The microbiology section comprises courses and seminars which are designed for students with different backgrounds in general biology, biochemistry and molecular biology and different levels of professional training.

 

 

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BIO-126 Diversity of Microorganisms	An introduction to microbiology for undergraduate students in the 2nd semester which emphasizes the following main topics: Prokaryotic innovations in the course of evolution Abilities of microorganisms to spread and differentiate The multitude of physiological abilities present in prokaryotes The role of microbes in geochemical cycling How microbes were discovered as agents of diseases and How microbes are domesticated for agriculture, health and food production. The self study course includes exercises which allow the student to test his/her knowledge of microbiological terms and the ability to use them properly. Test questions are offered via the internet. Results of exercises and virtual experiments are summarized by individual student or by groups and the reports are offered to the entire class as download documents.
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BIO-146 Biochemistry and Physiology of Prokaryotes	Emphasizes the multitude of biochemical processes found in prokaryotes and the proteogenomics of enzymes which regulate cellular physiology. The course focuses on the following themes. Nutrition of prokaryotes and biochemistry of major metabolic pathways Mechanisms of energy conversion in phototrophs and chemotrophs Enzymes and biochemical pathways for autotrophy Genome mining for metabolic abilities Energetics of chemolithotrophs Bio-Thermodynamics Membrane topology and proton translocation Electron transport and anaerobic respiration Fermentations Applications of microbial physiology to the degradation of xenobiotics Acetogenesis and Methanogenesis Interactions in trophic networks Regulation of metabolism and transcriptomics The course can be chosen as a free topic and is part of the biology curriculum. It addresses biology students in their 4th study semester. „Problem solving" is offered via the internet with examples taken from published scientific papers as well as with data from actual research experiments and using online data banks. The solutions are presented by students in short oral contributions and/or as writen contributions to the internet discussion groups.
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BIO 293 Evolution and Ecology of Microorganisms	The course emphasizes the evolution of microorganisms in an ecological and geochemical context. Students study in the field and in the laboratory the ecology of diverse microbial communities in their natural habitats and their interactions with the environment under variable and often extreme conditions. The emphasis lies on analyzing ecosystem processes with microbial involvement from the cellular level to community interactions to global scale geochemical processes. It addresses students in their 3rd study year. This is a „self-designed" course; the students choose the subjects they would like to discuss from a list of lecture topics which are offered via the internet and supported with information from original scientific papers and from internet sites. Microbial ecosystems & ecosystem determinants Adaptation of Prokaryotes to environmental conditions How energetics determines microbial lifestyles Microbial interactions Application of molecular tools to the study of prokaryotic communities Phylogeny, evolution and genomics of microorganisms Technically applied microbial ecology Deriving general concepts from microbial ecology and diversity The course also emphazises thermodynamic modelling as a means to understand metabolic interactions as well as mathematical simulations with self-designed computer models illustrating mass and energy fluxes in complex microbial food webs, reaction kinetics and the handling of large data sets originating from continuous measurement of ecological determinants. It is the aim of the course to arrive at generally valid ecological concepts which will guide the student to better understand the importance of the enormous variety of processes and the diversity of organisms that make up the global microbiota.
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Seminar Geomicrobiology	This is a seminar course for the discussion and evaluation of original scientific papers related to the Processes which led to the present day microbial diversity Evolutionary ecology or how the environment selects for particular microbial traits The prokaryotes' contribution to the evolution of life on earth and possibly on other planets Microbial involvement in geochemical cycling Microbe-mineral interactions Primary production and Earth systems processes The seminar addresses advanced students who want to learn how to access and search the world-wide scientific literature via the internet and to produce summaries and syntheses for presentations.
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Seminar Microbiology Research Colloquium	The colloquium brings advanced students and postgraduate investigators together in byweekly sessions to present and discuss their latest research results, to put these results into perspective by comparing them with published facts and to define, with the input of others, their next research steps.
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Special Microbiology Seminars	The seminars comprise contributions (lectures and discussions) by visiting speakers as well as practicing sessions for seminars held by collaborators at scientific meetings and other institutions.
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Course structure	The course was originally offered to undergraduate engineering students in the 2nd study semester. It is a lecture course based on a textbook and supplemented with weekly self-assessment exercises which are offered and corrected via the internet. With the change to the Bachelor / Master study plan, this course became part of the Biotechnology training for engineering students in the 4th semester.
Aim of the course	To familiarize engineers with a number of biological concepts which will allow them to make considerate use of the structures and processes invented by nature in technical designs and solutions. They learn about the basic principles of life which led to and which are necessary to maintain organismic diversity and which are essential if one is to make use of biological resources. And last but not least, during the course engineers are trained to evaluating risks of new techniques and of preventing damage to natural ecosystems.
Course sections	The course is divided into two sections; part I (Biology) deals with molecular, microbiological and biotechnological aspects; part II (Environment) is devoted to ecological issues.
Contents	In part I the student are made aware of major biological inventions which were invented predominantly in the microbial world, selected for and optimized in the course of evolution as well as about the richness of living organisms and metabolic and energetic life styles which resulted as a consequence of these inventions. We begin by examining the characteristics and the functional role of the biological macromolecules on which the structure, chemical functioning, propagation and adaptation of biological cells are based. These molecules form nanobiological structures which function in energy conversion, biosynthesis and perception as well as in information storage and processing. The global diversity of biological processes is manifest in the variety of mass and energy transformation patterns which are all based on a few basic thermodynamic and chemical principles.   Biotechnologists make use of the metabolic abilities of microorganisms and altered genotypes wherever it is technologically feasible and biologically possible. Process microbiologists aim to optimize and regulate the growth and the synthetic potential of microorganisms and environmental engineers exploit the abilities of microbes to degrade harmful chemicals which were introduced into the environment and which guarantee the proper functioning of global geochemical cycles in spite of man-made disturbances.   Environmental conditions which allow microorganisms to fulfill their natural geochemical functions, as well as those favoring the development of pathogens which can become health hazards, are study areas dealt with in ecological and epidemiological microbiology.   In part II we expand our view of biological processes to the higher organisms and illustrate their ecological role with a few case studies. The principles of evolution demonstrable in higher organisms emerge from inventions developed by prokaryotes. The process of evolution is the basis of the diversity of organisms and life styles found in various habitats. The complex relationships between organisms and their environment are discussed on four levels of organisation, mainly single organisms, populations, communities and ecosystems. Basic knowledge about the structure and functioning of ecosystems is not only important form a biological point of view, it is a mandatory prerequisite for sustainable exploitation of biological resources for food, basic raw materials and energy.   Biological processes are dynamic, and ecosystems go through phases of stability and instability. Knowledge about these phases is important if one intends to modify natural systems by technical measures. The course ends with a discussion about the most common biomes on earth, the ecological principles which govern them and the characteristics that make them extraordinary.
Final Report	The internet course was tested with more than 700 students over a 3 year period. Experiences are presented in the final report in a written form and as a power point presentation. Both documents as well as a pdf file containing the power point presentation can be downloaded.

