Search result: Catalogue data in Spring Semester 2021

Biology Master Information
Elective Major Subject Areas
Elective Major: Ecology and Evolution
Compulsory Concept Courses
NumberTitleTypeECTSHoursLecturers
701-0323-00LPlant EcologyO3 credits2VJ. Alexander
AbstractThis class focuses on ecological processes involved with plant life, mechanisms of plant adaptation, plant-animal and plant-soil interactions, plant strategies and implications for the structure and function of plant communities. The discussion of original research examples familiarises students with research questions and methods, and how to evaluate results and interpretations.
ObjectiveAfter attending this course, you will be able to:
1. Use your understanding of plant ecological theory to interpret primary data (tables, graphs) from ecological studies.
2. Critically evaluate evidence and conclusions presented in ecological studies based on your understanding of plant ecological processes.
3. Apply your knowledge of plant ecology to make general predictions about major responses of plant communities to biotic and environmental perturbations.
4. Evaluate the main methodological approaches used to study ecological processes in plants, and decide when they should be applied to address a research question.
ContentPlant communities can be spectacularly diverse, which has long puzzled ecologists since all plants compete for the same few limiting resources. Plants also represent the matrix of ecological communities, and the structure and dynamics of plant populations drives the functioning of terrestrial ecosystems. This course provides insight into these broad themes by providing an introduction to the essential ecological processes involved with plant life. We use original research examples to discuss how ecological questions are studied and how results are interpreted. Specific topics include:

- Plant functional traits (e.g. leaf economics, phenology), and how they determine interactions between plants and their physical environment.
- Plant life-history, and the different ecological strategies plants have developed to grow, survive and reproduce.
- Intra- and interspecific competition as regulators of plant population dynamics and multispecies coexistence.
- Interactions between plants and their friends (e.g. symbiotic fungi, pollinators) and enemies (e.g. herbivores, pathogens) above- and below-ground.
- Plant functional types and rules in the assembly of plant communities.
Lecture notesHandouts and further reading will be available electronically through the course Moodle at the beginning of the semester.
Prerequisites / NoticePrerequisites
- General knowledge of plant biology
- Basic knowledge of plant sytematics
- General ecological concepts
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
701-0310-00LConservation Biology Information W2 credits2GF. Knaus
AbstractIn this course, the students explore ecological approaches, philosophical foundations, and practical implementations of conservation activities. Based on case studies, they are introduced to different views, values and ideals inherent in these activities.
ObjectiveStudents of this course are able to:
- understand the historical development and the current state of biodiversity and estimate possible future trends
- explain the economic legal, political and philosophical foundations of conservation activities
- define different possibilities of how conservation can be implemented in practice
- identify and critically appraise normative elements in conservation
- analyse and evaluate a nature conservation project from conception to successful completion.
ContentThe course covers the following content:
- Describe and analyse the past, current and future human impacts on biodiversity.
- Explore alternative approaches to nature conservation and their implementation for example species or habitat protection, restorations, parks, etc.
- Discuss the ethical, moral, legal, and economic reasons for conservation.
- Understand the main theories relevant to conservation such as the vulnerability of small populations, ecosystem services, biodiversity, etc.
- Explore practical examples during excursions and provide an analysis and evaluation of concrete case studies.
Lecture notesKein Skript
LiteratureKüster H. 1999: Geschichte der Landschaft in Mitteleuropa. Von der Eiszeit bis zur Gegenwart. Beck, München, Germany. 424p.
Piechocki R. 2010: Landschaft, Heimat, Wildnis. Schutz der Natur - aber welcher und warum? Beck'sche Reihe, Beck, München, Germany. 266p.
Primack R.B. 2008: A primer of Conservation Biology. Fourth Edition. Sinauer Associates, Sunderland MA, USA. 349p.
Prerequisites / NoticeKenntnisse aus den folgenden LV sind vorausgesetzt:
- Allgemeine Biologie I
- Allgemeine Biologie II
- Biologie III: Ökologie
- Biologie IV: Diversität der Pflanzen und Tiere
701-1450-00LConservation GeneticsW3 credits4GR. Holderegger, M. Fischer, F. Gugerli
AbstractThe course deals with conservation genetics and its practical applications. It introduces the genetic theories of conservation genetics, such as inbreeding depression, adaptive genetic diversity or fragmentation. The course also shows how genetic methods such as eDNA and metabarcoding are used in conservation management, and it critically discusses the benefits and limits of conservation genetics.
ObjectiveGenetic and evolutionary argumentation is an important feature of conservation biology. The course equips students with knowledge on conservation genetics and its applications in conservation management. The course introduces the main theories of conservation genetics and shows how genetic methods are used in conservation management. In addition, it critically discusses the benefits and limits of conservation genetics. Practical examples dealing with animals and plants are presented.
ContentThere are 4 hours of lectures, presentations and group work per week. Students also have to spend about 3 hours per week on preparatory work for the following week. Every week, one subject will be presented by one of three lecturers.

Overview of themes:
Barcoding, eDNA metabarcoding and genetic monitoring; effects of small population size, genetic drift and inbreeding; neutral and adaptive genetic diversity; hybridization; gene flow, fragmentation and connectivity.

Specific topics:
(1) Species and individual identification: barcoding; metabarcoding; eDNA; estimation of census population size; habitat use and genetic monitoring.
(2) Inbreeding and inbreeding depression: small population size; bottlenecks; genetic drift; inbreeding and inbreeding depression; effective population size.
(3) Adaptive genetic diversity: neutral and adaptive genetic variation; importance of adaptive genetic diversity; methods to measure adaptive genetic variation.
(4) Hybridization and monitoring of genetic diversity: gene introgression; gene flow across species boundaries; demographic swamping; monitoring of genetic diversity.
(5) Half day excursion: practical example of conservation genetics on fragmentation.
(6) Discussion and evaluation of excursion; gene flow: historical and contemporary gene flow and dispersal; fragmentation and connectivity.
(7) Oral examination.
Lecture notesNo script; handouts and material for downloading will be provided.
LiteratureThere is no textbook for this course, but the following books are recommended:
Allendorf F.W., Luikart G.; Aitken S.N. 2013. Conservation and the Genetics of Populations, 2nd edition. Wiley, Oxford.
Frankham R., Ballou J.D., Briscoe D.A. 2010. Introduction to Conservation Genetics, 2nd edition. Cambridge University Press, Cambridge.

The following book and booklets in German are targeted to conservation professionals:
Holderegger R., Segelbacher G. (eds.). 2016. Naturschutzgenetik. Ein Handbuch für die Praxis. Haupt, Bern.
Csencsics D., Gugerli F. 2017. Naturschutzgenetik. WSl Berichte 60: 1-82 (free download: Link)
Prerequisites / NoticeRequirements:
Students must have a good background in genetics as well as in ecology and evolution. The courses "Population and Quantitative Genetics" or "Evolutionary Genetics" should have been attended.

Examination:
A final oral examination on the content of the course and the excursion are integral parts of the course.

Teaching forms:
The course needs the active participation of students. It consists of lectures, group work, presentations, discussions, reading and a half-day excursion.
701-1424-00LGuarda-Workshop in Evolutionary Biology Information
This course has limited spaces. To register for this course you have to sign in via mystudies and via the website of the University of Basel Link.
W3 credits4PS. Bonhoeffer
AbstractThis one week course is intended for students with a keen interest in evolutionary biology. The aim of the course is to develop a research project in small teams of 4-5 students. The students receive guidance by the "faculty" consisting of Prof. D. Ebert (U Basel) and Prof. S Bonhoeffer (ETHZ). Additionally two internationally reknown experts are invited every year.
Objectivesee link Link
Contentsee link Link
Lecture notesnone
Literaturenone
Prerequisites / NoticeAs the number of participants is limited, application for the course is necessary. Please apply for the course using the course website (see link Link).
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551-0216-00LField Course in Mycology Restricted registration - show details
Number of participants limited to 8.
W3 credits3.5PR. Berndt, M. A. Garcia Otalora
AbstractThis 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.
ObjectiveRecognizing 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.
ContentIntroduction 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 notesScripts will be handed out.
LiteratureTechnical literature will be provided in the lecture room.
Prerequisites / NoticeThe 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.
751-5110-00LInsects in AgroecosystemsW2 credits2VC. De Moraes, A. Kantsa, D. Lucas Gomes Marques Barbosa
AbstractThis class will focus on insect-plant interactions in agroecosystems, and how the unique man-made agricultural community effects insect populations leading to pest outbreaks. Key concepts in pest prediction and management will be discussed from an ecological perspective.
ObjectiveAt the end of this course, students will understand what biotic and abiotic factors contribute to pest outbreaks, why some modern pest management techniques have failed over time, and the trade-offs associated with the use of different pest control methods. Our approach will allow students to apply their knowledge to a variety of pest management situations. Additionally, students will learn about current research goals in agroecology and how these goals are being addressed by scientists engaged in agricultural research.
ContentThe focus of this course will be on understanding how the ecologies of agricultural systems differ from natural ecosystems, and how these difference affect the population dynamics of insect pests and natural enemies. Each section of the course is centered around a basic ecological, biological or engineering theme such as host shift, physiological time, or sampling techniques. Different management techniques will be discussed, as well as the ecological basis behind why these techniques work and why they sometimes fail. The role of insects in spreading economically important plant diseases will also be discussed. Recent advances in research will also be addressed throughout the course and reinforced with periodic readings of primary literature.
Lecture notesProvided to students through ILIAS
LiteratureSelected required readings (peer reviewed literature, selected book chapters).
701-1418-00LModelling Course in Population and Evolutionary Biology Information Restricted registration - show details
Number of participants limited to 20.

Priority is given to MSc Biology and Environmental Sciences students.
W4 credits6PS. Bonhoeffer, V. Müller
AbstractThis course provides a "hands-on" introduction into mathematical/computational modelling of biological processes with particular emphasis on evolutionary and population-biological questions. The models are developed using the Open Source software R.
ObjectiveThe aim of this course is to provide a practical introduction into the modelling of fundamental biological questions. The participants will receive guidance to develop mathematical/computational models in small teams. The participants chose two modules with different levels of difficulty from a list of projects.

The participant shall get a sense of the utility of modelling as a tool to investigate biological problems. The simpler modules are based mostly on examples from the earlier lecture "Ecology and evolution: populations" (script accessible at the course webpage). The advanced modules address topical research questions. Although being based on evolutionary and population biological methods and concepts, these modules also address topics from other areas of biology.
Contentsee Link
Lecture notesDetailed handouts describing both the modelling and the biological background are available to each module at the course website. In addition, the script of the earlier lecture "Ecology and evolution: populations" can also be downloaded, and contains further background information.
Prerequisites / NoticeThe course is based on the open source software R. Experience with R is useful but not required for the course. Similarly, the course 701-1708-00L Infectious Disease Dynamics is useful but not required.
701-0364-00LFlora and Vegetation of the Alps Restricted registration - show details
Zur dieser Vorlesung gehört eine 4-tägige Exkursion (max. 24 Plätze) nach Davos. Für eine Teilnahme an der Exkursion muss die Lehrveranstaltung «Böden und Vegetation der Alpen» (Nr. 701-0362-00) separat belegt werden.
W1 credit1VA. Widmer
AbstractThis course provides an introduction to the flora and vegetation of the Alps. This includes the climatic conditions at different elevations, the origin of Alpine plants, centers of diversity, ecological requirements and adaptations to prevailing environmental conditions, as well as characteristic plant communities at different altitudes and soil types.
ObjectiveThe students
- understand how climatic and edaphic factors affect the occurrence and distribution of alpine plants
- know characteristic plant species of the subalpine and alpine elevational belts in the Alps
- are familiar with characteristic plant communities on acidic, basic and ultramafic soils in the subalpine and alpine elevational belts.
ContentClimatic conditions at different elevations in the Alps; origin and distribution patterns; centers of diversity; ecological requirements and adaptations to prevailing environmental conditions; altitudinal belts; characteristic plant communities on different bedrock (dolomite, acidic and basic silicates, serpentine).
Lecture notesCourse material will be provided.
LiteratureLandolt E. 2003: Unsere Alpenflora. 7.Aufl., SAC-Verlag.
Prerequisites / NoticeSolid background in systematic botany and successful participation in the course "Systematic Biology: Plants" (Nr. 701-0360-00). It is further recommended that students have also participated in the block course "Plant Diversity" (Nr. 701-2314-00L), or alternatively the two courses "Plant Diversity: Colline/Montane" (701-0314-00L) and "Plant Diversity: Subalpine/Alpine" (701-0314-01L).

Notice:
To this lecture belongs the course "Soils and Vegetation of the Alps" (No. 701-0362-00) which currently includes three excursion days in the Davos region. The course is expected to take place between July 12 and 17, 2021. More detailed information will follow at the beginning of the spring semester 2021. Program changes and adjustments due to the corona situation are possible and will be communicated promptly.

Please note that this course will be taught in German.
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.
701-1410-01LQuantitative Approaches to Plant Population and Community EcologyW2 credits2VJ. Alexander, T. Walker
AbstractThis course presents leading problems in plant population, community and ecosystem ecology and modern tools to address them. Topics include parameterising models of plant population dynamics, using biological networks to investigate species coexistence, exploring the physiological and functional basis of plant life history strategies and quantifying how plants influence ecosystem functioning.
ObjectiveStudents will attain deep insight into topics at the cutting edge of plant ecological research, whilst developing specific skills that can later be applied to basic and applied ecological problems.
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.
701-1462-00LEvolution of Social Behavior and Biological Communication Restricted registration - show details
Number of participants limited to 24.
W3 credits2VM. Mescher
AbstractThis course addresses presents core concepts in the study of behavior and biological communication from a Darwinian perspective, with a focus on the evolution of sociality and the emergence of higher-level biological organization. It will entail lectures and discussion of selected readings from relevant primary and secondary literature.
ObjectiveStudents will become familiar with the application of Darwinian evolutionary theory to the study of behavior, communication, and social organization. They will also gain insight into the relevance of these topics for broader intellectual questions in biology, as well as for the organization of human societies.
ContentThis course will begin with an exploration of key concepts, including the central role of information in biology and Darwinian explanations for the emergence of adaptation and functional complexity in biological systems. We will then discuss the application of these concepts to the study of behavior and communication, with a focus on the evolution of social interactions. Significant attention will also be given to the evolution of cooperation among individual organisms and the emergence and maintenance of complex social organization. Finally, we will discuss the implications of the material covered for understanding human behavior and for the organization of human societies, including implications for implementing collective action to address global environmental challenges. These topics will be covered by lectures and discussion of relevant readings selected by the instructor. Evaluations will be based on in-class or take-home examinations, as well as participation in classroom discussions.
701-1426-00LAdvanced Evolutionary Genetics
Does not take place this semester.
W3 credits4GT. Städler
AbstractThe field of evolutionary genetics rests on genetic and evolutionary principles, (often) mathematical models, and molecular data. The explosion in the availability of genome-wide data makes competencies in "making sense" of such data more and more relevant. This course will cover selected topics that are both fundamental and/or currently very active research fields.
ObjectiveThis course deals with (some of) the conceptual foundations of evolutionary genetics in the age of genomics, going well beyond the introductory material that is part of the BSc curriculum. The principal aim is for students to gain a thorough appreciation for the underlying ideas and models of key evolutionary processes, and to witness how these are being tested and refined vis-à-vis the recent deluge of genome-wide sequence data. The course focuses on theoretical concepts and ways to infer the action of evolutionary processes from molecular data; as such it is also designed to facilitate understanding of the burgeoning scientific literature in molecular ecology and evolution. These aims require students to be actively engaged in reading original papers, discussing ideas and data among themselves, and presenting their interpretations in group talks.
ContentThere are 4 hours of lectures, student presentations, and/or group work per week. Students are expected to spend 4 additional hours per week on preparatory study for the following week. Every week, one subject will be presented and overseen by one of the two lecturers.

