Search result: Catalogue data in Spring Semester 2021
|Elective Major Subject Areas|
|Elective Major: Microbiology and Immunology|
|Elective Compulsory Master Courses|
|701-1310-00L||Environmental Microbiology||W||3 credits||2V||M. H. Schroth, M. Lever|
|Abstract||Microorganisms catalyze a large number of reactions that are of great importance to terrestrial and aquatic environments. To improve our understanding of the dynamics of a specific environment, it is important to gain a better understanding of microbial structures and their functions under varying environmental conditions.|
|Objective||Students will learn basic concepts in microbial ecology. Qualitative and quantitative concepts will be presented to assess microbial communities and associated processes in terrestrial and aquatic environments. Microbial diversity in such ecosystems will be illustrated in discussions of selected habitats.|
|Content||Lectures will cover general concepts of environmental microbiology including (i) quantification of microbial processes, (ii) energy fluxes in microbial ecosystems, (iii) application of state-of-the-art microbiological and molecular tools, and (iv) use of isotope methods for identification of microbial structures and functions. |
Topics to illustrate the microbial diversity of terrestrial and aquatic ecosystems will include (i) interactions between microbes and mineral/metallic solid phases, (ii) microbial carbon and nutrient cycling, (iii) microbial processes involved in the turnover of greenhouse gases, (iv) biofilms and microbial mats, (v) bioremediation, (vi) microorganisms in extreme habitats, and (vii) microbial evolution and astrobiology.
|Lecture notes||available at time of lecture - will be distributed electronically as pdf's|
|Literature||Brock Biology of Microorganisms, Madigan M. et al., Pearson, 14th ed., 2015|
|551-1100-00L||Infectious Agents: From Molecular Biology to Disease|
Number of participants limited to 22.
Requires application until 2 weeks before the start of the semester; selected applicants will be notified one week before the first week of lectures.
(if you missed the deadline, please come to the first date to see, if there are any slots left)
|W||4 credits||2S||W.‑D. Hardt, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander, further lecturers|
|Abstract||Literature seminar for students at the masters level and PhD students. Introduction to the current research topics in infectious diseases; Introduction to key pathogens which are studied as model organisms in this field; Overview over key research groups in the field of infectious diseases in Zürich.|
|Objective||Working with the current research literature. Getting to know the key pathogens serving as model organisms and the research technologies currently used in infection biology.|
|Content||for each model pathogen (or key technology):|
1. introduction to the pathogen
2. Discussion of one current research paper.
The paper will be provided by the respective supervisor. He/she will give advice (if required) and guide the respective literature discussion.
|Lecture notes||Teachers will provide the research papers to be discussed.|
Students will prepare handouts for the rest of the group for their assigned seminar.
|Literature||Teachers will provide the research papers to be discussed.|
|Prerequisites / Notice||Restricted to max 22 students. Please sign up until two weeks before the beginning of the semester via e-mail to firstname.lastname@example.org and include the following information: 551-1100-00L; your name, your e-mail address, university/eth, students (specialization, semester), PhD students (research group, member of a PhD program? which program?). The 22 students admitted to this seminar will be selected and informed by e-mail in the week befor the beginning of the semester by W.-D. Hardt.|
The first seminar date will serve to form groups of students and assign a paper to each group.
|551-1118-00L||Cutting Edge Topics: Immunology and Infection Biology II||W||2 credits||2S||A. Oxenius, B. Becher, C. Halin Winter, N. C. Joller, M. Kopf, S. R. Leibundgut, C. Münz, F. Sallusto, R. Spörri, M. van den Broek, University lecturers|
|Abstract||Weekly seminar about cutting edge topics in immunology and infection biology. Internationally renowned experts present their current research followed by an open discussion.|
|Objective||Weekly seminar about cutting edge topics in immunology and infection biology. Internationally renowned experts present their current research followed by an open discussion.|
The aim of this course is to confront students with current research topics and with scientific presentation. The course offers the opportunity to gain in depth knowledge about diverse topics which are often only briefly touched in the concept courses and to engage in discussion with experts in the field.
|Content||Immunology and infection biology.|
The specific topics are variable and depend each semester on the list of invited experts.
