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.     

Assessing spatial variability of SO2 field as detected by an air quality network using Self-Organizing Maps,cluster, and Principal Component Analysis

In Bilbao (Spain), an air quality network measures sulphur dioxide levels at 4 locations. The objective of this paper is to develop a practical methodology to identify redundant sensors and evaluate a network's capability to correctly follow and represent SO₂ fields in Bilbao, in the frame of a continuous network optimization process.The methodology is developed and tested at this particular location, but it is general enough to be useable at other places as well, since it is not tied neither to the particular geographical characteristics of the place nor to the phenomenology of the air quality over the area.To assess the spatial variability of SO₂ measured at 4 locations in the area, three different techniques have been used: Self-Organizing Maps (SOMs), cluster analysis (CA) and Principal Component Analysis (PCA). The results show that the three techniques yield the same results, but the information obtained via PCA can be helpful not only for that purpose but also to throw light on the major mechanisms involved. This might be used in future network optimization stages. The main advantage of cluster analysis and SOMs is that they provide readily interpretable results. All the calculations have been carried out using the freely available software R.     

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.     

Epiphytische Flechten im Wandel von Immissionen und Klima ? Ergebnisse einer Vergleichskartierung 1989/2007 in Nordwestdeutschland

Zusammenfassung   Hintergrund, Ziel und Zweck Borkenbewohnende (epiphytische) Flechten reagieren sehr empfindlich auf verschiedene Umwelteinflüsse wie Stoffgehalte in der Atmosph?re und Temperaturen. Sie haben als Bioindikatoren für Luftverunreinigungen einen hohen Stellenwert bei Umweltuntersuchungen. Basierend auf einer 1989 durchgeführten Kartierung borkenbewohnender (epiphytischer) Flechten in einem landwirtschaftlich intensiv genutzten Raum Nordwestdeutschlands erfolgte 2007 eine Wiederholungsuntersuchung. Dabei galt es, m?gliche Ver?nderungen der Immissionssituation und des Klimas zu erkennen. Material und Methoden Die Studie basiert auf einer vergleichenden Kartierung epiphytischer Flechten von 355 Tr?gerb?umen an 45 Monitoringpunkten. Die angewandte Methode orientiert sich an der 1989 angewandten halb-quantitativen Erfassung. Ergebnisse Es stellten sich gravierende Ver?nderungen in der Vegetation rindenbewohnender Flechten heraus. Insgesamt war eine Erh?hung der Artenzahl an nahezu allen Monitoringpunkten festzustellen. Es wurde eine sehr starke Abnahme s?uretoleranter Arten und eine deutliche Zunahme basen- und n?hrstofffordernder Flechtenarten festgestellt. Darüber hinaus zeigte sich eine deutliche Zunahme w?rmeliebender Flechtenarten mit einem Verbreitungsschwerpunkt in Südeuropa bei gleichzeitigem Rückgang von Arten mit einem boreal-montanem Verbreitungsschwerpunkt. Diskussion Die festgestellte Entwicklung steht im Einklang mit überregionalen Beobachtungen. Sie wird im Wesentlichen auf eine gro?r?umig ver?nderte Immissionssituation, d. h. einer Abnahme der atmosph?rischen SO₂-Belastung und Zunahme der Ammoniakbelastung zurückgeführt. Ebenso treten deutliche Auswirkungen der Klimaerw?rmung hervor. Schlussfolgerungen Mit relativ geringem Untersuchungsaufwand lie?en sich Ver?nderungen bei den epiphytischen Flechten in den letzten 18 Jahren aufzeigen. Diese sind relevant für die Beurteilung regional und kleinr?umig ver?nderter Umweltbedingungen, die auch für andere Organismen und ?kosysteme l?ngerfristig von gro?er Bedeutung sind. Empfehlungen und Ausblick Unter Verwendung standardisierter Methoden vermitteln epiphytische Flechten ein differenziertes Bild der Luftbelastungssituation in Ballungsr?umen und in landwirtschaftlich genutzten Regionen. Darüber hinaus sind sie offensichtlich gute Indikatoren für Temperatur?nderungen ihrer Umgebung. Weiterer Forschungsbedarf besteht für die Verwendung epiphytischer Flechten zum Biomonitoring von Klimaver?nderungen.