Each weekly topic will be introduced by a lecture (max. 2 x 45 minutes), highlighting key concepts and historically important papers. The (slight) majority of the time will be spent with group presentations based on recent important papers, and discussions of the relevant concepts.

Specific proposed topics (subject to change):
(1) The coalescent in structured populations (e.g. spatial sampling and its genealogical consequences, demographic inference from sequence data, spurious bottlenecks).
(2) Population subdivision: evolutionary processes and measures (e.g. spatial models, absolute and relative measures of divergence, Jost's (2008) fundamental insights and their reception).
(3) Speciation genetics and modes of species divergence (e.g. intrinsic postzygotic barriers, Dobzhansky-Muller incompatibilities, snowball effect, genomic islands of divergence).
(4) The interplay of linkage, recombination, and selection (e.g. selective sweeps, background selection, Hill-Robertson interference, adaptation).
(5) Evolutionary consequences of mating systems (e.g. clonal vs. sexual reproduction, bottlenecks, colonizing potential, efficacy of natural selection).
(6) Genomics of virulence evolution (e.g. pathogenicity islands, mobile genetic elements, chromosomal rearrangements).
Lecture notesNo script; handouts and material for downloading will be provided.
LiteratureThere is no textbook for this course. Relevant literature will be provided for each weekly session, selected mostly from the primary research literature.
Prerequisites / NoticeRequirements:
Students must have a good background in genetics, basic population genetics, as well as evolutionary biology. At a minimum, either the course "Population and Quantitative Genetics" or the course "Ecological Genetics" should have been attended, and ideally, both of these ("Evolutionary Genetics" in the D-BIOL curriculum).

Teaching Forms:
The course consists of lectures, readings, group work, student presentations, and discussions. Active participation and preparation of students is critical for a successful learning experience and outcome.
701-0314-00LPlant Diversity: Colline/Montane Restricted registration - show details
Participation in LV 701-0360-00L (Systematic Biology of Plants) or comparable knowledge (after consultation with the lecturer).
Enrollment for target group until 19.02.2021.
Waiting list until 31.3.2021.
W3 credits6PR. Berndt
AbstractThe practical focuses on the vegetation and flora of the colline and montane belts of Switzerland. It comprises five day excursions to typical and botanically rich locations. During the excursions the students will deepen their knowledge of plant species and learn to recognize important vegetation units and their ecological characteristics.
ObjectiveKnowledge of the flora and ecological conditions of the most important vegetation units of the colline and montane belts of Switzerland. Consolidation of taxonomic and plant morphological knowledge. Experience in plant determination using scientific determination keys. Basic collecting and herbarium techniques.
ContentThis course gives an introduction to the flora and vegetation of the colline and montane belts of Switzerland. During five excursions the students will become acquainted with the most important vegetation types, their species diversity and the respective environmental conditions.
Besides deepening the knowledge of plant species and vegetation a focus will be laid on how man shaped the cultural landscape and continues to change it.
Literature-Stützel T. 2015. Botanische Bestimmungsübungen (3. Aufl.). UTB, Ulmer Verlag.

-Hess H.E., Landolt E., Hirzel R. & Baltisberger M. 2015: Bestimmungsschlüssel zur Flora der Schweiz. 7., aktualisierte und überarbeitete Aufl., Birkhäuser Verlag, Basel/Boston/Berlin.
Prerequisites / NoticeParticipants need to know the teaching contents of the lecture « Plant Systematics » (LV 701 0360 00L) and the associated exercises and excursions.
It is expected that the participants know how to use a determination key (Hess et al. 2015. Bestimmungsschlüssel zur Flora der Schweiz) and understand the necessary botanical terminology (e.g. Stützel 2015).

Students from other universities are requested to contact the lecturers.

Program: Depending on actual CoVid situation the program may be changed on short notice!
15.-19. 6.: Day excursions (destinations to be announced)
22.6. (morning): Exam (9-11 Uhr, HIL E1)

The excursions will take place under any weather conditions. The participants should be equipped appropriately to cope with rough and steep terrain and adverse weather conditions. Sturdy mountain boots are mandatory!

Course fees:
No course fees.
701-0314-01LPlant Diversity: Subalpine/Alpine Restricted registration - show details
Prerequisite: Enrollment and successful performance assessment of LV 701-0360-00L (Systematic Biology: Plants).

Enrollment for target group until 19.02.2021
Waiting list until 31.03.2021.

The registration form must be handed in by 05.03.2021. Unconfirmed places are allocated to students on the waiting list.
W3 credits6PA. Guggisberg
AbstractThe practical focuses on the flora and vegetation of the northern Alps and covers from the upper montane to the lower alpine zone. Depending on the status of the COVID-19 pandemic, students are offered a mixture of individual activities and guided excursions to deepen their knowledge of plant species and to learn to recognize important vegetation units and their ecological characteristics.
ObjectiveGetting to know the most important vegetation types, their flora and ecological conditions in the northern Alps. Consolidation of taxonomic and plant morphological knowledge. Experience in plant determination using scientific determination keys.
ContentThis course provides an introduction to the flora and vegetation of the northern Alps. The students will become acquainted with the botanical richness of the Alps and the ecological specificities of the encountered habitats. They will not only gain knowledge in plant species, but also learn which environmental conditions do plants cope with and which adaptation they have evolved.

Following topics will be addressed in this course:

- Climatic and geological divisions of the Alps
- Effect of local conditions on vegetation of different altitudes
- Adaptation of plants to various alpine conditions
- Characteristic vegetation types of the subalpine and alpine zone (e.g. subalpine conifer forests, tall-herb communities and green alder scrubs, alpine grassland and scree vegetation, subalpine floodplain forest with fens) and their ecological conditions
- Interaction between plants and their environment: examples from pollination, reproduction and dispersal strategies.
Lecture notesA script is provided via Moodle.
Literature- Baltisberger M., Nyffeler R. & Widmer A. 2013: Systematische Botanik. 4., vollständig überarbeitete und erweiterte Aufl. v/d/f Hochschulverlag AG an der ETH Zürich.
- Stützel T. 2015. Botanische Bestimmungsübungen (3. Aufl.). UTB, Ulmer Verlag.
- Hess H.E., Landolt E., Hirzel R. & Baltisberger M. 2015: Bestimmungsschlüssel zur Flora der Schweiz. 7., aktualisierte und überarbeitete Aufl., Birkhäuser Verlag, Basel/Boston/Berlin.
Prerequisites / NoticeWe only admit students to the practical who have successfully completed the introductory lectures in systematic botany together with the associated exercises and excursions (cf. course 701-0360-00L Systematic Biology: Plants). In addition, we expect that the participants know how to use a determination key (Bestimmungsschlüssel zur Flora der Schweiz) and understand the necessary terminology.

Students from other universities are requested to contact the lecturers.

Program:
27.6.-1.7.: individual activities and guided day excursions (to be announced)
3.7.: exam at ETH Zentrum

The excursions will take place under any weather conditions. The participants should be able to cope with rough and steep terrain and should bring appropriate equipment. Sturdy mountain boots are mandatory!

Course fees:
No course fees.
701-0362-00LSoils and Vegetation of the Alps (Excursion) Restricted registration - show details
Diese Exkursion (max. 24 Plätze) gehört zur Vorlesung «Flora und Vegetation der Alpen» (701-0364-00; A. Widmer). Sie kann nur gleichzeitig mit der Vorlesung oder nach bestandener Prüfung belegt werden. Alternativ ist eine Teilnahme möglich mit bestandenen Prüfungen in «Boden- und Wasserchemie» (701-0533-00L; R. Kretzschmar, D.I. Christl, L. Winkel) und «Pedosphäre» (701-0501-00L; R. Kretzschmar).
W2 credits2PA. Widmer, R. Kretzschmar
AbstractThe excursion in the area of Davos illustrates how climatic and edaphic factors shape the distribution of alpine plants. Visits of multiple sites on different bedrocks in the subalpine and alpine elevational belts reveal connections between climatic conditions, soil formation and vegetation development.
ObjectiveThe students
- understand how parent rock, topography, climate, and vegetation influence soil forming processes and resulting soil properties (e.g. nutrients, water) in the Alps.
- understand, how climatic and edaphic factors affect the occurrence and distribution of alpine plants.
- are familiar with characteristic plant communities on acidic, basic and ultramafic bedrock in the subalpine and alpine elevational belts.
- know characteristic plant species and plant communities of the subalpine and alpine elevational belts in the Alps.
Content4-day excursion in the area of Davos with visits of sites on different bedrock (dolomite, gneiss/mica schist, amphibolite, serpentinite) in the subalpine and alpine elevational belts.
Structure, development and characteristics of the soils and of their effects on the vegetation; characteristic plant species and communities on different soil types.
Lecture notesA guide to the excursion will be made available.
LiteratureLandolt E. 2003: Unsere Alpenflora. 7.Aufl., SAC-Verlag.
Prerequisites / NoticePlease note that this course will be taught in German.
701-1480-00LEvolutionary Developmental Biology Restricted registration - show details
Number of participants limited to 24.
Waiting list will be deleted after 05.03.2021.
W3 credits1SM. La Fortezza, G. Velicer
AbstractStudents will be introduced to fundamental concepts and current open questions in the field of evolutionary developmental biology (Evo-Devo) primarily through reading, analysing and jointly discussing key literature.
ObjectiveThe course aims to expose students to major conceptual themes of the Evo-Devo field through discussion of key papers and to active areas of current Evo-Devo research. At the end of the course, students should be able to present, think critically about and discuss key Evo-Devo concepts.
ContentEvolutionary developmental biology (Evo-Devo) is a multidisciplinary field that studies the interplay between developmental and evolutionary processes. Major questions include: How do developmental systems evolve and diversify? Do developmental programs influence their own future evolution, and how? How does ecology affect the evolution of developmental programs, and vice versa? Fascinating and experimentally challenging, Evo-Devo first empirically emerged from comparative embryology. However, in recent decades this discipline has grown considerably to interconnect with many other fields, from genetics to sociobiology to microbiology. The course will examine questions such as those above and touch on the ongoing inter-disciplinary integration of Evo-Devo, including its interface with ecology (“Eco-Evo-Devo”) and the integration of aggregative microbial developmental systems into the field.
LiteratureRelevant literature:

Müller, G. (2007). Evo–devo: extending the evolutionary synthesis. Nature Reviews Genetics 8, 943-949. Link

Abouheif, E., et al (2014). Eco-evo-devo: the time has come. Advances in experimental medicine and biology 781, 107-25. Link

Moczek, A et al (2015). The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evolution & development 17, 198-219. Link

Gilbert, S. (2019). Evolutionary transitions revisited: Holobiont evo‐devo. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 12, 117762501877479 - 8. Link
Prerequisites / NoticeSignificant basic knowledge in especially evolutionary biology and developmental biology, and also cell biology and genetics, will be advantageous for readily understanding the course material.
401-0102-00LApplied Multivariate StatisticsW5 credits2V + 1UF. Sigrist
AbstractMultivariate statistics analyzes data on several random variables simultaneously. This course introduces the basic concepts and provides an overview of classical and modern methods of multivariate statistics including visualization, dimension reduction, supervised and unsupervised learning for multivariate data. An emphasis is on applications and solving problems with the statistical software R.
ObjectiveAfter the course, you are able to:
- describe the various methods and the concepts behind them
- identify adequate methods for a given statistical problem
- use the statistical software R to efficiently apply these methods
- interpret the output of these methods
ContentVisualization, multivariate outliers, the multivariate normal distribution, dimension reduction, principal component analysis, multidimensional scaling, factor analysis, cluster analysis, classification, multivariate tests and multiple testing
Lecture notesNone
Literature1) "An Introduction to Applied Multivariate Analysis with R" (2011) by Everitt and Hothorn
2) "An Introduction to Statistical Learning: With Applications in R" (2013) by Gareth, Witten, Hastie and Tibshirani

Electronic versions (pdf) of both books can be downloaded for free from the ETH library.
Prerequisites / NoticeThis course is targeted at students with a non-math background.

Requirements:
==========
1) Introductory course in statistics (min: t-test, regression; ideal: conditional probability, multiple regression)
2) Good understanding of R (if you don't know R, it is recommended that you study chapters 1,2,3,4, and 5 of "Introductory Statistics with R" from Peter Dalgaard, which is freely available online from the ETH library)

An alternative course with more emphasis on theory is 401-6102-00L "Multivariate Statistics" (only every second year).

