yet inclusive social–ecological system (SES)-centered risk and vulnerability framework and a list of indicators proven to be useful in past delta assessments. In total, 236 indicators were identified through a structured review of peer-reviewed literature performed for three globally relevant deltas—the Mekong, the Ganges–Brahmaputra–Meghna and the Amazon. These are meant to serve as a preliminary “library” of potential indicators to be used for future vulnerability assessments. Based on the reviewed studies, we identified disparities in the availability of indicators to populate some of the vulnerability domains of the proposed framework, as comprehensive social–ecological assessments were seldom implemented in the past. Even in assessments explicitly aiming to capture both the social and the ecological system, there were many more indicators for social susceptibility and coping/adaptive capacities as compared to those relevant for characterizing ecosystem susceptibility or robustness. Moreover, there is a lack of multi-hazard approaches accounting for the specific vulnerability profile of sub-delta areas. We advocate for more comprehensive, truly social–ecological assessments which respond to multi-hazard settings and recognize within-delta differences in vulnerability and risk. Such assessments could make use of the proposed framework and list of indicators as a starting point and amend it with new indicators that would allow capturing the complexity as well as the multi-hazard exposure in a typical delta SES.     

The food-print of Paris: long-term reconstruction of the nitrogen flows imported into the city from its rural hinterland

Between the tenth and twentieth century the population of Paris city increased from a few thousand to near 10 million inhabitants. In response to the growing urban demand during this period, the agrarian systems of the surrounding rural areas tremendously increased their potential for commercial export of agricultural products, made possible by a surplus of agricultural production over local consumption by humans and livestock in these areas. Expressed in terms of nitrogen, the potential for export increased from about 60 kg N/km2/year of rural territory in the Middle Ages, to more than 5,000 kg N/km2/year from modern agriculture. As a result of the balance between urban population growth and rural productivity, the rural area required to supply Paris (i.e. its food-print) did not change substantially for several centuries, remaining at the size of the Seine watershed surrounding the city (around 60,000 km2). The theoretical estimate of the size of the supplying hinterland at the end of the eighteenth century is confirmed by the figures deduced from the analysis of the historical city toll data (octroi). During the second half of the twentieth century, the ‘food-print’ of Paris reduced in size, owing to an unprecedented increase in the potential for commercial export associated with modern agricultural systems based on chemical N fertilization. We argue that analysing the capacity of territories to satisfy the demand for nitrogen-containing food products of local or distant urban population and markets might provide new and useful insights when assessing world food resource allocation in the context of increasing population and urbanization.     

Binding of polycyclic aromatic hydrocarbons by humic acids formed during composting

Binding of two model polycyclic aromatic hydrocarbons (PAHs), phenanthrene and pyrene, by humic acids (HAs) isolated from an organic substrate at different stages of composting and a soil was investigated using a batch fluorescence quenching method and the modified Freundlich model. With respect to soil HA, the organic substrate HA fractions were characterized by larger binding affinities for both phenanthrene and pyrene. Further, isotherm deviation from linearity was larger for soil HA than for organic substrate HAs, indicating a larger heterogeneity of binding sites in the former. The composting process decreased the binding affinity and increased the heterogeneity of binding sites of HAs. The changes undergone by the HA fraction during composting may be expected to contribute to facilitate microbial accessibility to PAHs. The results obtained also suggest that bioremediation of PAH-contaminated soils with matured compost, rather than with fresh organic amendments, may result in faster and more effective cleanup.     

Lessons from Integrating Fishers of Arapaima in Small-Scale Fisheries Management at the Mamirauá Reserve,Amazon

Fishers and small-scale fisheries worldwide have been marginalized historically. Now it is clear that integrating fishers in management processes is key to resource conservation, but it is less clear how to do it. Here, based on a literature review and new information, we present and analyze a case in which the participation of fishers in the management process was crucial in recovering an overexploited small-scale fishery for the pirarucu (Arapaima spp.) in the Amazon Basin, Brazil. In 8 years of experimental management, from 1999 to 2006, the population of pirarucu increased 9-fold (from about 2200 to 20,650 individuals), harvest quotas increased 10-fold (from 120 to 1249 individuals), and fishers’ participation in the management process increased and they benefited from increased monetary returns. Additionally, the number of communities conducting the management scheme increased from 4 in 1999 to 108 in 2006, following the demands of fishers and regional government agencies. Based on our analysis, we suggest that the participation of fishers in the management of other small-scale fisheries in the world can be improved by focusing on (1) applying the knowledge and skills of fishers in resource monitoring and management, (2) bridging knowledge systems among all involved stakeholders, (3) collaborating with fishers that are interested in, and capable of conducting, resource conservation schemes, and (4) conducting management under conditions of uncertainty.     

Effects of Fireplace Use on Forest Vegetation and Amount of Woody Debris in Suburban Forests in Northwestern Switzerland

Urban forests are popular recreation areas in Europe. Several of these temperate broad-leaved forests also have a high conservation value due to sustainable management over many centuries. Recreational activities, particularly the use of fireplaces, can cause extensive damage to soil, ground vegetation, shrubs, and trees. Firewood collection depletes woody debris, leading to a loss of habitat for specialized organisms. We examined the effects of fireplace use on forest vegetation and the amount of woody debris by comparing disturbed and control plots in suburban forests in northwestern Switzerland. At frequently used fireplaces, we found reduced species densities in the ground vegetation and shrub layer and changes in plant species composition due to human trampling within an area of 150–200 m². Picnicking and grilling also reduced the height and changed the age structure of shrubs and young trees. The amount of woody debris was lower in disturbed plots than in control plots. Pieces of wood with a diameter of 0.6–7.6 cm were preferentially collected by fireplace users. The reduction in woody debris volume extended up to a distance of 16 m from the fire ring, covering an area of 800 m² at each picnic site. In order to preserve the ecological integrity of urban forests and to maintain their attractiveness as important recreation areas, we suggest depositing logging residues to be used as firewood and to restrict visitor movements near picnic sites.     

Review of Agri-Environment Indexes and Stewardship Payments

Agri-environment programs aim to secure environmental and social stewardship services through payments to farmers. A critical component of many agri-environment programs is an agri-environment index (AEI) used to quantify benefits and target investments. An AEI will typically comprise multiple indicators, which are weighted and combined using a utility function, to measure the benefit of investment options (e.g., projects, farms, regions). This article presents a review of AEIs with 11 case studies from agri-environment programs in the United States, Australia, and the United Kingdom. We identify a generic procedure used to define AEIs and explore the implications of alternative methodological approaches. We conclude that AEIs have become an extremely important policy instrument and make suggestions for their improvement.