Outbreaks of foodborne illness linked to consumptions of fresh, or partially processed, agricultural products are a growing concern in industrialized and developing countries. The incidence of human pathogens on fresh fruits and vegetables is often related to the use of recycled wastewaster in surface irrigation as well as high amounts of animal manure in agricultural management practice. Thereby the soil inhabiting fauna plays an important role in the transport and dissemination of microorganisms. The focus of the proposed project is on nematodes, well known vectors for bacteria and viruses in soil. The major goals are to: (1) survey human pathogens in soil and on/in free-living and plant parasitic nematodes in agriculture field sites irrigated with recycled wastewater or fertilized with fresh animal manure in Israel and the Palestinian Authority, (2) assess the function of nematodes as vectors in transmitting bacteria from microbial hot spots to plants, and (3) localize bacteria on and/or within the nematode and identify bacterial factors required for survival in the nematode host. Understanding the mechanisms involved in dissemination of human pathogens by nematodes will enhance the ability to develop practical means to minimize contamination of fresh produce and increase safety in food production.
Various species of pest insects cause substantial damage to agriculture every year, or transmit deadly diseases to animals and humans. A successful strategy to control pest insect populations is based on the Sterile Insect Technique (SIT), which uses the release of mass-reared, radiation sterilized male insects to cause infertile matings and thus reduce the pest population level. However, irradiation is not applicable to every insect species. Thus, new strategies based on genetic modifications of pest insects have been developed or are currently under investigation.The goal of the proposed research is to improve the development and ecological safety of genetically engineered (GE) insects created for enhanced biological control programs, including the SIT and new strategies based on conditional lethality. A major concern for GE insect release programs is transgene stability, and maintenance of their consistent expression. Transgene loss or intra-genomic movement could result in loss of strain attributes, and may ultimately lead to interspecies movement resulting in ecological risks. To address potential transgene instability, a new transposon vector that allows post-integration immobilization will be tested in the Mediterranean, Mexican and Oriental fruit fly tephritid pest species. In addition, the system will be established in the mosquito species Aedes and Anopheles - carriers of dengue and malaria.Random genomic insertion is also problematic for GE strain development due to genomic position effects that suppress transgene expression, and insertional mutations that negatively affect host fitness and viability. Diminished transgene expression could result in the unintended survival of conditional lethal individuals, or the inability to identify them. To target transgene vectors to defined genomic insertion sites having minimal negative effects on gene expression and host fitness, a recombinase-mediated cassette exchange (RMCE) strategy will be developed that. RMCE will also allow for stabilization of the target site, will be tested in tephritid and mosquito species, and will aid to the development of stabilized target-site strains for conditional lethal biocontrol. This will include a molecular and organismal evaluation of an RNAi-based lethality approach. Lethality based on an RNAi mechanism in the proposed insects would increase the species specificity and having multiple targets for lethality versus one target in existing systems. By seeking to improve transgene expressivity and stabilization of transposon-based vector systems, this proposal specifically addresses issues related to new GE insects by reducing their unintended spread after field release, and by limiting the possibilities for transgene introgression.
Cherry leaf roll virus (CLRV) is a plant pathogen of economic and ecologic importance. It is globally distributed in a wide range of forest, fruit, and ornamental trees and shrubs. In several areas of cherry and walnut production CLRV causes severe losses in yield and quality. With current reference to the rapid dissemination and strong symptom expression in Finnish birches and the Germany-wide distribution of CLRV in birches and elderberry, we continuously investigate and gradually reveal CLRV transmission pathways as by pollen, seeds or water. However, modes and interactions responsible for the wide intergeneric host transmission as well as for the exceptional CLRV epidemic in Fennoscandia still remain unknown. In this project systematic studies shall investigate biological vectors as a causal agent to finally derive control mechanisms and strategies to avoid new epidemics in different hosts and geographic regions. Detailed monitoring of the invertebrate fauna of birch stands/forests and elderberry plantations in Germany and Finland shall reveal potential vectors to subsequently study them in detail by approved virus detection methods and transmission experiments. Molecular analyses of the CLRV coat protein shall prove its role as a viral determinant for a virus/vector interaction. Consequently, this project essentially will contribute important answers on the CLRV epidemiology, and this will be a key element within the first network of research on plant viral pathogens in forest trees.