401-0102-00L and 401-6102-00L are mutually exclusive. You can register for only one of these two courses.
Elective Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0314-00LMicrobiology (Part II)W3 credits2VW.‑D. Hardt, L. Eberl, J. Piel, J. Vorholt-Zambelli
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ObjectiveThis concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
Elective Major: Neurosciences
The major in Neurosciences in the Master program Biology ETHZ will no longer be offered from autumn 2019 onwards.
Elective Compulsory Concept Courses
See D-BIOL Master Studies Guide
NumberTitleTypeECTSHoursLecturers
551-0326-00LCell Biology Information W6 credits4VS. Werner, H. Gehart, W. Kovacs, M. Schäfer, U. Suter, A. Wutz, further lecturers
AbstractThis Course introduces principle concepts, techniques, and experimental strategies used in modern Cell Biology. Major topics include: neuron-glia interactions in health and disease; mitochondrial dynamics; stem cell biology; growth factor action in development, tissue repair and disease; cell metabolism, in particular sensing and signaling mechanisms, cell organelles, and lipid metabolism.
Objective-To prepare the students for successful and efficient lab work by learning how to ask the right questions and to use the appropriate techniques in a research project.
-To convey knowledge about neuron-glia interactions in health and disease.
- To provide information on different types of stem cells and their function in health and disease
-To provide information on growth factor signaling in development, repair and disease and on the use of growth factors or their receptors as drug targets for major human diseases
-To convey knowledge on the mechanisms underlying repair of injured tissues
-To provide the students with an overview of mitochondrial dynamics.
-Providing an understanding of RNA processing reactions and their regulations.
-To provide a comprehensive understanding of metabolic sensing mechanisms occurring in different cell types and organelles in response to glucose, hormones, oxygen, nutrients as well as lipids, and to discuss downstream signaling pathways and cellular responses.
-To provide models explaining how disturbances in complex metabolic control networks and bioenergetics can lead to disease and to highlight latest experimental approaches to uncover the intricacies of metabolic control at the cellular and organismal level.
-Providing the background and context that foster cross-disciplinary scientific thinking.
551-0318-00LImmunology IIW3 credits2VA. Oxenius, M. Kopf, S. R. Leibundgut, E. Slack, further lecturers
AbstractIntroduction into the cellular and molecular basis of the immune system and immune responses against diverse pathogens, tumors, transplants, and self (autoimmunity)
ObjectiveThe lectures will provide a detailed understanding:
- how innate and adaptive immune responses interact at the cellular and molecular level.
- how the immune system recognizes and fights against pathogenic microorganisms including viruses, bacteria, and parasites.
- why lymphocytes tolerate self molecules.
- about function and dysfunction the intestinal immune system.
- immunopathology and inflammatory diseases.
ContentThe aim of lecture is to understand:
> How pathogens are recognized by the innate immune system
> Immune defense against various pathogens
> Immunology of the skin, lung and intestines
> Tumor immunology
> Migration and homing of immune cells
> tolerance and autoimmunity
> T cell memory
Lecture notesPresentations of the lecturers are available at the Moodle link
LiteratureRecommended: Kuby Immunology (Freeman)
551-0320-00LCellular Biochemistry (Part II)W3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
227-1034-00LComputational Vision (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: INI402

Mind the enrolment deadlines at UZH:
Link
W6 credits2V + 1UD. Kiper
AbstractThis course focuses on neural computations that underlie visual perception. We study how visual signals are processed in the retina, LGN and visual cortex. We study the morpholgy and functional architecture of cortical circuits responsible for pattern, motion, color, and three-dimensional vision.
ObjectiveThis course considers the operation of circuits in the process of neural computations. The evolution of neural systems will be considered to demonstrate how neural structures and mechanisms are optimised for energy capture, transduction, transmission and representation of information. Canonical brain circuits will be described as models for the analysis of sensory information. The concept of receptive fields will be introduced and their role in coding spatial and temporal information will be considered. The constraints of the bandwidth of neural channels and the mechanisms of normalization by neural circuits will be discussed.
The visual system will form the basis of case studies in the computation of form, depth, and motion. The role of multiple channels and collective computations for object recognition will
be considered. Coordinate transformations of space and time by cortical and subcortical mechanisms will be analysed. The means by which sensory and motor systems are integrated to allow for adaptive behaviour will be considered.
ContentThis course considers the operation of circuits in the process of neural computations. The evolution of neural systems will be considered to demonstrate how neural structures and mechanisms are optimised for energy capture, transduction, transmission and representation of information. Canonical brain circuits will be described as models for the analysis of sensory information. The concept of receptive fields will be introduced and their role in coding spatial and temporal information will be considered. The constraints of the bandwidth of neural channels and the mechanisms of normalization by neural circuits will be discussed.
The visual system will form the basis of case studies in the computation of form, depth, and motion. The role of multiple channels and collective computations for object recognition will
be considered. Coordinate transformations of space and time by cortical and subcortical mechanisms will be analysed. The means by which sensory and motor systems are integrated to allow for adaptive behaviour will be considered.
LiteratureBooks: (recommended references, not required)
1. An Introduction to Natural Computation, D. Ballard (Bradford Books, MIT Press) 1997.
2. The Handbook of Brain Theorie and Neural Networks, M. Arbib (editor), (MIT Press) 1995.
227-1046-00LComputer Simulations of Sensory Systems Information W3 credits3GT. Haslwanter
AbstractThis course deals with computer simulations of the human auditory, visual, and balance system. The lecture will cover the physiological and mechanical mechanisms of these sensory systems. And in the exercises, the simulations will be implemented with Python. The simulations will be such that their output could be used as input for actual neuro-sensory prostheses.
ObjectiveOur sensory systems provide us with information about what is happening in the world surrounding us. Thereby they transform incoming mechanical, electromagnetic, and chemical signals into “action potentials”, the language of the central nervous system.
The main goal of this lecture is to describe how our sensors achieve these transformations, how they can be reproduced with computational tools. For example, our auditory system performs approximately a “Fourier transformation” of the incoming sound waves; our early visual system is optimized for finding edges in images that are projected onto our retina; and our balance system can be well described with a “control system” that transforms linear and rotational movements into nerve impulses.
In the exercises that go with this lecture, we will use Python to reproduce the transformations achieved by our sensory systems. The goal is to write programs whose output could be used as input for actual neurosensory prostheses: such prostheses have become commonplace for the auditory system, and are under development for the visual and the balance system. For the corresponding exercises, at least some basic programing experience is required!!
ContentThe following topics will be covered:
• Introduction into the signal processing in nerve cells.
• Introduction into Python.
• Simplified simulation of nerve cells (Hodgkins-Huxley model).
• Description of the auditory system, including the application of Fourier transforms on recorded sounds.
• Description of the visual system, including the retina and the information processing in the visual cortex. The corresponding exercises will provide an introduction to digital image processing.
• Description of the mechanics of our balance system, and the “Control System”-language that can be used for an efficient description of the corresponding signal processing (essentially Laplace transforms and control systems).
Lecture notesFor each module additional material will be provided on the e-learning platform "moodle". The main content of the lecture is also available as a wikibook, under Link
LiteratureOpen source information is available as wikibook Link

For good overviews of the neuroscience, I recommend:

• Principles of Neural Science (5th Ed, 2012), by Eric Kandel, James Schwartz, Thomas Jessell, Steven Siegelbaum, A.J. Hudspeth
ISBN 0071390111 / 9780071390118
THE standard textbook on neuroscience.
NOTE: The 6th edition will be released on February 5, 2021!
• L. R. Squire, D. Berg, F. E. Bloom, Lac S. du, A. Ghosh, and N. C. Spitzer. Fundamental Neuroscience, Academic Press - Elsevier, 2012 [ISBN: 9780123858702].
This book covers the biological components, from the functioning of an individual ion channels through the various senses, all the way to consciousness. And while it does not cover the computational aspects, it nevertheless provides an excellent overview of the underlying neural processes of sensory systems.

• G. Mather. Foundations of Sensation and Perception, 2nd Ed Psychology Press, 2009 [ISBN: 978-1-84169-698-0 (hardcover), oder 978-1-84169-699-7 (paperback)]
A coherent, up-to-date introduction to the basic facts and theories concerning human sensory perception.

• The best place to get started with Python programming are the Link

On signal processing with Python, my upcoming book
• Hands-on Signal Analysis with Python (Due: January 13, 2021
ISBN 978-3-030-57902-9, Link)
will contain an explanation to all the required programming tools and packages.
Prerequisites / Notice• Since I have to gravel from Linz, Austria, to Zurich to give this lecture, I plan to hold this lecture in blocks (every 2nd week).
• In addition to the lectures, this course includes external lab visits to institutes actively involved in research on the relevant sensory systems.
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.
376-1306-00LClinical Neuroscience (University of Zurich) Information
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BIO389

Mind the enrolment deadlines at UZH:
Link
W3 credits3VG. Schratt, University lecturers
AbstractThe lecture series "Clinical Neuroscience" presents a comprehensive, condensed overview of the most important neurological diseases, their clinical presentation, diagnosis, therapy options and possible causes. Patient demonstrations (Übungen) follow every lecture that is dedicated to a particular disease.
ObjectiveBy the end of this module students should be able to:
- demonstrate their understanding and deep knowledge concerning the main neurological diseases
- identify and explain the different clinical presentation of these diseases, the methodology of diagnosis and the current therapies available
- summarize and critically review scientific literature efficiently and effectively
376-1414-01LCurrent Topics in Brain Research (FS)W1 credit1.5KI. Mansuy, F. Helmchen, further lecturers
AbstractDifferent national and international scientific guests are invited to present and discuss their most recent scientific results.
ObjectiveThe aim is to exchange scientific knowledge and data as well as to promote communication and collaboration among researchers. Students taking the course participate in all seminars within one semester and write a critical report about one seminar of their choice. Prof. Isabelle / Dr. Alberto Corcoba will send instructions for this report to students who have registered for the course one week before the start of the semester.
ContentVarious scientific guests from the fields of neuroepigenetics, neurochemistry, neuromorphology and neurophysiology will report on their latest scientific findings.
Lecture notesno handout
Literatureno literature
Elective Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0326-00LCell Biology Information W6 credits4VS. Werner, H. Gehart, W. Kovacs, M. Schäfer, U. Suter, A. Wutz, further lecturers
AbstractThis Course introduces principle concepts, techniques, and experimental strategies used in modern Cell Biology. Major topics include: neuron-glia interactions in health and disease; mitochondrial dynamics; stem cell biology; growth factor action in development, tissue repair and disease; cell metabolism, in particular sensing and signaling mechanisms, cell organelles, and lipid metabolism.
Objective-To prepare the students for successful and efficient lab work by learning how to ask the right questions and to use the appropriate techniques in a research project.
-To convey knowledge about neuron-glia interactions in health and disease.
- To provide information on different types of stem cells and their function in health and disease
-To provide information on growth factor signaling in development, repair and disease and on the use of growth factors or their receptors as drug targets for major human diseases
-To convey knowledge on the mechanisms underlying repair of injured tissues
-To provide the students with an overview of mitochondrial dynamics.
-Providing an understanding of RNA processing reactions and their regulations.
-To provide a comprehensive understanding of metabolic sensing mechanisms occurring in different cell types and organelles in response to glucose, hormones, oxygen, nutrients as well as lipids, and to discuss downstream signaling pathways and cellular responses.
-To provide models explaining how disturbances in complex metabolic control networks and bioenergetics can lead to disease and to highlight latest experimental approaches to uncover the intricacies of metabolic control at the cellular and organismal level.
-Providing the background and context that foster cross-disciplinary scientific thinking.
551-0318-00LImmunology IIW3 credits2VA. Oxenius, M. Kopf, S. R. Leibundgut, E. Slack, further lecturers
AbstractIntroduction into the cellular and molecular basis of the immune system and immune responses against diverse pathogens, tumors, transplants, and self (autoimmunity)
ObjectiveThe lectures will provide a detailed understanding:
- how innate and adaptive immune responses interact at the cellular and molecular level.
- how the immune system recognizes and fights against pathogenic microorganisms including viruses, bacteria, and parasites.
- why lymphocytes tolerate self molecules.
- about function and dysfunction the intestinal immune system.
- immunopathology and inflammatory diseases.
ContentThe aim of lecture is to understand:
> How pathogens are recognized by the innate immune system
> Immune defense against various pathogens
> Immunology of the skin, lung and intestines
> Tumor immunology
> Migration and homing of immune cells
> tolerance and autoimmunity
> T cell memory
Lecture notesPresentations of the lecturers are available at the Moodle link
LiteratureRecommended: Kuby Immunology (Freeman)
551-0320-00LCellular Biochemistry (Part II)W3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
Elective Major: Microbiology and Immunology
Compulsory Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0314-00LMicrobiology (Part II)O3 credits2VW.‑D. Hardt, L. Eberl, J. Piel, J. Vorholt-Zambelli
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ObjectiveThis concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
551-0318-00LImmunology IIO3 credits2VA. Oxenius, M. Kopf, S. R. Leibundgut, E. Slack, further lecturers
AbstractIntroduction into the cellular and molecular basis of the immune system and immune responses against diverse pathogens, tumors, transplants, and self (autoimmunity)
ObjectiveThe lectures will provide a detailed understanding:
- how innate and adaptive immune responses interact at the cellular and molecular level.
- how the immune system recognizes and fights against pathogenic microorganisms including viruses, bacteria, and parasites.
- why lymphocytes tolerate self molecules.
- about function and dysfunction the intestinal immune system.
- immunopathology and inflammatory diseases.
ContentThe aim of lecture is to understand:
> How pathogens are recognized by the innate immune system
> Immune defense against various pathogens
> Immunology of the skin, lung and intestines
> Tumor immunology
> Migration and homing of immune cells
> tolerance and autoimmunity
> T cell memory
Lecture notesPresentations of the lecturers are available at the Moodle link
LiteratureRecommended: Kuby Immunology (Freeman)
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, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander, further lecturers
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 Link 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 credits2SA. 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 credits3.5PR. Berndt, M. A. Garcia Otalora
AbstractThis 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.
ObjectiveRecognizing 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.
ContentIntroduction 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 notesScripts will be handed out.
LiteratureTechnical literature will be provided in the lecture room.
Prerequisites / NoticeThe 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.
551-1132-00LBasic VirologyW2 credits1VK. Tobler, C. Fraefel
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
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 credits2VB. Nguyen, W.‑D. Hardt, 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, 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.
ContentImportant 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 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:
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)
227-0390-00LElements 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.
751-4805-00LRecent Advances in Biocommunication Restricted registration - show details
Number of participants limited to 25.
W3 credits2SC. De Moraes
AbstractStudents 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.
ObjectiveStudents 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.
551-1103-00LMicrobial Biochemistry Information W4 credits2VJ. Vorholt-Zambelli, J. Piel
AbstractThe 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.
ObjectiveThe lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms.
ContentImportant 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
Microbial autotrophy
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
LiteratureWill be provided during the course.
Elective Master Courses
NumberTitleTypeECTSHoursLecturers
551-0512-00LCurrent Topics in Molecular and Cellular Neurobiology Restricted registration - show details
Does not take place this semester.
Number of participants limited to 8
W2 credits1SU. Suter
AbstractThe course is a literature seminar or "journal club". Each Friday a student, or a member of the Suter Lab in the Institute of Molecular Health Sciences, will present a paper from the recent literature.
ObjectiveThe course introduces you to recent developments in the fields of cellular and molecular neurobiology. It also supports you to develop your skills in critically reading the scientific literature. You should be able to grasp what the authors wanted to learn e.g. their goals, why the authors chose the experimental approach they used, the strengths and weaknesses of the experiments and the data presented, and how the work fits into the wider literature in the field. You will present one paper yourself, which provides you with practice in public speaking.
ContentYou will present one paper yourself. Give an introduction to the field of the paper, then show and comment on the main results (all the papers we present are available online, so you can show original figures with a beamer). Finish with a summary of the main points and a discussion of their significance.
You are expected to take part in the discussion and to ask questions. To prepare for this you should read all the papers beforehand (they will be announced a week in advance of the presentation).
Lecture notesPresentations will be made available after the seminars.
LiteratureWe cover a range of themes related to development and neurobiology. Before starting your preparations, you are required to check with Laura Montani (Link), who helps you with finding an appropriate paper.
Prerequisites / NoticeYou must attend at least 80% of the journal clubs, and give a presentation of your own. At the end of the semester there will be a 30 minute oral exam on the material presented during the semester. The grade will be based on the exam (45%), your presentation (45%), and a contribution based on your active participation in discussion of other presentations (10%).
551-0224-00LAdvanced Proteomics Restricted registration - show details
For master students from the 2nd semester on, also doctoral candidates and post docs.
W4 credits6GP. Picotti, L. Gillet, A. Leitner, P. Pedrioli
AbstractGoal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine.
Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises.
ObjectiveTo discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology.
ContentBlock course teaching current methods for the acquisition and processing of proteomic datasets.
Prerequisites / NoticeNumber of people: Not exceeding 30.
Students from ETHZ, Uni Zurich and University of Basel
Non-ETH students must register at ETH Zurich as special students Link
Elective Concept Courses
NumberTitleTypeECTSHoursLecturers
752-4006-00LFood Microbiology IIW3 credits2VM. Loessner, J. Klumpp
AbstractThe lecture deals with basic (sometimes advanced) methods for detection and differentiation of (not only food-borne) microorganisms; production of foods by microbial fermentation; different approaches for the preservation of foods; and a short overview on food legals aspects and hygiene measures.
ObjectiveThe second part of this 1 year-lecture deals with basic (sometimes advanced) methods for detection and differentiation of (not only foodborne) microorgansims; production of foods by microbial fermentations; different approaches for the preservation of foods; and a short overview on legal aspects and hygiene control measures.
ContentDetection and Differentiation of Microorganisms
Culture Methods, Microscopy, Enrichment and Separation, Detection of intracellular Metabolites and Enzymes, Immunological Methods, Gene Probes and Microarrays, Nucleic Acid Amplification, Expression of Reportergenes, Typing Methods