|551-1104-00L||Selected Topics in Forest Mycology||W||2 credits||1V||I. L. Brunner, M. Peter Baltensweiler, D. H. Rigling|
|Abstract||Lifestyles and functions of symbiotic, saprobic and pathogenic fungi, communities of mycorrhizas and its functional aspects, evolution and phylogenetic aspects of plant-fungal interactions, inter- and intraspecific interactions of mycelia, role of fungi in nutrient mobilisation and weathering.|
|Objective||In-depth knowledge of the biology and ecology of fungi in the forest. Self-examination of the current literature.|
|Content||In-depth treatment of selected topics of fungi in the forest ecosystem: Lifestyles and functions of symbiotic, saprobic and pathogenic fungi, communities of mycorrhizas and its functional aspects, evolution and phylogenetic aspects of plant-fungal interactions, inter- and intraspecific interactions of mycelia, role of fungi in nutrient mobilisation and weathering.|
Basics will be presented in lectures. In addition, individual study of the learning matter with the help of current literature and presentations.
|Lecture notes||Documents for the course will be handed out.|
|Literature||Smith S.E. and Read D.J. 1997. Mycorrhizal Symbiosis. Academic Press, 2nd ed., pp. 605.|
|551-0216-00L||Field Course in Mycology |
Number of participants limited to 8.
|W||3 credits||3.5P||R. Berndt, M. A. Garcia Otalora|
|Abstract||This mycology class combines field excursions and a practical training in the lab. The participants will be introduced to the species diversity and morphology of basidio- and ascomycetes, learn how fungi are collected for scientific purposes and how they are determined by macroscopic and microscopic characters using specialist literature. This year’s course will focus on lichenized fungi.|
|Objective||Recognizing fungal species diversity and learning to determine basidio- and ascomycete species.|
Collecting, documenting and preparing herbarium specimens of fungi for scientific purposes.
Introduction to the light microscopy of fungi.
Learning how to use specialist mycology literature and understanding the technical terminology.
Knowledge of the relevant macroscopic und microscopic characters of fungi.
|Content||Introduction to the taxonomy of basidio- and ascomycetes. Field excursions to study fungi in their habitats. Study and determination of the collections in the lab. Micromorphology of basidio- and ascomycetes (incl. lichenized fungi). Introduction to major groups of plant-pathogenic fungi, especially rust fungi.|
|Lecture notes||Scripts will be handed out.|
|Literature||Technical literature will be provided in the lecture room.|
|Prerequisites / Notice||The course is restricted to eight persons who are requested to enroll by a written application to the lecturers.|
Requirements: The participants need to read in advance selected chapters from mycology textbooks (to be announced) to gather the basic mycology knowledge necessary for the course.
|551-1132-00L||Basic Virology||W||2 credits||1V||K. Tobler, C. Fraefel|
|Abstract||Introduction into the basics of virology, including characterization of viruses, virus-cell interactions, virus-host interactions, virus-host population interactions, basics of prevention and prophylaxis as well as diagnostics.|
|Objective||Introduction into the basics of virology.|
|Content||Basics in virology. Characterization of viruses, virus-cell interactions, virus-host interactions, virus-host population interactions, basics of prevention and prophylaxis as well as diagnostics.|
|Lecture notes||The lecture uses the lecturer's 'Allgemeine Virologie' as a basis.|
The lecturer's slides as well as selected primary literature will be provided 24-48 hrs prior to the lecture in pdf format.
|Literature||Flint et al., 2009. Principles of Virology, 3rd Edition. |
ASM Press, Washington, DC, USA.
