Search result: Catalogue data in Spring Semester 2019

Biology Master Information
Elective Major Subject Areas
Elective Major: Microbiology and Immunology
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
701-1310-00LEnvironmental MicrobiologyW3 credits2VM. H. Schroth, M. Lever
AbstractMicroorganisms 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.
ObjectiveStudents 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.
ContentLectures 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 notesavailable at time of lecture - will be distributed electronically as pdf's
LiteratureBrock Biology of Microorganisms, Madigan M. et al., Pearson, 14th ed., 2015
551-1100-00LInfectious 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)
W4 credits2SW.‑D. Hardt, L. Eberl, U. F. Greber, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander
AbstractLiterature 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.
ObjectiveWorking with the current research literature. Getting to know the key pathogens serving as model organisms and the research technologies currently used in infection biology.
Contentfor 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 notesTeachers will provide the research papers to be discussed.
Students will prepare handouts for the rest of the group for their assigned seminar.
LiteratureTeachers will provide the research papers to be discussed.
Prerequisites / NoticeRestricted to max 22 students. Please sign up until two weeks before the beginning of the semester via e-mail to micro_secr@micro.biol.ethz.ch 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.
551-1118-00LCutting Edge Topics: Immunology and Infection Biology II Information W2 credits1SA. 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
AbstractWeekly seminar about cutting edge topics in immunology and infection biology. Internationally renowned experts present their current research followed by an open discussion.
ObjectiveWeekly 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.
ContentImmunology and infection biology.
The specific topics are variable and depend each semester on the list of invited experts.
551-1104-00LSelected Topics in Forest MycologyW2 credits1VI. L. Brunner, M. Peter Baltensweiler, D. H. Rigling
AbstractLifestyles 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.
ObjectiveIn-depth knowledge of the biology and ecology of fungi in the forest. Self-examination of the current literature.
ContentIn-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 notesDocuments for the course will be handed out.
LiteratureSmith S.E. and Read D.J. 1997. Mycorrhizal Symbiosis. Academic Press, 2nd ed., pp. 605.
551-0216-00LField Course in Mycology Restricted registration - show details
Number of participants limited to 8.
W3 credits3.5PA. Leuchtmann
AbstractField excursions with collecting of fungi, and study of collections in the course room. Main focus are small fungi (ascomycetes): you will receive insight into the diversity of fungi and an introduction to species identification. Furthermore, the ecology and function of fungi in selected habitats will be discussed, and selected examples of edible and poisonous mushrooms shown.
ObjectiveExtended knowledge in taxonomy and systematics of fungi, in particular Ascomycetes. Participants know about ecological functions of fungi as mutualists, saprobes or parasites of plants in various ecosystems.
ContentEinführung ins Reich der Pilze, Merkmale der Pilze und Überblick über deren systematische Gliederung. Exkursionen zum Sammeln von Ascomyceten in ausgewählten Lebensräumen. Kennenlernen von notwendigen Sammel- und Präparationstechniken, Einführung in die Ökologie und Funktion der Pilze, Untersuchung und Bestimmen von Pilzen mit optischen Hilfsmitteln im Kursraum, Einblick in Formenvielfalt ausgewählter Pilzgruppen (Ascomyecten), Beispiele von Gift- und Speisepilzen.
Lecture notesKursunterlagen werden abgegeben
LiteratureSpezialliteratur für die Bestimmung der Familien, Gattungen und Arten der mitteleuropäischen Mykoflora.
Prerequisites / NoticeDer Kurs ist auf maximal 8 Teilnehmende beschränkt. Schriftliche Anmeldung erforderlich. Das Kursgeld von Fr. 180.- muss von den Kursteilnehmern übernommen werden. Vor dem Kurs (Freitag 23. Aug. 2019) findet eine halbtägige Einführung in Zürich statt, deren Besuch ist obligatorisch.
551-1132-00LBasic Virology Information
Does not take place this semester.
W2 credits1V
AbstractIntroduction 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.
ObjectiveIntroduction into the basics of virology.
ContentBasics 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 notesThe 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.
LiteratureFlint 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 / NoticeBasic knowledge in molecular biology, cell biology, immunology.
551-0140-00LEpigeneticsW4 credits2VA. Wutz, U. Grossniklaus, R. Paro, R. Santoro
AbstractEpigenetics 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.
ObjectiveThe 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.
ContentTopics
- 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
751-4904-00LMicrobial Pest ControlW2 credits2GJ. Enkerli, G. Grabenweger, S. Kuske Pradal
AbstractThis 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.
ObjectiveTo 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.
ContentDefinitions 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 notesLecture notes comprising the basic aspects will be provided.
LiteratureAdditional literature will be indicated in the lecture
551-1126-00LTechnologies in Molecular MicrobiologyW4 credits2VH.‑M. Fischer, B. Christen, M. Christen, further lecturers
AbstractThe 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.
ObjectiveThe lecture course aims at providing principles of modern techniques used in molecular microbiology. Emphasis is on genetic, biochemical, and cellular analysis including also bioinformatics aspects. 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.
ContentImportant genetic, biochemical, biophysical, bioinformatic and structural 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
- Synthetic biology
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references, relevant papers and handouts will be provided during the lectures.
Prerequisites / NoticeThe following lecturers will contribute to the course:

Prof. Beat Christen (ETH)
Dr. Matthias Christen (ETH)
Prof. Hans-Martin Fischer (ETH)
Dr. Jonas Grossmann (FGCZ)
Dr. Florian Freimoser (Agroscope)
Dr. Bernd Roschitzki (FGCZ)
Dr. Roman Spörri (ETH)
227-0390-00LElements of MicroscopyW4 credits3GM. Stampanoni, G. Csúcs, A. Sologubenko
AbstractThe 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.
ObjectiveSolid introduction to the basics of microscopy, either with visible light, electrons or X-rays.
ContentIt 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.
LiteratureAvailable Online.
701-1708-00LInfectious Disease DynamicsW4 credits2VS. Bonhoeffer, R. D. Kouyos, R. R. Regös, T. Stadler
AbstractThis 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.
ObjectiveAttendees 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").
ContentAfter 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 notesSlides and script of the lecture will be available online.
LiteratureThe 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 / NoticeBasic knowledge of population dynamics and population genetics as well as linear algebra and analysis will be an advantage.
751-4505-00LPlant Pathology IIW2 credits2GB. McDonald
AbstractPlant 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.
ObjectiveAn 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.
ContentPlant 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 notesLecture notes will be available for purchase at the cost of reproduction.
LiteratureLecture notes will be available for purchase at the cost of reproduction.
Prerequisites / NoticePlant Pathology I provides a good preparation for Plant Pathology II, but is not a prerequisite for this course.
551-1700-00LIntroduction to Flow Cytometry Restricted registration - show details
Number of participants limited to 24.
W2 credits1VJ. Kisielow, L. Tortola, further lecturers
AbstractThe 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.
ObjectiveThe goal of this course is to provide the basic knowledge of flow and mass cytometry required for planning and execution of cytometric experiments.
ContentThe 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
- Sorting
- 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 notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references on immunophenotyping, analysis of proliferation, cell cycle, apoptosis and cell signalling will be discussed during the lectures.
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