Production of Foods with Microorganisms
Fermented Plant Products, Bread and Sour Dough, Fermented (alcoholic) Beverages, Fermented Milk Products, Fermented Meats, Traditional Fermented Foods, Coffee, Tea, Cacao, Tobacco, Fermentation Problems (Viruses, Antibiotics, Disinfectants)

Food Preservation I: Physical Methods
Low Water Activity, Low Temperature, Heat Treatment, High Pressure Treatment, Radiation

Food Preservation II: Chemical Methods
Natural Antimicrobial Substances, Smoking, Preservatives, Low pH, Modified Atmosphere Packaging

Food Preservation III: Biological Methods
Addition of Enzymes, Protective Cultures, Starter- and Ripening Cultures

Quality Assurance and Control
Legal Aspects and Regulations, Factory- and Personal Hygiene, Cleaning & Disinfection, GMP & HACCP
Lecture notesElectronic PDF copies of the presentation slides will be made available to all students.
LiteratureSuggestions in the first lecture
Prerequisites / NoticeThe lecture "Food Microbiology I" (or an equivalent course) is a prerequisite
529-0732-00LProteins and Lipids
Note for BSc Biology students: Only one of the two concept courses 529-0731-00 Nucleic Acids and Carbohydrates (autumn semester) or 529-0732-00 Proteins and Lipids (spring semester) can be counted for the Bachelor's degree.
W6 credits3GD. Hilvert
AbstractAn overview of the relationship between protein sequence, conformation and function.
ObjectiveOverview of the relationship between protein sequence, conformation and function.
ContentProteins, structures and properties, (bio)synthesis of polypeptides, protein folding and design, protein engineering, chemical modification of proteins, proteomics.
LiteratureGeneral Literature:
- T.E. Creighton: Proteins: Structures and Molecular Properties, 2nd Edition, H.W. Freeman and Company, New York, 1993.
- C. Branden, J. Tooze , Introduction to Protein Structure, Garland Publishing, New York, 1991.
- J. M. Berg, J. L. Tymoczko, L. Stryer: Biochemistry, 5th edition, H.W. Freeman and Company, New York, 2002.
- G.A. Petsko, D. Ringe: Protein Structure and Function, New Science Press Ltd., London, 2004.

Original Literature:
Citations from the original literature relevant to the individual lectures will be assigned weekly.
551-0326-00LCell Biology Information W6 credits4VS. Werner, H. Gehart, W. Kovacs, M. Schäfer, U. Suter, A. Wutz, further lecturers
AbstractThis Course introduces principle concepts, techniques, and experimental strategies used in modern Cell Biology. Major topics include: neuron-glia interactions in health and disease; mitochondrial dynamics; stem cell biology; growth factor action in development, tissue repair and disease; cell metabolism, in particular sensing and signaling mechanisms, cell organelles, and lipid metabolism.
Objective-To prepare the students for successful and efficient lab work by learning how to ask the right questions and to use the appropriate techniques in a research project.
-To convey knowledge about neuron-glia interactions in health and disease.
- To provide information on different types of stem cells and their function in health and disease
-To provide information on growth factor signaling in development, repair and disease and on the use of growth factors or their receptors as drug targets for major human diseases
-To convey knowledge on the mechanisms underlying repair of injured tissues
-To provide the students with an overview of mitochondrial dynamics.
-Providing an understanding of RNA processing reactions and their regulations.
-To provide a comprehensive understanding of metabolic sensing mechanisms occurring in different cell types and organelles in response to glucose, hormones, oxygen, nutrients as well as lipids, and to discuss downstream signaling pathways and cellular responses.
-To provide models explaining how disturbances in complex metabolic control networks and bioenergetics can lead to disease and to highlight latest experimental approaches to uncover the intricacies of metabolic control at the cellular and organismal level.
-Providing the background and context that foster cross-disciplinary scientific thinking.
551-0324-00LSystems Biology Information W6 credits4VP. Picotti, M. Claassen, U. Sauer, B. Snijder, B. Wollscheid
AbstractIntroduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects.
Objective- obtain an overview of global analytical methods
- obtain an overview of computational methods in systems biology
- understand the concepts of systems biology
ContentOverview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology.
Lecture notesno script
LiteratureThe course is not taught by a particular book, but some books are suggested for further reading:

- Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005
551-0320-00LCellular Biochemistry (Part II)W3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
551-0307-01LMolecular and Structural Biology II: Molecular Machines and Cellular Assemblies
D-BIOL students are obliged to take part I and part II as a two-semester course.
W3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course on advanced topics in Molecular Biology and Biochemistry will cover the structure and function of cellular assemblies. General topics in basic biochemistry will be further developed with examples of the function of large cellular machines involved in DNA packaging, translation, virus architecture, RNA processing, cell-cell interactions, and the molecular basis of CRISPER systems.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
literature:
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.
Elective Major: Cell Biology
Compulsory Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0326-00LCell Biology Information O6 credits4VS. Werner, H. Gehart, W. Kovacs, M. Schäfer, U. Suter, A. Wutz, further lecturers
AbstractThis Course introduces principle concepts, techniques, and experimental strategies used in modern Cell Biology. Major topics include: neuron-glia interactions in health and disease; mitochondrial dynamics; stem cell biology; growth factor action in development, tissue repair and disease; cell metabolism, in particular sensing and signaling mechanisms, cell organelles, and lipid metabolism.
Objective-To prepare the students for successful and efficient lab work by learning how to ask the right questions and to use the appropriate techniques in a research project.
-To convey knowledge about neuron-glia interactions in health and disease.
- To provide information on different types of stem cells and their function in health and disease
-To provide information on growth factor signaling in development, repair and disease and on the use of growth factors or their receptors as drug targets for major human diseases
-To convey knowledge on the mechanisms underlying repair of injured tissues
-To provide the students with an overview of mitochondrial dynamics.
-Providing an understanding of RNA processing reactions and their regulations.
-To provide a comprehensive understanding of metabolic sensing mechanisms occurring in different cell types and organelles in response to glucose, hormones, oxygen, nutrients as well as lipids, and to discuss downstream signaling pathways and cellular responses.
-To provide models explaining how disturbances in complex metabolic control networks and bioenergetics can lead to disease and to highlight latest experimental approaches to uncover the intricacies of metabolic control at the cellular and organismal level.
-Providing the background and context that foster cross-disciplinary scientific thinking.
Elective Compulsory Concept Courses
See D-BIOL Master Studies Guide
NumberTitleTypeECTSHoursLecturers
551-0324-00LSystems Biology Information W6 credits4VP. Picotti, M. Claassen, U. Sauer, B. Snijder, B. Wollscheid
AbstractIntroduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects.
Objective- obtain an overview of global analytical methods
- obtain an overview of computational methods in systems biology
- understand the concepts of systems biology
ContentOverview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology.
Lecture notesno script
LiteratureThe course is not taught by a particular book, but some books are suggested for further reading:

- Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005
551-0320-00LCellular Biochemistry (Part II)W3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
551-0318-00LImmunology IIW3 credits2VA. Oxenius, M. Kopf, S. R. Leibundgut, E. Slack, further lecturers
AbstractIntroduction into the cellular and molecular basis of the immune system and immune responses against diverse pathogens, tumors, transplants, and self (autoimmunity)
ObjectiveThe lectures will provide a detailed understanding:
- how innate and adaptive immune responses interact at the cellular and molecular level.
- how the immune system recognizes and fights against pathogenic microorganisms including viruses, bacteria, and parasites.
- why lymphocytes tolerate self molecules.
- about function and dysfunction the intestinal immune system.
- immunopathology and inflammatory diseases.
ContentThe aim of lecture is to understand:
> How pathogens are recognized by the innate immune system
> Immune defense against various pathogens
> Immunology of the skin, lung and intestines
> Tumor immunology
> Migration and homing of immune cells
> tolerance and autoimmunity
> T cell memory
Lecture notesPresentations of the lecturers are available at the Moodle link
LiteratureRecommended: Kuby Immunology (Freeman)
376-0209-00LMolecular Disease MechanismsW6 credits4VC. Wolfrum, H. Gahlon, M. Kopf
AbstractIn this course the mechanisms of disease development will be studied. Main topics will be:

1. Influence of environmental factors with an emphasis on inflammation and the immune response.
2. Mechanisms underlying disease progression in metabolic disorders, integrating genetic and environmental factors.
3. Mechanisms underlying disease progression in cancer, integrating genetic and environment
ObjectiveTo understand the mechanisms governing disease development with a special emphasis on genetic and environmental associated components
Lecture notesAll information can be found at:

Link

The enrollment key will be provided by email
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
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, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander, further lecturers
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 Link 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.
551-0512-00LCurrent Topics in Molecular and Cellular Neurobiology Restricted registration - show details
Does not take place this semester.
Number of participants limited to 8
W2 credits1SU. Suter
AbstractThe course is a literature seminar or "journal club". Each Friday a student, or a member of the Suter Lab in the Institute of Molecular Health Sciences, will present a paper from the recent literature.
ObjectiveThe course introduces you to recent developments in the fields of cellular and molecular neurobiology. It also supports you to develop your skills in critically reading the scientific literature. You should be able to grasp what the authors wanted to learn e.g. their goals, why the authors chose the experimental approach they used, the strengths and weaknesses of the experiments and the data presented, and how the work fits into the wider literature in the field. You will present one paper yourself, which provides you with practice in public speaking.
ContentYou will present one paper yourself. Give an introduction to the field of the paper, then show and comment on the main results (all the papers we present are available online, so you can show original figures with a beamer). Finish with a summary of the main points and a discussion of their significance.
You are expected to take part in the discussion and to ask questions. To prepare for this you should read all the papers beforehand (they will be announced a week in advance of the presentation).
Lecture notesPresentations will be made available after the seminars.
LiteratureWe cover a range of themes related to development and neurobiology. Before starting your preparations, you are required to check with Laura Montani (Link), who helps you with finding an appropriate paper.
Prerequisites / NoticeYou must attend at least 80% of the journal clubs, and give a presentation of your own. At the end of the semester there will be a 30 minute oral exam on the material presented during the semester. The grade will be based on the exam (45%), your presentation (45%), and a contribution based on your active participation in discussion of other presentations (10%).
551-1118-00LCutting Edge Topics: Immunology and Infection Biology II Information W2 credits2SA. 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.
551-1310-00LA Problem-Based Approach to Cellular Biochemistry Restricted registration - show details
Number of participants limited to 12.
W6 credits2GM. Peter, V. Korkhov, G. Neurohr, V. Panse, A. E. Smith, F. van Drogen
AbstractIndependent, guided acquisition of a defined area of research, identification of key open questions, development of an experimental strategy to address a defined question, and formulation of this strategy within the framework of a research grant.
ObjectiveWorking independently, students will acquire an overview of a defined research area, and identify important open questions. In addition, they will develop an experimental strategy to address a defined question, and to formulate this strategy within the framework of a research grant.
ContentThe students will work in groups of two to three, in close contact with a tutor (ETH Prof or senior scientist). A research overview with open questions and a research grant will be developed independently by the students, with guidance from the tutor through regular mandatory meetings. The students will write both the research overview with open questions and the grant in short reports, and present them to their colleagues.
LiteratureThe identification of appropriate literature is a component of the course.
Prerequisites / NoticeThis course will be taught in English, and requires extensive independent work.
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
551-0224-00LAdvanced Proteomics Restricted registration - show details
For master students from the 2nd semester on, also doctoral candidates and post docs.
W4 credits6GP. Picotti, L. Gillet, A. Leitner, P. Pedrioli
AbstractGoal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine.
Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises.
ObjectiveTo discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology.
ContentBlock course teaching current methods for the acquisition and processing of proteomic datasets.
Prerequisites / NoticeNumber of people: Not exceeding 30.
Students from ETHZ, Uni Zurich and University of Basel
Non-ETH students must register at ETH Zurich as special students Link
551-1126-00LTechnologies in Molecular MicrobiologyW4 credits2VB. Nguyen, W.‑D. Hardt, 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, 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.
ContentImportant 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 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:
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)
551-0338-00LCurrent Approaches in Single Cell Analysis (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BME327

Mind the enrolment deadlines at UZH:
Link
W2 credits2VB. Bodenmiller, University lecturers
AbstractIn this lecture, we will discuss the most important single cell
approaches, the questions they can address and current developments. We will cover single cell: genomics, transcriptomics, proteomics (CyTOF mass cytometry), metabolomics and highly multiplexed imaging. Finally, we will also discuss the latest approaches for the analysis of such generated highly multiplexed single cell data.
ObjectiveOn completion of this module the students should be able to:
- explain the basic principles of single cell analysis techniques
- identify and justify the limitations of the current single cell
technologies and suggest reasonable improvements
- know the basic challenges in data analysis imposed by the complex
multi parameter data.
Key skills:
On completion of this module the students should be able to:
- summarize and discuss the impact these technologies have on biology
and medicine
- design biological and biomedical experiments for which single cell
analysis is essential
ContentCurrently single cell analysis approaches revolutionize the way we study and understand biological systems. In all biological and biomedical settings, cell populations and tissues are highly heterogeneous; this heterogeneity plays a critical role in basic biological processes such as cell cycle, development and organismic function, but is also a major player in disease, e.g. for cancer development, diagnosis and treatment.
Currently, single cell analysis techniques are rapidly developing and
find broad application, as the single cell measurements not only enable
to study cell specific functions, but often reveal unexpected biological
mechanisms in so far (assumed) well understood biological processes.
In this lecture, we will discuss the most important single cell approaches, the questions they can address and current developments. We will cover single cell genomics, single cell transcriptomics, single cell proteomics (CyTOF mass cytometry), single cell metabolomics and highly multiplexed single cell imaging. Finally, we will also discuss the latest approaches for the analysis of such generated highly multiplexed single cell data.
551-1404-00LRNA and Proteins: Post-Transcriptional Regulation of Gene Expression (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BCH252