Vol I. ISBN 978-1-55581-479-3
Vol II. ISBN 978-1-55581-480-9
|Prerequisites / Notice||Basic knowledge in molecular biology, cell biology, immunology.|
|551-0140-00L||Epigenetics||W||4 credits||2V||A. Wutz, U. Grossniklaus, R. Paro, R. Santoro|
|Abstract||Epigenetics studies the inheritance of traits that cannot be attributed to changes in the DNA sequence. The lecture will present an overview of different epigenetic phenomena and provide detailed insight into the underlying molecular mechanisms. The role of epigenetic processes in the development of cancer and other disorders will be discussed.|
|Objective||The aim of the course is to gain an understanding of epigenetic mechanisms and their impact on the development of organisms, regenerative processes or manifestation of disease.|
- historical overview, concepts and comparison Genetics vs. Epigenetics
- Biology of chromatin: structure and function, organization in the nucleus and the role of histone modifications in processes like transcription and replication
- DNA methylation as an epigenetic modification
- Inheritance of epigenetic modifications during cell division: cellular memory
- Stability and reversibility of epigenetic modifications: cellular plasticity and stem cells
- Genomic imprinting in plants and mammals
- X chromosome inactivation and dosis compensation
- position effects, paramutations and transvection
- RNA-induced gene silencing
- The role of epigenetic processes in cancer development or cell aging
|751-4904-00L||Microbial Pest Control||W||2 credits||2G||J. Enkerli, G. Grabenweger|
|Abstract||This lecture provides conceptual as well as biological and ecological background on microbial pest management. Methods and techniques applied to develop and monitor microbial control agents are elucidated.|
|Objective||To know the most important groups of insect pathogens and their characteristics. To become familiar with the basic steps necessary for the development of microbial control agents. To understand the techniques and methods used to monitor field applications and the procedures involved in registration of products for microbial pest management.|
|Content||Definitions and general terms used in microbial control are presented. Biological and ecological aspects of all arthropod-pathogenic groups (virus, bacteria, fungi and nematodes) as well as their advantages and disadvantages in relation to biocontrol are discussed. Particular emphasis is put on hypocrealean and entomophthoralean fungi. Examples are used to demonstrate how projects in microbial control can be set up, how pathogens can be applied and how efficacy, non-target effects, persistence and dissemination are monitored. Furthermore, the necessary steps for product development, commercial aspects and registration requirements are discussed.|
|Lecture notes||Lecture notes comprising the basic aspects will be provided.|
|Literature||Additional literature will be indicated in the lecture|
|551-1126-00L||Technologies in Molecular Microbiology||W||4 credits||2V||B. Nguyen, W.‑D. Hardt, further lecturers|
|Abstract||The lecture course provides an advanced understanding of modern techniques used in molecular microbiology. Current technologies and research directions in molecular microbiology including applied aspects will be illustrated with paper discussions. The format is a lecture course enriched by group activities.|
|Objective||The lecture course aims at providing principles of modern techniques used in molecular microbiology. Emphasis is on genetic, biochemical, cellular, and community analysis . Discussion of a set of commonly applied technologies will assist students in evaluating current research in molecular microbiology and choosing appropriate methods for their own demands.|
|Content||Important genetic, biochemical, biophysical, and community analysis methods will be presented that are used to gain a deeper understanding of the molecular principles and mechanisms underlying basic physiological processes in prokaryotes. Applied aspects of molecular microbiology and current research in this area will also be covered.|
List of topics:
- Analysis of genes, genomes and transcriptomes
- Analysis of proteins, proteomes and microbial systems
|Lecture notes||Updated handouts will be provided during the class.|
|Literature||Current literature references, relevant papers and handouts will be provided during the lectures.|
|Prerequisites / Notice||The following lecturers will contribute to the course:|
Dr. Alex Brachmann (ETH)
Prof. Hans-Martin Fischer (ETH)
Dr. Florian Freimoser (Agroscope)
Dr. Jonas Grossmann (FGCZ)
Annika Hausmann (ETH)
Dr. Bidong Nguyen (ETH)
Dr. Bernd Roschitzki (FGCZ)
Dr. Roman Spörri (ETH)
|227-0390-00L||Elements of Microscopy||W||4 credits||3G||M. Stampanoni, G. Csúcs, A. Sologubenko|
|Abstract||The lecture reviews the basics of microscopy by discussing wave propagation, diffraction phenomena and aberrations. It gives the basics of light microscopy, introducing fluorescence, wide-field, confocal and multiphoton imaging. It further covers 3D electron microscopy and 3D X-ray tomographic micro and nanoimaging.|
|Objective||Solid introduction to the basics of microscopy, either with visible light, electrons or X-rays.|
|Content||It would be impossible to imagine any scientific activities without the help of microscopy. Nowadays, scientists can count on very powerful instruments that allow investigating sample down to the atomic level.|
The lecture includes a general introduction to the principles of microscopy, from wave physics to image formation. It provides the physical and engineering basics to understand visible light, electron and X-ray microscopy.
