Projects of the Environmental Genomics and Systems Biology Research Group
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ActinOmics: bioprospecting and genomics of actinobacteria isolated from the Marchica lagoon
The massive and excessive use of antibiotics in medicine has led to the emergence and spread of multi-resistant pathogens, rendering treatment with the usual antibiotics ineffective. Added to this phenomenon of antibiotic resistance is the emergence of new infectious diseases, often zoonotic, in humans. Hence the ...
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ToViPoRe: massive detection of tomato brown rugose fruit virus by high-throughput sequencing
Swiss agriculture is at risk with the emergence of a new viral disease epidemic caused by the Tomato Brown Rugose Fruit Virus (ToBRFV), also know as Jordan virus. This plant disease attacking tomato and peppers can lead to a complete yield loss thus generating significant economic losses for Swiss growers. ...
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EBDOmics – Comparative genomics of Enterobacter spp. causing Bulb Decay of Onions
Enterobacter bulb disease of onions (EBDO) is caused by members of the Enterobacter cloacae complex. This includes a diverse group of Enterobacter species that occur as clinical isolates and in the environment. Although EBDO has been known for several years, no systematic study has been conducted on their correct ...
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Turf Pathogen Screening System using Loop Mediated Isothermal Amplification
The objective is the development of a real-time pathogen screening system for a group of global relevant turf grass diseases using loop mediated isothermal amplification, LAMP technology. From a turf sample, DNA isolated and amplified using LAMP. Pathogen occurrence in the sample will be detected directly with the ...
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Fire Blight App for Central Asia
Based on the existing tick app in Switzerland, we will develop an app for smartphones that can inform local populations in Central Asia about fire blight, simultaneously allowing a citizen science approach for mapping the spread of this dangerous pome fruit disease. Utilizing the gathered data, a more precise ...
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Antibiotic resistances in Enterobacteria
Atypical Enterobacteria are frequently misidentified in clinical diagnostics due to unsettled taxonomy and noisy reference databases. Despite of their environmental origin, they regularly appear in clinical samples and increasingly display multi-drug resistances (MDRs) that are acquired during adaptation to ...
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Acceptance of an app for contact-tracing of SARS-CoV-2 in the Swiss population
The survey of 1929 adults in Switzerland in the period from 17 - 26 April 2020 suggests that a large majority of the population in any case or probably intends to a) install an app for contact-tracing of SARS-CoV-2, b) report infections in the app and c) comply with the app's request for contact reduction or ...
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Evaluation of benefits and risk of assisted migration in Fagus species
Risk and benefits of assisted introduction of drought-resistant Fagus species in Europe European beech (Fagus sylvatica) is one of the economically most important broadleaved trees in Europe. Its natural geographical diffusion area is however expected to experience a major shift as a consequence of global ...
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ChitinOMix – A multidisciplinary project to understand the effect of chitin soil amendment on the plant response, natural microbial community and the fate of human pathogenic bacteria
The consumption of fruit and vegetables are considered as important for a healthy and balanced diet and recognized as a significant source of vitamins and fibre. Authorities encourage the consumption of fresh plant produce, but food safety of fresh fruits and vegetables continues to be a major concern. By now it is ...
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Silent pathway awakening to discover novel antibacterial compounds from actinomycetes
There is a tremendous need for novel antibiotics due to the global resistance crisis. Actinomycetes are the most important sources of secondary metabolites. They provide an enormous potential to discover novel antibiotics. Actinobacteria remain an underexploited reservoir of interesting products, ...
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Fighting bites with bytes: Promoting public health with crowdsourced tick prevention
Ticks are on the rise and transmit several infectious diseases, leading to serious illness or even death. The smartphone App “Zecke–Tick Prevention helps people, to remember the tick bite location and to check it for potential Lyme disease symptoms. In an interdisciplinary approach, ZHAW-scientists want to find out ...
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CarbonATE - microbiological methanation
The European Union aims at a transition towards a renewable energy system by strengthening biomass exploitation. Within P2G concept bio-methanation of CO2 from biomass conversion systems with H2 enables an overall emission reduction. For this methanation process the amount of gases serving as potential CO2 ...
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LAMP Diagnostic in Ornamentals
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Preservation of Central Asian fruit tree forest ecosystems from bacterial pathogen Erwinia amylovora (fire blight)
Fire blight is a severe bacterial disease of apple and pear that can quickly destroy whole orchards. In the last few years it arrived also in Central Asia, where pomaceous fruit plants represent the dominant species in mid-altitude forests and constitute a critical foundation for the entire ecosystem. Fire blight is ...
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MinION2FixID: fast and reliable legume root nodule bacteria identification using nanopore sequencing technology
Rhizobia are bacterial symbionts associated with legumes that are of paramount importance for the fixation of atmospheric nitrogen in the soil. The success of this process (and ultimately the performance of the plant) depends on the type of root nodule bacteria, which should be adequate to each plant species. ...
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XhortOMICs: Diagnostic and epidemiological tools for the Xanthomonas hortorum species-level clade based on OMICs technologies
Despite its recent re-emergence and increased prevalence in many countries, the research on Xanthomonas hortorum species-level clade members has been very limited until now. It is thus important to have an increased knowledge thereof to be able to react to its increasing occurrence. Therefore, the overall aim of the ...
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Development of a fast and exact method for R. solanacearum detection in Swiss surface water samples
The broad-host range plant pathogen Ralstonia solanacearum is a treat for Swiss agriculture and therefore classified as quarantine organism. The current detection methods are, however, cumbersome. Testing surface water at strategic sites, especially downstream of locations where potential host plants are present, ...
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Effect of cryopreservation on genome mutation rate - examples of grapevine
Grapevine genetic resources are maintained in field collections being challenged by repeating biotic and abiotic stresses. Plant adapt to stress by increased mutation rates. Hence, long-term field collections may not be optimal to maintain original cultivars (and clones in grapevine). This project will quantify ...
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Off Flavour control in land-based salmon production
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Characterization of nitrogen dynamics in an aquaponic system
An aquaponic (AP) system combines a recirculating aquaculture system (production of aquatic animals, mostly fish) with a hydroponic system (production of plants) and recycles water and nutrients between these two main components. Nutrient-rich water from the aquaculture component is directed to the ...