Mind the enrolment deadlines at UZH:
Link
W3 credits2VUniversity lecturers
AbstractThe course introduces the cellular processes and molecular mechanisms involved in regulating genome expression at the post-transcriptional level.
Topics will include :
-RNA processing, and transport;
-protein synthesis and translational control, trafficking and degradation;
-RNA-guided regulation (RNA interference, microRNAs);
-molecular surveillance and quality control mechanisms
Objective-Outline the cellular processes
used by eukaryotic and prokaryotic cells
to control gene expression at the post-
transcriptional level.
-Describe the molecular mechanisms
underlying post-transcriptional gene
regulation
-Identify experimental approaches
used to study post-transcriptional gene
regulation and describe their strengths
and weaknesses.
551-1412-00LMolecular and Structural Biology IV: Visualizing Macromolecules by X-Ray Crystallography and EMW4 credits2VN. Ban, D. Böhringer, T. Ishikawa, M. A. Leibundgut, K. Locher, M. Pilhofer, K. Wüthrich, further lecturers
AbstractThis course provides an in-depth discussion of two main methods to determine the 3D structures of macromolecules and complexes at high resolution: X-ray crystallography and cryo-electron microscopy. Both techniques result in electron density maps that are interpreted by atomic models.
ObjectiveStudents will obtain the theoretical background to understand structure determination techniques employed in X-ray crystallography and electron microscopy, including diffraction theory, crystal growth and analysis, reciprocal space calculations, interpretation of electron density, structure building and refinement as well as validation. The course will also provide an introduction into the use of cryo-electron tomography to visualize complex cellular substructures at sub-nanometer resolutions, effectively bridging the resolution gap between optical microscopy and single particle cryo-electron microscopy. Lectures will be complemented with practical sessions where students will have a chance to gain hands on experience with sample preparation, data processing and structure building and refinement.
Content- History of Structural Molecular Biology

- X-ray diffraction from macromolecular crystals

- Data collection and statistics, phasing methods

- Crystal symmetry and space groups

- X-ray data processing

- Principle of cryo-EM for biological macromolecules I, including hardware of TEM and detectors, image formation principle (phase contrast, spherical aberration, CTF), 3D reconstruction (central-section theorem, backprojection, missing information)

- Single particle analysis, including principle (projection matching, random conical tilt, angular reconstitution)

- Tomography I, including basics and subtomogram averaging

- Tomography - recent techniques, including cryo-FIB
- EM specimen preparation (cryo, negative stain), initial EM data processing

- EM and X-ray structure building, refinement, validation and interpretation

- Model building and refinement
551-1414-00LMolecular and Structural Biology V: Studying Macromolecules by NMR and EPRW4 credits2VF. Allain, A. D. Gossert, G. Jeschke, K. Wüthrich
AbstractThe course provides an overview of experimental methods for studying function and structure of macromolecules at atomic resolution in solution. The two main methods used are Nuclear Magnetic Resonance (NMR) spectroscopy and Electron Paramagnetic Resonance (EPR) spectroscopy.
ObjectiveInsight into the methodology, areas of application and limitations of these two methods for studying biological macromolecules. Practical exercises with spectra to have hands on understanding of the methodology.
ContentPart I: Historical overview of structural biology.
Part II: Basic concepts of NMR and initial examples of applications.
2D NMR and isotope labeling for studying protein function and molecular interactions at atomic level.
Studies of dynamic processes of proteins in solution.
Approaches to study large particles.
Methods for determination of protein structures in solution.
Part III: NMR methods for structurally characterizing RNA and protein-RNA complexes.
Part IV: EPR of biomolecules
Literature1) Wüthrich, K. NMR of Proteins and Nucleic Acids, Wiley-Interscience.
2) Dominguez et al, Prog Nucl Magn Reson Spectrosc. 2011 Feb;58(1-2):1-61.
3) Duss O et al, Methods Enzymol. 2015;558:279-331.
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.
376-1306-00LClinical Neuroscience (University of Zurich) Information
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BIO389

Mind the enrolment deadlines at UZH:
Link
W3 credits3VG. Schratt, University lecturers
AbstractThe lecture series "Clinical Neuroscience" presents a comprehensive, condensed overview of the most important neurological diseases, their clinical presentation, diagnosis, therapy options and possible causes. Patient demonstrations (Übungen) follow every lecture that is dedicated to a particular disease.
ObjectiveBy the end of this module students should be able to:
- demonstrate their understanding and deep knowledge concerning the main neurological diseases
- identify and explain the different clinical presentation of these diseases, the methodology of diagnosis and the current therapies available
- summarize and critically review scientific literature efficiently and effectively
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.
551-1103-00LMicrobial Biochemistry Information W4 credits2VJ. Vorholt-Zambelli, J. Piel
AbstractThe 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.
ObjectiveThe lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms.
ContentImportant 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
Microbial autotrophy
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
LiteratureWill be provided during the course.
701-1480-00LEvolutionary Developmental Biology Restricted registration - show details
Number of participants limited to 24.
Waiting list will be deleted after 05.03.2021.
W3 credits1SM. La Fortezza, G. Velicer
AbstractStudents will be introduced to fundamental concepts and current open questions in the field of evolutionary developmental biology (Evo-Devo) primarily through reading, analysing and jointly discussing key literature.
ObjectiveThe course aims to expose students to major conceptual themes of the Evo-Devo field through discussion of key papers and to active areas of current Evo-Devo research. At the end of the course, students should be able to present, think critically about and discuss key Evo-Devo concepts.
ContentEvolutionary developmental biology (Evo-Devo) is a multidisciplinary field that studies the interplay between developmental and evolutionary processes. Major questions include: How do developmental systems evolve and diversify? Do developmental programs influence their own future evolution, and how? How does ecology affect the evolution of developmental programs, and vice versa? Fascinating and experimentally challenging, Evo-Devo first empirically emerged from comparative embryology. However, in recent decades this discipline has grown considerably to interconnect with many other fields, from genetics to sociobiology to microbiology. The course will examine questions such as those above and touch on the ongoing inter-disciplinary integration of Evo-Devo, including its interface with ecology (“Eco-Evo-Devo”) and the integration of aggregative microbial developmental systems into the field.
LiteratureRelevant literature:

Müller, G. (2007). Evo–devo: extending the evolutionary synthesis. Nature Reviews Genetics 8, 943-949. Link

Abouheif, E., et al (2014). Eco-evo-devo: the time has come. Advances in experimental medicine and biology 781, 107-25. Link

Moczek, A et al (2015). The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evolution & development 17, 198-219. Link

Gilbert, S. (2019). Evolutionary transitions revisited: Holobiont evo‐devo. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 12, 117762501877479 - 8. Link
Prerequisites / NoticeSignificant basic knowledge in especially evolutionary biology and developmental biology, and also cell biology and genetics, will be advantageous for readily understanding the course material.
Elective Major: Molecular Health Sciences
Compulsory Concept Courses
NumberTitleTypeECTSHoursLecturers
376-0209-00LMolecular Disease MechanismsO6 credits4VC. Wolfrum, H. Gahlon, M. Kopf
AbstractIn this course the mechanisms of disease development will be studied. Main topics will be:

1. Influence of environmental factors with an emphasis on inflammation and the immune response.
2. Mechanisms underlying disease progression in metabolic disorders, integrating genetic and environmental factors.
3. Mechanisms underlying disease progression in cancer, integrating genetic and environment
ObjectiveTo understand the mechanisms governing disease development with a special emphasis on genetic and environmental associated components
Lecture notesAll information can be found at:

Link

The enrollment key will be provided by email
Elective Compulsory Concept Courses
See D-BIOL Master Studies Guide
NumberTitleTypeECTSHoursLecturers
551-0326-00LCell Biology Information W6 credits4VS. Werner, H. Gehart, W. Kovacs, M. Schäfer, U. Suter, A. Wutz, further lecturers
AbstractThis Course introduces principle concepts, techniques, and experimental strategies used in modern Cell Biology. Major topics include: neuron-glia interactions in health and disease; mitochondrial dynamics; stem cell biology; growth factor action in development, tissue repair and disease; cell metabolism, in particular sensing and signaling mechanisms, cell organelles, and lipid metabolism.
Objective-To prepare the students for successful and efficient lab work by learning how to ask the right questions and to use the appropriate techniques in a research project.
-To convey knowledge about neuron-glia interactions in health and disease.
- To provide information on different types of stem cells and their function in health and disease
-To provide information on growth factor signaling in development, repair and disease and on the use of growth factors or their receptors as drug targets for major human diseases
-To convey knowledge on the mechanisms underlying repair of injured tissues
-To provide the students with an overview of mitochondrial dynamics.
-Providing an understanding of RNA processing reactions and their regulations.
-To provide a comprehensive understanding of metabolic sensing mechanisms occurring in different cell types and organelles in response to glucose, hormones, oxygen, nutrients as well as lipids, and to discuss downstream signaling pathways and cellular responses.
-To provide models explaining how disturbances in complex metabolic control networks and bioenergetics can lead to disease and to highlight latest experimental approaches to uncover the intricacies of metabolic control at the cellular and organismal level.
-Providing the background and context that foster cross-disciplinary scientific thinking.
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
551-1310-00LA Problem-Based Approach to Cellular Biochemistry Restricted registration - show details
Number of participants limited to 12.
W6 credits2GM. Peter, V. Korkhov, G. Neurohr, V. Panse, A. E. Smith, F. van Drogen
AbstractIndependent, guided acquisition of a defined area of research, identification of key open questions, development of an experimental strategy to address a defined question, and formulation of this strategy within the framework of a research grant.
ObjectiveWorking independently, students will acquire an overview of a defined research area, and identify important open questions. In addition, they will develop an experimental strategy to address a defined question, and to formulate this strategy within the framework of a research grant.
ContentThe students will work in groups of two to three, in close contact with a tutor (ETH Prof or senior scientist). A research overview with open questions and a research grant will be developed independently by the students, with guidance from the tutor through regular mandatory meetings. The students will write both the research overview with open questions and the grant in short reports, and present them to their colleagues.
LiteratureThe identification of appropriate literature is a component of the course.
Prerequisites / NoticeThis course will be taught in English, and requires extensive independent work.
551-0512-00LCurrent Topics in Molecular and Cellular Neurobiology Restricted registration - show details
Does not take place this semester.
Number of participants limited to 8
W2 credits1SU. Suter
AbstractThe course is a literature seminar or "journal club". Each Friday a student, or a member of the Suter Lab in the Institute of Molecular Health Sciences, will present a paper from the recent literature.
ObjectiveThe course introduces you to recent developments in the fields of cellular and molecular neurobiology. It also supports you to develop your skills in critically reading the scientific literature. You should be able to grasp what the authors wanted to learn e.g. their goals, why the authors chose the experimental approach they used, the strengths and weaknesses of the experiments and the data presented, and how the work fits into the wider literature in the field. You will present one paper yourself, which provides you with practice in public speaking.
ContentYou will present one paper yourself. Give an introduction to the field of the paper, then show and comment on the main results (all the papers we present are available online, so you can show original figures with a beamer). Finish with a summary of the main points and a discussion of their significance.
You are expected to take part in the discussion and to ask questions. To prepare for this you should read all the papers beforehand (they will be announced a week in advance of the presentation).
Lecture notesPresentations will be made available after the seminars.
LiteratureWe cover a range of themes related to development and neurobiology. Before starting your preparations, you are required to check with Laura Montani (Link), who helps you with finding an appropriate paper.
Prerequisites / NoticeYou must attend at least 80% of the journal clubs, and give a presentation of your own. At the end of the semester there will be a 30 minute oral exam on the material presented during the semester. The grade will be based on the exam (45%), your presentation (45%), and a contribution based on your active participation in discussion of other presentations (10%).
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
701-1350-00LCase Studies in Environment and HealthW4 credits2VK. McNeill, T. Julian, M. Scheringer
AbstractThis course will focus on a few individual chemicals and pathogens from different standpoints: their basic chemistry or biology, their environmental behavior, (eco)toxicology, and human health impacts. The course will draw out the common points in each chemical or pathogen's history.
ObjectiveThis course aims to illustrate how the individual properties of chemicals and pathogens along with societal pressures lead to environmental and human health crises. The ultimate goal of the course is to identify common aspects that will improve prediction of environmental crises before they occur. Students are expected to participate actively in the course, which includes the critical reading of the pertinent literature and class presentations.
ContentEach class will feature the case study of a different chemical or pathogen that have had a profound effect on human health and the environment. The instructors will present eight to ten of these and the students will present a poster on their own pollutant or pathogen in groups of two. Students will be expected to contribute to the in class discussions and, on their selected topics, to lead the discussion.
Lecture notesHandouts will be provided as needed.
LiteratureHandouts will be provided as needed.
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, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander, further lecturers
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 Link 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.
227-0396-00LEXCITE Interdisciplinary Summer School on Bio-Medical Imaging Restricted registration - show details
The school admits 60 MSc or PhD students with backgrounds in biology, chemistry, mathematics, physics, computer science or engineering based on a selection process.