Although the use of genetically modified plants for bioremediation, or the in situ cleaning of contaminated sites, has been known for quite some time, little attention has so far been paid to the production of antibodies in plants and their ex vivo application in selective depletion. Therefore, highly affine and specific antibodies against algal toxins using microcystin as an example will be produced in plants at low cost within this research project. The basis is a monoclonal antibody (Mab 10E7, species: mouse) generated in a former research project. The sequence of the variable domains will be determined, optimized for plants and sub cloned into suitable plant transformation vectors, which already contain constant antibody sequences. In addition, a scFv fragment containing different tag sequences and fusion proteins will be constructed. Leaf-based (tobacco) as well as seed-based (barley) systems will be used.Affinity-purified plant-produced antibodies (plantibodies) will be characterized in detail for their binding properties using microtitre plate-ELISA and surface plasmon resonance (SPR). The monoclonal mouse antibody will be used as reference. To assure cost-efficiency for future applications, roughly purified fractions (sequential pH and temperature treatment followed by filtration) will be tested for the upscaling. Following immobilization of the plantibody fractions on suitable substrates, for instance membranes, porous polymer monoliths or in porous glasses, their application for depletion will be defined using model water samples spiked fortified with microcystins.
Ziel des Projekts ist die Entwicklung von speziellen Limiter-Techniken für Strömungs- und Transportprobleme. Im Mittelpunkt der geplanten Arbeiten stehen hochauflösende Finite-Elemente-Verfahren zur Simulation von Ozeanströmungen auf unstrukturierten Gittern. In erster Linie sollen die von den Antragstellern entwickelten und analysierten Ansätze an problemspezifische Anisotropien angepasst werden, die in geophysikalischen Anwendungen auftreten. Die neuen Limiter werden in der Lage sein, die horizontalen und vertikalen Komponenten separat zu beschränken, um eine übermäßige Verschmierung durch die numerische Diffusion zu verhindern. Darüber hinaus sollen die bisherigen Limiter-Konzepte auf Vektorfelder - insbesondere Geschwindigkeiten und diffuse Flüsse - erweitert werden. Um die Positivitätserhaltung im Rahmen eines vertikalen Wirbelviskositätsmodells zu garantieren, ist eine Sonderbehandlung für heterogene Diffusionskoeffizienten und nichtlineare Quellterme vorgesehen. Die anisotropen Flusskorrektur-Schemata und Ableitungslimiter sollen in die Software-Pakete UTBEST3D und FESOM integriert werden. Die erwartete Reduktion der unphysikalischen Vermischung soll durch detaillierte numerische Studien quantifiziert werden.
This proposal is a continuation of the project 'GeoKernels': Kernel-Based Methods for Geo- and Environmental Sciences (200021-113944/1). The projects deal with the fundamental developments in the field of intelligent geospatial data analysis and modelling using Machine Learning algorithms. The first phase of the GeoKernels project provided a general methodology for using the state-of-the-art models in machine learning (where kernel methods establish one of the main successful areas) for spatio-temporal data analysis and modelling. Real life data lie on some lower-dimensional manifolds in the original high-dimensional geo-feature space. For environmental data these natural low-dimensional geo-manifolds are induced by rivers, relief features, urban structures, hydro-geological formations, etc. During PhaseI in the GeoKernels methodology, semi-supervised learning was applied to the stated problems in an efficient and elegant manner. The continuation of the project (Phase2) is aimed at advancing the data-driven GeoKernels modelling methodology, bringing it closer to the need of real-life operational use, from one side, and developing new methods concerned with geomanifold modelling by feature extraction and interpretable predictions with multiple kernel learning. The new developments will provide more transparency to the data-driven methods and will bring more flexibility for modelling complex environmental processes. The methods are particularly targeted at applications in natural hazards assessments and forecasting, topo-climatic modelling and renewable resources evaluation. Due to the established collaboration, the results of this multidisciplinary project will improve spatial data collection and management process in different scientific fields, will develop new procedures of environmental pattern recognition and modelling approaches using recent achievements in machine learning. The main results will be presented at the international conferences and workshops and published in scientific journals and books. The results, including the software modules (Machine Learning Office) and online interactive case studies will be available at the website of the project for the research and educational purposes (www.geokernels.org).