During selected exercises in the lab, several sophisticated instrument will be explained and their capabilities demonstrated.
|701-1708-00L||Infectious Disease Dynamics||W||4 credits||2V||S. Bonhoeffer, R. D. Kouyos, R. R. Regös, T. Stadler|
|Abstract||This course introduces into current research on the population biology of infectious diseases. The course discusses the most important mathematical tools and their application to relevant diseases of human, natural or managed populations.|
|Objective||Attendees will learn about:|
* the impact of important infectious pathogens and their evolution on human, natural and managed populations
* the population biological impact of interventions such as treatment or vaccination
* the impact of population structure on disease transmission
Attendees will learn how:
* the emergence spread of infectious diseases is described mathematically
* the impact of interventions can be predicted and optimized with mathematical models
* population biological models are parameterized from empirical data
* genetic information can be used to infer the population biology of the infectious disease
The course will focus on how the formal methods ("how") can be used to derive biological insights about the host-pathogen system ("about").
|Content||After an introduction into the history of infectious diseases and epidemiology the course will discuss basic epidemiological models and the mathematical methods of their analysis. We will then discuss the population dynamical effects of intervention strategies such as vaccination and treatment. In the second part of the course we will introduce into more advanced topics such as the effect of spatial population structure, explicit contact structure, host heterogeneity, and stochasticity. In the final part of the course we will introduce basic concepts of phylogenetic analysis in the context of infectious diseases.|
|Lecture notes||Slides and script of the lecture will be available online.|
|Literature||The course is not based on any of the textbooks below, but they are excellent choices as accompanying material:|
* Keeling & Rohani, Modeling Infectious Diseases in Humans and Animals, Princeton Univ Press 2008
* Anderson & May, Infectious Diseases in Humans, Oxford Univ Press 1990
* Murray, Mathematical Biology, Springer 2002/3
* Nowak & May, Virus Dynamics, Oxford Univ Press 2000
* Holmes, The Evolution and Emergence of RNA Viruses, Oxford Univ Press 2009
|Prerequisites / Notice||Basic knowledge of population dynamics and population genetics as well as linear algebra and analysis will be an advantage.|
|751-4505-00L||Plant Pathology II||W||2 credits||2G||B. McDonald|
|Abstract||Plant Pathology II focuses on disease control in agroecosystems based on biological control, pesticide applications and breeding of resistant crop cultivars. The genetics of pathogen-plant interactions will be explored in detail as a basis for understanding the development of boom-and-bust cycles and methods that may be used to prevent the evolution of pathogen virulence and fungicide resistance.|
|Objective||An understanding of the how biological control, pesticides and plant breeding can be used to achieve sustainable disease control. An understanding of the genetic basis of pathogen-plant interactions and appropriate methods for using resistance to control diseases in agroecosystems.|
|Content||Plant Pathology II will focus on disease control in agroecosystems based on biological control, pesticide applications and breeding of resistant crop cultivars. The genetics of pathogen-plant interactions will be explored in detail as a basis for understanding the development of boom-and-bust cycles and methods that may be used to prevent the evolution of pathogen virulence and fungicide resistance.|
Lecture Topics and Tentative Schedule
Week 1 Biological control: biofumigation, disease declines, suppressive soils.
Week 2 Biological control: competitive exclusion, hyperparasitism.
Week 3 Chemical control: History of fungicides in Europe, fungicide properties, application methods.
Week 4 Fungicide categories and modes of action, antibiotics, fungicide development, fungicide safety and risk assessment (human health).
Week 5 Resistance to fungicides. Genetics of fungicide resistance, ABC transporters, risk assessment, fitness costs. FRAC risk assessment model vs. population genetic risk assessment model.
Week 6 Genetics of pathogen-plant interaction: genetics of pathogens, genetics of plant resistance, major gene and quantitative resistance, acquired resistance. Flor's GFG hypothesis and the quadratic check, the receptor and elicitor model of GFG, the guard model of GFG.
Week 7 Resistance gene structure and genome distribution, conservation of LRR motifs across eukaryotes. Genetic basis of quantitative resistance. QTLs and QRLs. Connections between MGR and QR. Durability of QR.
Week 8 Genetic resistance: Costs, benefits and risks.
Week 9 Non-host resistance. Types of NHR. NHR in Arabidopsis with powdery mildews. NHR in maize and rice. Avirulence genes and pathogen elicitors. PAMPs, effectors, type-III secretion systems, harpins in bacteria. Fungal avirulence genes.
Week 10 Easter holiday no class.
Week 11 Sechselauten holiday no class.