Students have to apply for acceptance. To apply a curriculum vitae and an application letter need to be submitted.
Further information can be found at: Link.
W4 credits6GS. Kozerke, G. Csúcs, J. Klohs-Füchtemeier, S. F. Noerrelykke, M. P. Wolf
AbstractTwo-week summer school organized by EXCITE (Center for EXperimental & Clinical Imaging TEchnologies Zurich) on biological and medical imaging. The course covers X-ray imaging, magnetic resonance imaging, nuclear imaging, ultrasound imaging, optoacoustic imaging, infrared and optical microscopy, electron microscopy, image processing and analysis.
ObjectiveStudents understand basic concepts and implementations of biological and medical imaging. Based on relative advantages and limitations of each method they can identify preferred procedures and applications. Common foundations and conceptual differences of the methods can be explained.
ContentTwo-week summer school on biological and medical imaging. The course covers concepts and implementations of X-ray imaging, magnetic resonance imaging, nuclear imaging, ultrasound imaging, optoacoustic imaging, infrared and optical microscopy and electron microscopy. Multi-modal and multi-scale imaging and supporting technologies such as image analysis and modeling are discussed. Dedicated modules for physical and life scientists taking into account the various backgrounds are offered.
Lecture notesPresentation slides, Web links
Prerequisites / NoticeThe school admits 60 MSc or PhD students with backgrounds in biology, chemistry, mathematics, physics, computer science or engineering based on a selection process. To apply a curriculum vitae, a statement of purpose and applicants references need to be submitted. Further information can be found at: Link
227-0946-00LMolecular Imaging - Basic Principles and Biomedical ApplicationsW3 credits2V + 1AD. Razansky
AbstractConcept: What is molecular imaging.
Discussion/comparison of the various imaging modalities used in molecular imaging.
Design of target specific probes: specificity, delivery, amplification strategies.
Biomedical Applications.
ObjectiveMolecular Imaging is a rapidly emerging discipline that translates concepts developed in molecular biology and cellular imaging to in vivo imaging in animals and ultimatly in humans. Molecular imaging techniques allow the study of molecular events in the full biological context of an intact organism and will therefore become an indispensable tool for biomedical research.
ContentConcept: What is molecular imaging.
Discussion/comparison of the various imaging modalities used in molecular imaging.
Design of target specific probes: specificity, delivery, amplification strategies.
Biomedical Applications.
551-1132-00LBasic VirologyW2 credits1VK. Tobler, C. Fraefel
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.
376-1306-00LClinical Neuroscience (University of Zurich) Information
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BIO389

Mind the enrolment deadlines at UZH:
Link
W3 credits3VG. Schratt, University lecturers
AbstractThe lecture series "Clinical Neuroscience" presents a comprehensive, condensed overview of the most important neurological diseases, their clinical presentation, diagnosis, therapy options and possible causes. Patient demonstrations (Übungen) follow every lecture that is dedicated to a particular disease.
ObjectiveBy the end of this module students should be able to:
- demonstrate their understanding and deep knowledge concerning the main neurological diseases
- identify and explain the different clinical presentation of these diseases, the methodology of diagnosis and the current therapies available
- summarize and critically review scientific literature efficiently and effectively
376-1392-00LMechanobiology: Implications for Development, Regeneration and Tissue EngineeringW3 credits2GG. Shivashankar
AbstractThis course will emphasize the importance of mechanobiology to cell determination and behavior. Its importance to regenerative medicine and tissue engineering will also be addressed. Finally, this course will discuss how age and disease adversely alter major mechanosensitive developmental programs.
ObjectiveThe goal of this course is to provide an introduction to the emerging field of “Mechanobiology”.
ContentWe will focus on cells and tissues and introduce the major methods employed in uncovering the principles of mechanobiology. We will first discuss the cellular mechanotransduction mechanisms and how they regulate genomes. This will be followed by an analysis of the mechanobiological underpinnings of cellular differentiation, cell-state transitions and homeostasis. Developing on this understanding, we will then introduce the mechanobiological basis of cellular ageing and its impact on tissue regeneration, including neurodegeneration and musculoskeletal systems. We will then highlight the importance of tissue organoid models as routes to regenerative medicine. We will also discuss the impact of mechanobiology on host-pathogen interactions. Finally, we will introduce the broad area of mechanopathology and the development of cell-state biomarkers as readouts of tissue homeostasis and disease pathologies. Collectively, the course will provide a quantitate framework to understand the mechanobiological processes at cellular scale and how they intersect with tissue function and diseases.

Lecture 1: Introduction to the course: forces, signalling and cell behaviour
Lecture 2: Methods to engineer and sense mechanobiological processes
Lecture 3: Mechanisms of cellular mechanosensing and cytoskeletal remodelling
Lecture 4: Nuclear mechanotransduction pathways
Lecture 5: Genome organization, regulation and genome integrity
Lecture 6: Differentiation, development and reprogramming
Lecture 7: Tissue microenvironment, cell behaviour and homeostasis
Lecture 8: Cellular aging and tissue regeneration
Lecture 9: Neurodegeneration and regeneration
Lecture 10: Musculoskeletal systems and regeneration
Lecture 11: Tissue organoid models and regenerative medicine
Lecture 12: Microbial systems and host-pathogen interactions
Lecture13: Mechanopathology and cell-state biomarkers
Lecture14: Concluding lecture and case studies
Lecture notesn/a
LiteratureTopical Scientific Manuscripts
551-0364-00LFunctional Genomics
Information for UZH students:
Enrolment to this course unit only possible at ETH. No enrolment to module BIO 254 at UZH.

Please mind the ETH enrolment deadlines for UZH students: Link
W3 credits2VC. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, further lecturers
AbstractFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data.
ObjectiveFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. Such data provide the basis for systems biology efforts to elucidate the structure, dynamics and regulation of cellular networks.
ContentThe curriculum of the Functional Genomics course emphasizes an in depth understanding of new technology platforms for modern genomics and advanced genetics, including the application of functional genomics approaches such as advanced sequencing, proteomics, metabolomics, clustering and classification. Students will learn quality controls and standards (benchmarking) that apply to the generation of quantitative data and will be able to analyze and interpret these data. The training obtained in the Functional Genomics course will be immediately applicable to experimental research and design of systems biology projects.
Prerequisites / NoticeThe Functional Genomics course will be taught in English.
551-0338-00LCurrent Approaches in Single Cell Analysis (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BME327

Mind the enrolment deadlines at UZH:
Link
W2 credits2VB. Bodenmiller, University lecturers
AbstractIn this lecture, we will discuss the most important single cell
approaches, the questions they can address and current developments. We will cover single cell: genomics, transcriptomics, proteomics (CyTOF mass cytometry), metabolomics and highly multiplexed imaging. Finally, we will also discuss the latest approaches for the analysis of such generated highly multiplexed single cell data.
ObjectiveOn completion of this module the students should be able to:
- explain the basic principles of single cell analysis techniques
- identify and justify the limitations of the current single cell
technologies and suggest reasonable improvements
- know the basic challenges in data analysis imposed by the complex
multi parameter data.
Key skills:
On completion of this module the students should be able to:
- summarize and discuss the impact these technologies have on biology
and medicine
- design biological and biomedical experiments for which single cell
analysis is essential
ContentCurrently single cell analysis approaches revolutionize the way we study and understand biological systems. In all biological and biomedical settings, cell populations and tissues are highly heterogeneous; this heterogeneity plays a critical role in basic biological processes such as cell cycle, development and organismic function, but is also a major player in disease, e.g. for cancer development, diagnosis and treatment.
Currently, single cell analysis techniques are rapidly developing and
find broad application, as the single cell measurements not only enable
to study cell specific functions, but often reveal unexpected biological
mechanisms in so far (assumed) well understood biological processes.
In this lecture, we will discuss the most important single cell approaches, the questions they can address and current developments. We will cover single cell genomics, single cell transcriptomics, single cell proteomics (CyTOF mass cytometry), single cell metabolomics and highly multiplexed single cell imaging. Finally, we will also discuss the latest approaches for the analysis of such generated highly multiplexed single cell data.
551-1404-00LRNA and Proteins: Post-Transcriptional Regulation of Gene Expression (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BCH252

Mind the enrolment deadlines at UZH:
Link
W3 credits2VUniversity lecturers
AbstractThe course introduces the cellular processes and molecular mechanisms involved in regulating genome expression at the post-transcriptional level.
Topics will include :
-RNA processing, and transport;
-protein synthesis and translational control, trafficking and degradation;
-RNA-guided regulation (RNA interference, microRNAs);
-molecular surveillance and quality control mechanisms
Objective-Outline the cellular processes
used by eukaryotic and prokaryotic cells
to control gene expression at the post-
transcriptional level.
-Describe the molecular mechanisms
underlying post-transcriptional gene
regulation
-Identify experimental approaches
used to study post-transcriptional gene
regulation and describe their strengths
and weaknesses.
636-0111-00LSynthetic Biology I
Attention: This course was offered in previous semesters with the number: 636-0002-00L "Synthetic Biology I". Students that already passed course 636-0002-00L cannot receive credits for course 636-0111-00L.
W4 credits3GS. Panke, J. Stelling
AbstractTheoretical & practical introduction into the design of dynamic biological systems at different levels of abstraction, ranging from biological fundamentals of systems design (introduction to bacterial gene regulation, elements of transcriptional & translational control, advanced genetic engineering) to engineering design principles (standards, abstractions) mathematical modelling & systems desig
ObjectiveAfter the course, students will be able to theoretically master the biological and engineering fundamentals required for biological design to be able to participate in the international iGEM competition (see Link).
ContentThe overall goal of the course is to familiarize the students with the potential, the requirements and the problems of designing dynamic biological elements that are of central importance for manipulating biological systems, primarily (but not exclusively) prokaryotic systems. Next, the students will be taken through a number of successful examples of biological design, such as toggle switches, pulse generators, and oscillating systems, and apply the biological and engineering fundamentals to these examples, so that they get hands-on experience on how to integrate the various disciplines on their way to designing biological systems.
Lecture notesHandouts during classes.
LiteratureMark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press
Uri Alon, An Introduction to Systems Biology, Chapman & Hall
Prerequisites / Notice1) Though we do not place a formal requirement for previous participation in particular courses, we expect all participants to be familiar with a certain level of biology and of mathematics. Specifically, there will be material for self study available on Link as of mid January, and everybody is expected to be fully familiar with this material BEFORE THE CLASS BEGINS to be able to follow the different lectures. Please contact Link for access to material
2) The course is also thought as a preparation for the participation in the international iGEM synthetic biology summer competition (Link, Link). This competition is also the contents of the course Synthetic Biology II. Link
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.
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.
Elective Major: Biochemistry
Compulsory Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0320-00LCellular Biochemistry (Part II)O3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
Compulsory Master Course
NumberTitleTypeECTSHoursLecturers
551-1310-00LA Problem-Based Approach to Cellular Biochemistry Restricted registration - show details
Number of participants limited to 12.
O6 credits2GM. Peter, V. Korkhov, G. Neurohr, V. Panse, A. E. Smith, F. van Drogen
AbstractIndependent, guided acquisition of a defined area of research, identification of key open questions, development of an experimental strategy to address a defined question, and formulation of this strategy within the framework of a research grant.
ObjectiveWorking independently, students will acquire an overview of a defined research area, and identify important open questions. In addition, they will develop an experimental strategy to address a defined question, and to formulate this strategy within the framework of a research grant.
ContentThe students will work in groups of two to three, in close contact with a tutor (ETH Prof or senior scientist). A research overview with open questions and a research grant will be developed independently by the students, with guidance from the tutor through regular mandatory meetings. The students will write both the research overview with open questions and the grant in short reports, and present them to their colleagues.
LiteratureThe identification of appropriate literature is a component of the course.
Prerequisites / NoticeThis course will be taught in English, and requires extensive independent work.
Elective Compulsory Concept Courses
See D-BIOL Master Studies Guide
NumberTitleTypeECTSHoursLecturers
551-0326-00LCell Biology Information W6 credits4VS. Werner, H. Gehart, W. Kovacs, M. Schäfer, U. Suter, A. Wutz, further lecturers
AbstractThis Course introduces principle concepts, techniques, and experimental strategies used in modern Cell Biology. Major topics include: neuron-glia interactions in health and disease; mitochondrial dynamics; stem cell biology; growth factor action in development, tissue repair and disease; cell metabolism, in particular sensing and signaling mechanisms, cell organelles, and lipid metabolism.
Objective-To prepare the students for successful and efficient lab work by learning how to ask the right questions and to use the appropriate techniques in a research project.
-To convey knowledge about neuron-glia interactions in health and disease.
- To provide information on different types of stem cells and their function in health and disease
-To provide information on growth factor signaling in development, repair and disease and on the use of growth factors or their receptors as drug targets for major human diseases
-To convey knowledge on the mechanisms underlying repair of injured tissues
-To provide the students with an overview of mitochondrial dynamics.
-Providing an understanding of RNA processing reactions and their regulations.
-To provide a comprehensive understanding of metabolic sensing mechanisms occurring in different cell types and organelles in response to glucose, hormones, oxygen, nutrients as well as lipids, and to discuss downstream signaling pathways and cellular responses.
-To provide models explaining how disturbances in complex metabolic control networks and bioenergetics can lead to disease and to highlight latest experimental approaches to uncover the intricacies of metabolic control at the cellular and organismal level.
-Providing the background and context that foster cross-disciplinary scientific thinking.
551-0307-01LMolecular and Structural Biology II: Molecular Machines and Cellular Assemblies
D-BIOL students are obliged to take part I and part II as a two-semester course.
W3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course on advanced topics in Molecular Biology and Biochemistry will cover the structure and function of cellular assemblies. General topics in basic biochemistry will be further developed with examples of the function of large cellular machines involved in DNA packaging, translation, virus architecture, RNA processing, cell-cell interactions, and the molecular basis of CRISPER systems.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
literature:
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
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
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, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander, further lecturers
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 Link 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.
551-1402-00LMolecular and Structural Biology VI: Biophysical Analysis of Macromolecular Mechanisms
This course is strongly recommended for the Masters Major "Biology and Biophysics".
W4 credits2VR. Glockshuber, T. Ishikawa, S. Jonas, B. Schuler, E. Weber-Ban
AbstractThe course is focussed on biophysical methods for characterising conformational transitions and reaction mechanisms of proteins and biological mecromolecules, with focus on methods that have not been covered in the Biology Bachelor Curriculum.
ObjectiveThe goal of the course is to give the students a broad overview on biopyhsical techniques available for studying conformational transitions and complex reaction mechanisms of biological macromolecules. The course is particularly suited for students enrolled in the Majors "Structural Biology and Biophysics", "Biochemistry" and "Chemical Biology" of the Biology MSc curriculum, as well as for MSc students of Chemistry and Interdisciplinary Natural Sciences".
ContentThe biophysical methods covered in the course include advanced reaction kinetics, methods for the thermodynamic and kinetic analysis of protein-ligand interactions, static and dynamic light scattering, analytical ultracentrifugation, spectroscopic techniques such as fluorescence anisotropy, fluorescence resonance energy transfer (FRET) and single molecule fluorescence spectrosopy, modern electron microscopy techniques, atomic force microscopy, and isothermal and differential scanning calorimetry.
Lecture notesCourse material from the individual lecturers wil be made available at the sharepoint website

Link
Prerequisites / NoticeFinished BSc curriculum in Biology, Chemistry or Interdisciplinary Natural Sciences. The course is also adequate for doctoral students with research projects in structural biology, biophysics, biochemistry and chemical biology.
551-0224-00LAdvanced Proteomics Restricted registration - show details
For master students from the 2nd semester on, also doctoral candidates and post docs.
W4 credits6GP. Picotti, L. Gillet, A. Leitner, P. Pedrioli
AbstractGoal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine.
Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises.
ObjectiveTo discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology.
ContentBlock course teaching current methods for the acquisition and processing of proteomic datasets.
Prerequisites / NoticeNumber of people: Not exceeding 30.
Students from ETHZ, Uni Zurich and University of Basel
Non-ETH students must register at ETH Zurich as special students Link
551-0364-00LFunctional Genomics
Information for UZH students:
Enrolment to this course unit only possible at ETH. No enrolment to module BIO 254 at UZH.