The spread of highly pathogenic avian influenza (HPAI) is a global threat to all countries with a poultry industry, semi-commercial production and backyard poultry and has already caused enormous economic losses. Since 1997, H5N1 viruses which have infected humans have included Haemagglutinins from several clades and variable genotypes. Therefore, all HPAI H5N1 viruses must be considered a potential threat to public health. This increases the scope of viruses with pandemic potential and the importance of continued surveillance of H5N1 avian influenza outbreaks. WHO and the OIE are urging countries worldwide to initiate surveillance programmes tailored to an early detection of cases of HPAI. There is an international demand to reduce random sampling and redirect the scarce resources to a targeted sampling, which focuses on the high-risk population, which is even more true for developing countries e.g. in Africa, which are almost devoid of surveillance capacity. In these cases, risk-based surveillance, and aiming at the most probable source of disease to save scarce resources are even more justified. This project aims: 1) To develop a statistical risk based framework for the combined analysis of surveillance data on avian influenza virus originating from various sources. 2) To develop a model for the assessment and optimisation of the effectiveness of different surveillance strategies for avian influenza. 3) To develop models to assess the effectiveness of different control strategies to prevent infection and spread of HPAI in commercial poultry. The approach is based on the Swiss Tropical Institute's competence in Bayesian spatial risk analyses, transmission modelling of vector borne and zoonotic diseases and its international network in Africa and Asia. This project will focus on Switzerland but within the global context of transport, trade and wild bird migration. It will collaborate with all involved institutions in Switzerland dealing with domestic poultry and wild birds. Expected results and innovations are: 1. Risk maps and contributions to risk maps for LPAI and HPAI on wild and domestic birds in Switzerland. 2. Decision tree for AI risk based surveillance in Switzerland applicable also to low income countries. 3. Risk based surveillance map and sampling plan for AI in Switzerland. 4. Performance indicators of surveillance sensitivity and cost-effectiveness of surveillance of AI in Switzerland and 5. A transmission model of HPAI adapted to Switzerland capable to simulate different intervention strategies.
Untersuchung verschiedener Verfahren zur Optimierung der Rotte. Erfassung der Arthropodenfauna. Beziehungen der Tierwelt der Deponie zur Umgebung. Die Bedeutung der Insekten als Vektoren von Mikroorganismen.
Forest structure is altered by humans for long times (Bramanti et al. 2009). The long lasting modification of forests pursuant to human demands modified the living conditions for birds as well as for many other animals. This included changes in resource availability (e.g., food, foraging, nesting sites) and changes of interspecific interactions, e.g., parasitism and predation (Knoke et al. 2009; Ellis et al. 2012). Also species compositions and the survivability of populations and even species are affected. The loss of foraging sites and suitable places for reproduction, the limitation of mobility due to fragmented habitats and the disturbances by humans itself may lead to more stressed individuals and less optimal living conditions. In certain cases species are not able to deal with the modified requirements and their populations will shrink and even vanish. Depending on the intensity of management and the remaining forest structure, biodiversity is more or less endangered. Especially in systems of two or more strongly connected taxa changing conditions that affect at least one part may subsequently affect the other, too. One system of interspecific communities that recently attracted the attention of biologists includes birds, blood parasites (haemosporidians) and their transmitting vectors. For instance, avian malaria (Plasmodium relictum) represents the reason for extreme declines in the avifauna of Hawaii since the introduction of respective vectors (e.g. Culicidae) during the 20th century (van Riper et al. 1986, Woodworth et al. 2005). With the current knowledge of this topic we are not able to predict if such incidences could also occur in Germany. All in all, different management strategies and intensity of forest management may influence the network of birds, vectors and blood parasites and change biodiversity. To elucidate this ecological complex, and to understand the interactions of the triad of songbirds as vertebrate hosts, dipteran vectors and haemosporidians within changing local conditions, I intend to collect data on the three taxa in differently managed forest areas, the given forest structure and the climatic conditions. I will try to explain the role of abiotic factors on infection dynamics, in detail the role of forest management intensity. Data acquisition takes place at three spatially divided locations: inside the Biodiversity Exploratory Schwäbische Alb, at the Mooswald in Freiburg, and inside the Schwarzwald.
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