Week 12 Host-specific toxins. GFG for toxins and connection to apoptosis. Fitness costs of virulence alleles. Diversifying selection in NIP1.
Week 13 Boom and bust cycles for resistance genes and fungicides and coevolutionary processes. Pathogen genetic structure and evolutionary potential. Genetic structure of pathogen populations in agroecosystems, risk assessment for pathogen evolution and breeding strategies for durable resistance.
Week 14 Resistance gene and fungicide deployment strategies for agroecosystems.
Week 15 Genetic engineering approaches to achieve disease resistant crops.
|Lecture notes||Lecture notes will be available for purchase at the cost of reproduction.|
|Literature||Lecture notes will be available for purchase at the cost of reproduction.|
|Prerequisites / Notice||Plant Pathology I provides a good preparation for Plant Pathology II, but is not a prerequisite for this course.|
|551-1700-00L||Introduction to Flow Cytometry |
Number of participants limited to 24.
|W||2 credits||1V||J. Kisielow, L. Tortola, further lecturers|
|Abstract||The lecture provides an introduction to flow cytometry. We will cover the technology basics, experimental design, data acquisition and analysis of flow and mass cytometry. In addition, various research applications will be discussed. The format is a lecture course enriched by a visit to the ETH Flow Cytometry Core Facility and practical demonstration of the use of analysis and sorting instruments.|
|Objective||The goal of this course is to provide the basic knowledge of flow and mass cytometry required for planning and execution of cytometric experiments.|
|Content||The lecture course aims at teaching principles of flow cytometry. The emphasis is on theoretical principles (signal detection, fluorochromes, signal spill-over and compensation) as well as practical aspects of experimental design and performance (sample preparation, controls, data acquisition and analysis).|
List of topics:
- Principles of Flow Cytometry
- Signal processing
- Compensation and Controls
- Data analysis, gating and presentation
- Panel design
- Mass cytometry
- High-dimensional data analysis
- Practical demonstration (hardware and software)
Modern flow cytometric techniques for immunophenotyping, analysis of proliferation, cell cycle, apoptosis and cell signalling will be introduced.
|Lecture notes||Updated handouts will be provided during the class.|
|Literature||Current literature references on immunophenotyping, analysis of proliferation, cell cycle, apoptosis and cell signalling will be discussed during the lectures.|
|751-4805-00L||Recent Advances in Biocommunication |
Number of participants limited to 25.
|W||3 credits||2S||C. De Moraes|
|Abstract||Students will gain insight into the role of sensory cues and signals in mediating interactions within and between species. There will be a primary, but not exclusive, focus on chemical signaling in interactions among plants, insects and microbes. The course will focus on the discussion of current literature addressing key conceptual questions and state-of-the-art research techniques and methods.|
|Objective||Students will gain insight into the role of sensory cues and signals in mediating interactions within and between species. There will be a primary, but not exclusive, focus on chemical signaling in interactions among plants, insects and microbes. The course will focus on the discussion of current literature addressing key conceptual questions and state-of-the-art research techniques and methods. Students will engage in discussion and critical analyses of relevant papers and present their evaluations in a seminar setting.|
|551-1103-00L||Microbial Biochemistry||W||4 credits||2V||J. Vorholt-Zambelli, J. Piel|
|Abstract||The lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms. Emphasis is on processes that are specific to bacteria and archaea and that contribute to the widespread occurrence of prokaryotes. Applied aspects of microbial biochemistry will be pointed out as well as research fields of current scientific interest.|
|Objective||The lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms.|
|Content||Important biochemical processes specific to bacteria and archaea will be presented that contribute to the widespread occurrence of prokaryotes. Applied aspects of microbial biochemistry will be pointed out as well as research fields of current scientific interest. Emphasis is on concepts of energy generation and assimilation. |
List of topics:
Microbial Biochemistry and origin of life
Methanogenesis and methylotrophy
Anaerobic oxidation of methane
Complex: (Ligno-)Cellulose and in demand for bioenergy
Challenging: Aromatics and hydrocarbons
Living on a diet and the anaplerotic provocation
20 amino acids: the making of
Extending the genetic code
The 21st and 22nd amino acid
Some exotic biochemistry: nucleotides, cofactors
Ancient biochemistry? Iron-sulfur clusters, polymers
Secondary metabolites: playground of evolution
|Literature||Will be provided during the course.|
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