Please mind the ETH enrolment deadlines for UZH students: Link
W3 credits2VC. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, further lecturers
AbstractFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data.
ObjectiveFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. Such data provide the basis for systems biology efforts to elucidate the structure, dynamics and regulation of cellular networks.
ContentThe curriculum of the Functional Genomics course emphasizes an in depth understanding of new technology platforms for modern genomics and advanced genetics, including the application of functional genomics approaches such as advanced sequencing, proteomics, metabolomics, clustering and classification. Students will learn quality controls and standards (benchmarking) that apply to the generation of quantitative data and will be able to analyze and interpret these data. The training obtained in the Functional Genomics course will be immediately applicable to experimental research and design of systems biology projects.
Prerequisites / NoticeThe Functional Genomics course will be taught in English.
551-1126-00LTechnologies in Molecular MicrobiologyW4 credits2VB. Nguyen, W.‑D. Hardt, 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, 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.
ContentImportant 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 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:
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)
227-0396-00LEXCITE Interdisciplinary Summer School on Bio-Medical Imaging Restricted registration - show details
The school admits 60 MSc or PhD students with backgrounds in biology, chemistry, mathematics, physics, computer science or engineering based on a selection process.

Students have to apply for acceptance. To apply a curriculum vitae and an application letter need to be submitted.
Further information can be found at: Link.
W Dr4 credits6GS. Kozerke, G. Csúcs, J. Klohs-Füchtemeier, S. F. Noerrelykke, M. P. Wolf
AbstractTwo-week summer school organized by EXCITE (Center for EXperimental & Clinical Imaging TEchnologies Zurich) on biological and medical imaging. The course covers X-ray imaging, magnetic resonance imaging, nuclear imaging, ultrasound imaging, optoacoustic imaging, infrared and optical microscopy, electron microscopy, image processing and analysis.
ObjectiveStudents understand basic concepts and implementations of biological and medical imaging. Based on relative advantages and limitations of each method they can identify preferred procedures and applications. Common foundations and conceptual differences of the methods can be explained.
ContentTwo-week summer school on biological and medical imaging. The course covers concepts and implementations of X-ray imaging, magnetic resonance imaging, nuclear imaging, ultrasound imaging, optoacoustic imaging, infrared and optical microscopy and electron microscopy. Multi-modal and multi-scale imaging and supporting technologies such as image analysis and modeling are discussed. Dedicated modules for physical and life scientists taking into account the various backgrounds are offered.
Lecture notesPresentation slides, Web links
Prerequisites / NoticeThe school admits 60 MSc or PhD students with backgrounds in biology, chemistry, mathematics, physics, computer science or engineering based on a selection process. To apply a curriculum vitae, a statement of purpose and applicants references need to be submitted. Further information can be found at: Link
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.
551-0338-00LCurrent Approaches in Single Cell Analysis (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BME327

Mind the enrolment deadlines at UZH:
Link
W2 credits2VB. Bodenmiller, University lecturers
AbstractIn this lecture, we will discuss the most important single cell
approaches, the questions they can address and current developments. We will cover single cell: genomics, transcriptomics, proteomics (CyTOF mass cytometry), metabolomics and highly multiplexed imaging. Finally, we will also discuss the latest approaches for the analysis of such generated highly multiplexed single cell data.
ObjectiveOn completion of this module the students should be able to:
- explain the basic principles of single cell analysis techniques
- identify and justify the limitations of the current single cell
technologies and suggest reasonable improvements
- know the basic challenges in data analysis imposed by the complex
multi parameter data.
Key skills:
On completion of this module the students should be able to:
- summarize and discuss the impact these technologies have on biology
and medicine
- design biological and biomedical experiments for which single cell
analysis is essential
ContentCurrently single cell analysis approaches revolutionize the way we study and understand biological systems. In all biological and biomedical settings, cell populations and tissues are highly heterogeneous; this heterogeneity plays a critical role in basic biological processes such as cell cycle, development and organismic function, but is also a major player in disease, e.g. for cancer development, diagnosis and treatment.
Currently, single cell analysis techniques are rapidly developing and
find broad application, as the single cell measurements not only enable
to study cell specific functions, but often reveal unexpected biological
mechanisms in so far (assumed) well understood biological processes.
In this lecture, we will discuss the most important single cell approaches, the questions they can address and current developments. We will cover single cell genomics, single cell transcriptomics, single cell proteomics (CyTOF mass cytometry), single cell metabolomics and highly multiplexed single cell imaging. Finally, we will also discuss the latest approaches for the analysis of such generated highly multiplexed single cell data.
551-1412-00LMolecular and Structural Biology IV: Visualizing Macromolecules by X-Ray Crystallography and EMW4 credits2VN. Ban, D. Böhringer, T. Ishikawa, M. A. Leibundgut, K. Locher, M. Pilhofer, K. Wüthrich, further lecturers
AbstractThis course provides an in-depth discussion of two main methods to determine the 3D structures of macromolecules and complexes at high resolution: X-ray crystallography and cryo-electron microscopy. Both techniques result in electron density maps that are interpreted by atomic models.
ObjectiveStudents will obtain the theoretical background to understand structure determination techniques employed in X-ray crystallography and electron microscopy, including diffraction theory, crystal growth and analysis, reciprocal space calculations, interpretation of electron density, structure building and refinement as well as validation. The course will also provide an introduction into the use of cryo-electron tomography to visualize complex cellular substructures at sub-nanometer resolutions, effectively bridging the resolution gap between optical microscopy and single particle cryo-electron microscopy. Lectures will be complemented with practical sessions where students will have a chance to gain hands on experience with sample preparation, data processing and structure building and refinement.
Content- History of Structural Molecular Biology

- X-ray diffraction from macromolecular crystals

- Data collection and statistics, phasing methods

- Crystal symmetry and space groups

- X-ray data processing

- Principle of cryo-EM for biological macromolecules I, including hardware of TEM and detectors, image formation principle (phase contrast, spherical aberration, CTF), 3D reconstruction (central-section theorem, backprojection, missing information)

- Single particle analysis, including principle (projection matching, random conical tilt, angular reconstitution)

- Tomography I, including basics and subtomogram averaging

- Tomography - recent techniques, including cryo-FIB
- EM specimen preparation (cryo, negative stain), initial EM data processing

- EM and X-ray structure building, refinement, validation and interpretation

- Model building and refinement
551-1414-00LMolecular and Structural Biology V: Studying Macromolecules by NMR and EPRW4 credits2VF. Allain, A. D. Gossert, G. Jeschke, K. Wüthrich
AbstractThe course provides an overview of experimental methods for studying function and structure of macromolecules at atomic resolution in solution. The two main methods used are Nuclear Magnetic Resonance (NMR) spectroscopy and Electron Paramagnetic Resonance (EPR) spectroscopy.
ObjectiveInsight into the methodology, areas of application and limitations of these two methods for studying biological macromolecules. Practical exercises with spectra to have hands on understanding of the methodology.
ContentPart I: Historical overview of structural biology.
Part II: Basic concepts of NMR and initial examples of applications.
2D NMR and isotope labeling for studying protein function and molecular interactions at atomic level.
Studies of dynamic processes of proteins in solution.
Approaches to study large particles.
Methods for determination of protein structures in solution.
Part III: NMR methods for structurally characterizing RNA and protein-RNA complexes.
Part IV: EPR of biomolecules
Literature1) Wüthrich, K. NMR of Proteins and Nucleic Acids, Wiley-Interscience.
2) Dominguez et al, Prog Nucl Magn Reson Spectrosc. 2011 Feb;58(1-2):1-61.
3) Duss O et al, Methods Enzymol. 2015;558:279-331.
551-1103-00LMicrobial Biochemistry Information W4 credits2VJ. Vorholt-Zambelli, J. Piel
AbstractThe 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.
ObjectiveThe lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms.
ContentImportant 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
Microbial autotrophy
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
LiteratureWill be provided during the course.
Elective Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0326-00LCell Biology Information W6 credits4VS. Werner, H. Gehart, W. Kovacs, M. Schäfer, U. Suter, A. Wutz, further lecturers
AbstractThis Course introduces principle concepts, techniques, and experimental strategies used in modern Cell Biology. Major topics include: neuron-glia interactions in health and disease; mitochondrial dynamics; stem cell biology; growth factor action in development, tissue repair and disease; cell metabolism, in particular sensing and signaling mechanisms, cell organelles, and lipid metabolism.
Objective-To prepare the students for successful and efficient lab work by learning how to ask the right questions and to use the appropriate techniques in a research project.
-To convey knowledge about neuron-glia interactions in health and disease.
- To provide information on different types of stem cells and their function in health and disease
-To provide information on growth factor signaling in development, repair and disease and on the use of growth factors or their receptors as drug targets for major human diseases
-To convey knowledge on the mechanisms underlying repair of injured tissues
-To provide the students with an overview of mitochondrial dynamics.
-Providing an understanding of RNA processing reactions and their regulations.
-To provide a comprehensive understanding of metabolic sensing mechanisms occurring in different cell types and organelles in response to glucose, hormones, oxygen, nutrients as well as lipids, and to discuss downstream signaling pathways and cellular responses.
-To provide models explaining how disturbances in complex metabolic control networks and bioenergetics can lead to disease and to highlight latest experimental approaches to uncover the intricacies of metabolic control at the cellular and organismal level.
-Providing the background and context that foster cross-disciplinary scientific thinking.
551-0324-00LSystems Biology Information W6 credits4VP. Picotti, M. Claassen, U. Sauer, B. Snijder, B. Wollscheid
AbstractIntroduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects.
Objective- obtain an overview of global analytical methods
- obtain an overview of computational methods in systems biology
- understand the concepts of systems biology
ContentOverview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology.
Lecture notesno script
LiteratureThe course is not taught by a particular book, but some books are suggested for further reading:

- Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005
529-0732-00LProteins and Lipids
Note for BSc Biology students: Only one of the two concept courses 529-0731-00 Nucleic Acids and Carbohydrates (autumn semester) or 529-0732-00 Proteins and Lipids (spring semester) can be counted for the Bachelor's degree.
W6 credits3GD. Hilvert
AbstractAn overview of the relationship between protein sequence, conformation and function.
ObjectiveOverview of the relationship between protein sequence, conformation and function.
ContentProteins, structures and properties, (bio)synthesis of polypeptides, protein folding and design, protein engineering, chemical modification of proteins, proteomics.
LiteratureGeneral Literature:
- T.E. Creighton: Proteins: Structures and Molecular Properties, 2nd Edition, H.W. Freeman and Company, New York, 1993.
- C. Branden, J. Tooze , Introduction to Protein Structure, Garland Publishing, New York, 1991.
- J. M. Berg, J. L. Tymoczko, L. Stryer: Biochemistry, 5th edition, H.W. Freeman and Company, New York, 2002.
- G.A. Petsko, D. Ringe: Protein Structure and Function, New Science Press Ltd., London, 2004.

Original Literature:
Citations from the original literature relevant to the individual lectures will be assigned weekly.
551-0314-00LMicrobiology (Part II)W3 credits2VW.‑D. Hardt, L. Eberl, J. Piel, J. Vorholt-Zambelli
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ObjectiveThis concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
551-0318-00LImmunology IIW3 credits2VA. Oxenius, M. Kopf, S. R. Leibundgut, E. Slack, further lecturers
AbstractIntroduction into the cellular and molecular basis of the immune system and immune responses against diverse pathogens, tumors, transplants, and self (autoimmunity)
ObjectiveThe lectures will provide a detailed understanding:
- how innate and adaptive immune responses interact at the cellular and molecular level.
- how the immune system recognizes and fights against pathogenic microorganisms including viruses, bacteria, and parasites.
- why lymphocytes tolerate self molecules.
- about function and dysfunction the intestinal immune system.
- immunopathology and inflammatory diseases.
ContentThe aim of lecture is to understand:
> How pathogens are recognized by the innate immune system
> Immune defense against various pathogens
> Immunology of the skin, lung and intestines
> Tumor immunology
> Migration and homing of immune cells
> tolerance and autoimmunity
> T cell memory
Lecture notesPresentations of the lecturers are available at the Moodle link
LiteratureRecommended: Kuby Immunology (Freeman)
551-0307-01LMolecular and Structural Biology II: Molecular Machines and Cellular Assemblies
D-BIOL students are obliged to take part I and part II as a two-semester course.
W3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course on advanced topics in Molecular Biology and Biochemistry will cover the structure and function of cellular assemblies. General topics in basic biochemistry will be further developed with examples of the function of large cellular machines involved in DNA packaging, translation, virus architecture, RNA processing, cell-cell interactions, and the molecular basis of CRISPER systems.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
literature:
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.
Elective Major: Molecular Plant Biology
Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
551-0120-01LPlant Biology Colloquium (Spring Semester)
This compulsory course is required only once. It may be taken in autumn as course 551-0120-00 "Plant Biology Colloquium (Autumn Semester)" or in spring as course 551-0120-01 "Plant Biology Colloquium (Spring Semester)".
W2 credits1KC. Sánchez-Rodríguez, K. Bomblies, W. Gruissem, A. Rodriguez-Villalon, O. Voinnet, S. C. Zeeman
AbstractCurrent topics in Molecular Plant Biology presented by internal and external speakers from accademia.
ObjectiveGetting insight into actual areas and challenges of Molecular Plant Biology.
ContentLink
Elective Compulsory Concept Courses
See D-BIOL Master Studies Guide
NumberTitleTypeECTSHoursLecturers
529-0732-00LProteins and Lipids
Note for BSc Biology students: Only one of the two concept courses 529-0731-00 Nucleic Acids and Carbohydrates (autumn semester) or 529-0732-00 Proteins and Lipids (spring semester) can be counted for the Bachelor's degree.
W6 credits3GD. Hilvert
AbstractAn overview of the relationship between protein sequence, conformation and function.
ObjectiveOverview of the relationship between protein sequence, conformation and function.
ContentProteins, structures and properties, (bio)synthesis of polypeptides, protein folding and design, protein engineering, chemical modification of proteins, proteomics.
LiteratureGeneral Literature:
- T.E. Creighton: Proteins: Structures and Molecular Properties, 2nd Edition, H.W. Freeman and Company, New York, 1993.
- C. Branden, J. Tooze , Introduction to Protein Structure, Garland Publishing, New York, 1991.
- J. M. Berg, J. L. Tymoczko, L. Stryer: Biochemistry, 5th edition, H.W. Freeman and Company, New York, 2002.
- G.A. Petsko, D. Ringe: Protein Structure and Function, New Science Press Ltd., London, 2004.

