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Studies and continuing education in environmental genomics and system biology

The production of pyoverdines by ten different Pseudomonas strains (Picture: J. Meyer).
Laboratory analysis of a soil probe



The Environmental Genomics and Systems Biology Research Group is involved in the development of the following modules, both of which are part of the Minor Field Diagnostics and Analytics, but which can also be attended as stand-alone modules.

Biosynthesis and Analytics (BSA, 3rd semester module for the B.Sc. in Environmental Engineering)

Vitally important processes such as growth, energy generation, reproduction, pathogen defence etc. can only be explained in the context of the underlying biochemical building blocks and processes. A real understanding of the way that living processes operate and are controlled at the cellular and sub-cellular levels is only possible through a combination of biology, chemistry and physics. During theoretical lectures and lab-based practical courses, students will be introduced to the chemical mechanisms operating in organisms and shown how to investigate biochemical processes methodically by means of laboratory experiments.

Molecular biological analysis and application (MBAA, 4th semester module for the B.Sc. in Environmental Engineering)

Molecular biological diagnosis and analysis is increasingly used in the field and is therefore gaining practical significance in several areas of natural resource sciences. The aim of this module is to become acquainted with these methods and procedures as well as to use specific methods and to examine their practical significance and application. The module gives an overview of their application in nature conservation and environmental protection, as well as in agriculture and eco technologies. Methods of analysis and for appraisal of findings are acquired. The module is an emerging project and some changes may be made.

Semester theses

The following semester’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:

  • Victor Bühlmann (2018): Transport of bacteria through natural soil.
  • Philipp von Ow (2018): Biokontrolle mittels Mikroorganismen als Bekämpfungsmassnahme gegen pathogene Organismen in Aquaponik.
  • Severin Erb (2018): "The big fight" - Antibiotika-Resistenz im Gewässer.
  • Nora Vogel (2018): Gentiana sp. - Genetische und phänotypische Untersuchungen im Jurapark Aargau.
  • Mirjam Kurz (2018): Molecular analysis of the distribution of two ancestral populations of Erwinia amylovora in Europe using CRISPR data.
  • Alexia Roschi (2017): Molekularer Nachweis der Streptomycinresistenz im Feuerbranderreger Erwinia amylovora.
  • Mireia Marcé Escursell (PDF 210,6 KB) (2016): Differential fitness of Erwinia amylovora isolates carrying different variants of the rpsL gene leading to high level of streptomycin resistance.
  • Priska Stierli (2016): Vergleich und Charakterisierung von Genomsequenzen der neuen Spezies Erwinia gerundensis.
  • Nicola Rhyner (2016): Application of MALDI-TOF mass spectrometry profiling for inter- and intrapopulation discrimination of Orchidaceae.
  • Sarah Schuhmacher & Dominique Wildi (2015): Quantifizierung der mikrobiellen Populationen in der Rhizosphäre von Weizen.

Bachelor theses

The following bachelor’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:

  • Mirjam Kurz (2018): Evidence for hybridization between exotic Fagus orientalis and native Fagus sylvatica in a forest stand of Switzerland.
  • Dominik Rutz (2018): Assembly, annotation and comparative genomics of the genomes of Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T.
  • Daniela Lüthi (2017): Comparative genomics of Collimonas sp. CCOS 246 to related species.
  • Mathieu Robin (2015): Genetic evidence of damage caused by wild animals.
  • Yvonne Bollinger (2014) :Design of open space parks following the example of Zurich’s Vulkanplatz.
  • Joël Wieser (2014): Investigation into the habitat type of the native orchid Serapias vomeracea (ploughshare serapias).

Master theses

The following master’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:

  • Nicola Rhyner (2019): Using microsatellite markers to assess post-stocking survival and genetic structure of atlantic trout (Salmo trutta L.) in a pre-alpine water system. [Collaboration with Aquaculture Systems Research Group]
  • Andrea Bohny (2019): Microbial and chemical characterization of biofilms in an aquaponic system. [Collaboration with Ecological Engineering Research Group and ETH Zurich]
  • Moritz Kaufmann (2019): Evolution of multidrug resistance in pEL60 plasmids. [MS-LS ACLS]
  • Jonas Siegrist (2019): Genome mining of polyketide and nonribosomal peptide synthases in actinomycetes. [MS-LS ACLS, Collaboration with Martin Sievers (ICBT)]
  • Anuschka Neira (2019): Biodiversity of soil bacteria in greenhouses. [MSc ENR; Collaboration with Soil Ecology Research Group]
  • Nadine Antenen (2017): The impact of hydropower on microbial diversity and community structure in floodplains. [Collaboration with Ecohydrology Research Group]
  • Julia Eichmann (2016): Expression analyses of selected genes of Vitis vinifera during early infection stages of its major pathogens Plasmopara viticola and Botrytis cinerea.  [Collaboration with Viticulture Research Group]

Ph.D. theses

The following Ph.D. theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:

  • Michael Gétaz (2018): Genomic investigations of the strawberry quarantine bacteria pathogen Xanthomonas Fragaria for a better integrative pest management.
  • Michela Ruinelli (2017): Genomic investigations of members of the Pseudomonas syringae species complex associated with Prunus spp. and kiwifruit.

Continuing education

FLASH-SAMBA Applied Microbial Genomics course, Curitiba (Brasilien), 07.11-11.11.2016

This International Course is being offered at Pontifícia Universidade Católica do Paraná (PUCPR) in Curitiba in the context of a partnership between the Brazilian and the Swiss Governments, represented by PUCPR and ZHAW University respectively. The aim is to bring to the attendants (students and scientists) the necessary tools and skills to execute bacterial gene, MLST and genomics analysis using bioinformatics. You will learn the principles of gene and genome sequencing; how to use the most common gene and genomic analysis software and how to interpret those tons of data that will become more and more popular once the costs of genome sequencing will continue to drop.

News release on the ZHAW Webpage