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„Alpecole" is an interdisciplinary teaching approach on aspects of alpine ecology. The course will be developed between 2002 and 2004. It brings together a number of researchers from different Swiss Universities which contribute special topics to an overarching internet course on "Alpine Ecology and Environments". This internet course will prepare students for field courses where they will gain direct experience with alpine ecosystems.

Content	A variety of alpine ecosystems are considered and the course includes modules on a wide range of integrated topics. Where appropriate, local and global aspects will be brought together.
Interests	The course will be of interest to students studying biology, geography/geosciences, environmental sciences and related subjects at the graduate and postgraduate level, in Swiss and other European universities.
Contribution	The Microbial Ecology Group is contributing to the module "Life in aquatic ecosystems: Selection under extreme and extremely variable conditions" with the following contents Habitat definitions and dimensions Abiotic aquatic ecosystem determinants Life strategies under harsh environmental conditions Biogeochemical cycles in high mountain aquatic environments Uses and influences of man on high mountain aquatic ecosystems Workshop topics related to mountain aquatic ecology are Impact of land use changes on aquatic habitats Aquatic ecosystems as landscape elements Marketing and protection of aquatic resources in the Alps Water related economic development of mountain areas Vulnerability, destruction and restoration of mountain aquatic ecosystems Coping with hazardous natural events: technical and biological measures Response of biogeochemical and hydrological cycles to global environmental changes

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Simulation & Modelling

 

 

Simulation and Modelling

„SYMOLIFE", an on-line simulation and modelling course for life sciences and systems biology SYMOLIFE consists of internet-supported, interactive modelling and simulation learning modules for life science students. The unit is based on commercially available software (Simulink, Matlab, etc.). The course will teach participants to develop simple models based on proper mathematical equations for the description of physical, chemical and biological life processes, to define the boundary conditions under which they take place and solve the equations with the aid of the computer. During the first phase of the project, three modules (Physics, Biochemistry and Microbiology) were prepared. During the second phase we will develop a number of models for metabolic processes, epidemiology and physiology . Examples of exercises of the physics module include Stochastic processes Recognition of patterns Diffusion equations Neuronal networks Examples of exercises of the biochemistry module include Enzyme kinetics Inhibition of enzymes Mechanisms of substrate recognition and binding Relaxation kinetics Examples of exercises of the microbiology module include Growth patterns and processes Trophic interactions between prokaryotes Multicompartments in biogeochemical cycles Population dynamics in predator-prey interactions Diffusion in biofilms

Collaborators

Peter F. Meier and Stefan Schafroth (Physics) Antonio Baici and Thomas Hirt (Biochemistry) Kurt Hanselmann and Roman Kälin (Microbiology) Christoph Fuchs (MNF)

 

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