Original Literature:
Citations from the original literature relevant to the individual lectures will be assigned weekly.
551-0324-00LSystems Biology Information W6 credits4VP. Picotti, M. Claassen, U. Sauer, B. Snijder, B. Wollscheid
AbstractIntroduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects.
Objective- obtain an overview of global analytical methods
- obtain an overview of computational methods in systems biology
- understand the concepts of systems biology
ContentOverview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology.
Lecture notesno script
LiteratureThe course is not taught by a particular book, but some books are suggested for further reading:

- Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005
551-0320-00LCellular Biochemistry (Part II)W3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
551-0314-00LMicrobiology (Part II)W3 credits2VW.‑D. Hardt, L. Eberl, J. Piel, J. Vorholt-Zambelli
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ObjectiveThis concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
551-0326-00LCell Biology Information W6 credits4VS. Werner, H. Gehart, W. Kovacs, M. Schäfer, U. Suter, A. Wutz, further lecturers
AbstractThis Course introduces principle concepts, techniques, and experimental strategies used in modern Cell Biology. Major topics include: neuron-glia interactions in health and disease; mitochondrial dynamics; stem cell biology; growth factor action in development, tissue repair and disease; cell metabolism, in particular sensing and signaling mechanisms, cell organelles, and lipid metabolism.
Objective-To prepare the students for successful and efficient lab work by learning how to ask the right questions and to use the appropriate techniques in a research project.
-To convey knowledge about neuron-glia interactions in health and disease.
- To provide information on different types of stem cells and their function in health and disease
-To provide information on growth factor signaling in development, repair and disease and on the use of growth factors or their receptors as drug targets for major human diseases
-To convey knowledge on the mechanisms underlying repair of injured tissues
-To provide the students with an overview of mitochondrial dynamics.
-Providing an understanding of RNA processing reactions and their regulations.
-To provide a comprehensive understanding of metabolic sensing mechanisms occurring in different cell types and organelles in response to glucose, hormones, oxygen, nutrients as well as lipids, and to discuss downstream signaling pathways and cellular responses.
-To provide models explaining how disturbances in complex metabolic control networks and bioenergetics can lead to disease and to highlight latest experimental approaches to uncover the intricacies of metabolic control at the cellular and organismal level.
-Providing the background and context that foster cross-disciplinary scientific thinking.
551-0307-01LMolecular and Structural Biology II: Molecular Machines and Cellular Assemblies
D-BIOL students are obliged to take part I and part II as a two-semester course.
W3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course on advanced topics in Molecular Biology and Biochemistry will cover the structure and function of cellular assemblies. General topics in basic biochemistry will be further developed with examples of the function of large cellular machines involved in DNA packaging, translation, virus architecture, RNA processing, cell-cell interactions, and the molecular basis of CRISPER systems.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
literature:
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
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
551-0138-00LRegulation of Plant Primary MetabolismW2 credits1VS. C. Zeeman
AbstractPlants are the primary producers of our ecosystem. This course will survey the pathways of plant metabolism. Emphasis will be placed on the mechanisms of carbon dioxide assimilation, carbohydrate metabolism, and the regulation of metabolic fluxes. The course will also highlight the classical and state-of-the-art research methods.
ObjectiveThe aim of the course is to confer a broad understanding of plant metabolism, to give insight into the methods of plant biology research, and to promote critical evaluation of scientific literature.
ContentThe course will include a combination of lectures and coursework/active-learning exercises (e.g. research paper presentations)
551-0224-00LAdvanced Proteomics Restricted registration - show details
For master students from the 2nd semester on, also doctoral candidates and post docs.
W4 credits6GP. Picotti, L. Gillet, A. Leitner, P. Pedrioli
AbstractGoal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine.
Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises.
ObjectiveTo discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology.
ContentBlock course teaching current methods for the acquisition and processing of proteomic datasets.
Prerequisites / NoticeNumber of people: Not exceeding 30.
Students from ETHZ, Uni Zurich and University of Basel
Non-ETH students must register at ETH Zurich as special students Link
751-5110-00LInsects in AgroecosystemsW2 credits2VC. De Moraes, A. Kantsa, D. Lucas Gomes Marques Barbosa
AbstractThis class will focus on insect-plant interactions in agroecosystems, and how the unique man-made agricultural community effects insect populations leading to pest outbreaks. Key concepts in pest prediction and management will be discussed from an ecological perspective.
ObjectiveAt the end of this course, students will understand what biotic and abiotic factors contribute to pest outbreaks, why some modern pest management techniques have failed over time, and the trade-offs associated with the use of different pest control methods. Our approach will allow students to apply their knowledge to a variety of pest management situations. Additionally, students will learn about current research goals in agroecology and how these goals are being addressed by scientists engaged in agricultural research.
ContentThe focus of this course will be on understanding how the ecologies of agricultural systems differ from natural ecosystems, and how these difference affect the population dynamics of insect pests and natural enemies. Each section of the course is centered around a basic ecological, biological or engineering theme such as host shift, physiological time, or sampling techniques. Different management techniques will be discussed, as well as the ecological basis behind why these techniques work and why they sometimes fail. The role of insects in spreading economically important plant diseases will also be discussed. Recent advances in research will also be addressed throughout the course and reinforced with periodic readings of primary literature.
Lecture notesProvided to students through ILIAS
LiteratureSelected required readings (peer reviewed literature, selected book chapters).
751-4904-00LMicrobial Pest ControlW2 credits2GJ. Enkerli, G. Grabenweger
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
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.
551-1103-00LMicrobial Biochemistry Information W4 credits2VJ. Vorholt-Zambelli, J. Piel
AbstractThe 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.
ObjectiveThe lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms.
ContentImportant 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
Microbial autotrophy
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
LiteratureWill be provided during the course.
701-1480-00LEvolutionary Developmental Biology Restricted registration - show details
Number of participants limited to 24.
Waiting list will be deleted after 05.03.2021.
W3 credits1SM. La Fortezza, G. Velicer
AbstractStudents will be introduced to fundamental concepts and current open questions in the field of evolutionary developmental biology (Evo-Devo) primarily through reading, analysing and jointly discussing key literature.
ObjectiveThe course aims to expose students to major conceptual themes of the Evo-Devo field through discussion of key papers and to active areas of current Evo-Devo research. At the end of the course, students should be able to present, think critically about and discuss key Evo-Devo concepts.
ContentEvolutionary developmental biology (Evo-Devo) is a multidisciplinary field that studies the interplay between developmental and evolutionary processes. Major questions include: How do developmental systems evolve and diversify? Do developmental programs influence their own future evolution, and how? How does ecology affect the evolution of developmental programs, and vice versa? Fascinating and experimentally challenging, Evo-Devo first empirically emerged from comparative embryology. However, in recent decades this discipline has grown considerably to interconnect with many other fields, from genetics to sociobiology to microbiology. The course will examine questions such as those above and touch on the ongoing inter-disciplinary integration of Evo-Devo, including its interface with ecology (“Eco-Evo-Devo”) and the integration of aggregative microbial developmental systems into the field.
LiteratureRelevant literature:

Müller, G. (2007). Evo–devo: extending the evolutionary synthesis. Nature Reviews Genetics 8, 943-949. Link

Abouheif, E., et al (2014). Eco-evo-devo: the time has come. Advances in experimental medicine and biology 781, 107-25. Link

Moczek, A et al (2015). The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evolution & development 17, 198-219. Link

Gilbert, S. (2019). Evolutionary transitions revisited: Holobiont evo‐devo. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 12, 117762501877479 - 8. Link
Prerequisites / NoticeSignificant basic knowledge in especially evolutionary biology and developmental biology, and also cell biology and genetics, will be advantageous for readily understanding the course material.
551-0364-00LFunctional Genomics
Information for UZH students:
Enrolment to this course unit only possible at ETH. No enrolment to module BIO 254 at UZH.

Please mind the ETH enrolment deadlines for UZH students: Link
W3 credits2VC. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, further lecturers
AbstractFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data.
ObjectiveFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. Such data provide the basis for systems biology efforts to elucidate the structure, dynamics and regulation of cellular networks.
ContentThe curriculum of the Functional Genomics course emphasizes an in depth understanding of new technology platforms for modern genomics and advanced genetics, including the application of functional genomics approaches such as advanced sequencing, proteomics, metabolomics, clustering and classification. Students will learn quality controls and standards (benchmarking) that apply to the generation of quantitative data and will be able to analyze and interpret these data. The training obtained in the Functional Genomics course will be immediately applicable to experimental research and design of systems biology projects.
Prerequisites / NoticeThe Functional Genomics course will be taught in English.
Elective Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0307-01LMolecular and Structural Biology II: Molecular Machines and Cellular Assemblies
D-BIOL students are obliged to take part I and part II as a two-semester course.
W3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course on advanced topics in Molecular Biology and Biochemistry will cover the structure and function of cellular assemblies. General topics in basic biochemistry will be further developed with examples of the function of large cellular machines involved in DNA packaging, translation, virus architecture, RNA processing, cell-cell interactions, and the molecular basis of CRISPER systems.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
literature:
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.
751-4805-00LRecent Advances in Biocommunication Restricted registration - show details
Number of participants limited to 25.
W3 credits2SC. De Moraes
AbstractStudents 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.
ObjectiveStudents 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.
Elective Major: Systems Biology
Compulsory Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0324-00LSystems Biology Information O6 credits4VP. Picotti, M. Claassen, U. Sauer, B. Snijder, B. Wollscheid
AbstractIntroduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects.
Objective- obtain an overview of global analytical methods
- obtain an overview of computational methods in systems biology
- understand the concepts of systems biology
ContentOverview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology.
Lecture notesno script
LiteratureThe course is not taught by a particular book, but some books are suggested for further reading:

- Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005
Elective Compulsory Concept Courses
See D-BIOL Master Studies Guide
NumberTitleTypeECTSHoursLecturers
551-0320-00LCellular Biochemistry (Part II)W3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
551-0314-00LMicrobiology (Part II)W3 credits2VW.‑D. Hardt, L. Eberl, J. Piel, J. Vorholt-Zambelli
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ObjectiveThis concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
Elective Compulsory Master Courses I: Computation
NumberTitleTypeECTSHoursLecturers
636-0702-00LStatistical Models in Computational BiologyW6 credits2V + 1U + 2AN. Beerenwinkel
AbstractThe course offers an introduction to graphical models and their application to complex biological systems. Graphical models combine a statistical methodology with efficient algorithms for inference in settings of high dimension and uncertainty. The unifying graphical model framework is developed and used to examine several classical and topical computational biology methods.
ObjectiveThe goal of this course is to establish the common language of graphical models for applications in computational biology and to see this methodology at work for several real-world data sets.
ContentGraphical models are a marriage between probability theory and graph theory. They combine the notion of probabilities with efficient algorithms for inference among many random variables. Graphical models play an important role in computational biology, because they explicitly address two features that are inherent to biological systems: complexity and uncertainty. We will develop the basic theory and the common underlying formalism of graphical models and discuss several computational biology applications. Topics covered include conditional independence, Bayesian networks, Markov random fields, Gaussian graphical models, EM algorithm, junction tree algorithm, model selection, Dirichlet process mixture, causality, the pair hidden Markov model for sequence alignment, probabilistic phylogenetic models, phylo-HMMs, microarray experiments and gene regulatory networks, protein interaction networks, learning from perturbation experiments, time series data and dynamic Bayesian networks. Some of the biological applications will be explored in small data analysis problems as part of the exercises.
Lecture notesno
Literature- Airoldi EM (2007) Getting started in probabilistic graphical models. PLoS Comput Biol 3(12): e252. doi:10.1371/journal.pcbi.0030252
- Bishop CM. Pattern Recognition and Machine Learning. Springer, 2007.
- Durbin R, Eddy S, Krogh A, Mitchinson G. Biological Sequence Analysis. Cambridge university Press, 2004
401-0102-00LApplied Multivariate StatisticsW5 credits2V + 1UF. Sigrist
AbstractMultivariate statistics analyzes data on several random variables simultaneously. This course introduces the basic concepts and provides an overview of classical and modern methods of multivariate statistics including visualization, dimension reduction, supervised and unsupervised learning for multivariate data. An emphasis is on applications and solving problems with the statistical software R.
ObjectiveAfter the course, you are able to:
- describe the various methods and the concepts behind them
- identify adequate methods for a given statistical problem
- use the statistical software R to efficiently apply these methods
- interpret the output of these methods
ContentVisualization, multivariate outliers, the multivariate normal distribution, dimension reduction, principal component analysis, multidimensional scaling, factor analysis, cluster analysis, classification, multivariate tests and multiple testing
Lecture notesNone
Literature1) "An Introduction to Applied Multivariate Analysis with R" (2011) by Everitt and Hothorn
2) "An Introduction to Statistical Learning: With Applications in R" (2013) by Gareth, Witten, Hastie and Tibshirani

Electronic versions (pdf) of both books can be downloaded for free from the ETH library.
Prerequisites / NoticeThis course is targeted at students with a non-math background.

Requirements:
==========
1) Introductory course in statistics (min: t-test, regression; ideal: conditional probability, multiple regression)
2) Good understanding of R (if you don't know R, it is recommended that you study chapters 1,2,3,4, and 5 of "Introductory Statistics with R" from Peter Dalgaard, which is freely available online from the ETH library)

An alternative course with more emphasis on theory is 401-6102-00L "Multivariate Statistics" (only every second year).

401-0102-00L and 401-6102-00L are mutually exclusive. You can register for only one of these two courses.
227-0396-00LEXCITE Interdisciplinary Summer School on Bio-Medical Imaging Restricted registration - show details
The school admits 60 MSc or PhD students with backgrounds in biology, chemistry, mathematics, physics, computer science or engineering based on a selection process.

Students have to apply for acceptance. To apply a curriculum vitae and an application letter need to be submitted.
Further information can be found at: Link.
W4 credits6GS. Kozerke, G. Csúcs, J. Klohs-Füchtemeier, S. F. Noerrelykke, M. P. Wolf
AbstractTwo-week summer school organized by EXCITE (Center for EXperimental & Clinical Imaging TEchnologies Zurich) on biological and medical imaging. The course covers X-ray imaging, magnetic resonance imaging, nuclear imaging, ultrasound imaging, optoacoustic imaging, infrared and optical microscopy, electron microscopy, image processing and analysis.
ObjectiveStudents understand basic concepts and implementations of biological and medical imaging. Based on relative advantages and limitations of each method they can identify preferred procedures and applications. Common foundations and conceptual differences of the methods can be explained.
ContentTwo-week summer school on biological and medical imaging. The course covers concepts and implementations of X-ray imaging, magnetic resonance imaging, nuclear imaging, ultrasound imaging, optoacoustic imaging, infrared and optical microscopy and electron microscopy. Multi-modal and multi-scale imaging and supporting technologies such as image analysis and modeling are discussed. Dedicated modules for physical and life scientists taking into account the various backgrounds are offered.
Lecture notesPresentation slides, Web links
Prerequisites / NoticeThe school admits 60 MSc or PhD students with backgrounds in biology, chemistry, mathematics, physics, computer science or engineering based on a selection process. To apply a curriculum vitae, a statement of purpose and applicants references need to be submitted. Further information can be found at: Link
Elective Compulsory Master Courses II: Biology
NumberTitleTypeECTSHoursLecturers
551-1310-00LA Problem-Based Approach to Cellular Biochemistry Restricted registration - show details
Number of participants limited to 12.
W6 credits2GM. Peter, V. Korkhov, G. Neurohr, V. Panse, A. E. Smith, F. van Drogen
AbstractIndependent, guided acquisition of a defined area of research, identification of key open questions, development of an experimental strategy to address a defined question, and formulation of this strategy within the framework of a research grant.
ObjectiveWorking independently, students will acquire an overview of a defined research area, and identify important open questions. In addition, they will develop an experimental strategy to address a defined question, and to formulate this strategy within the framework of a research grant.
ContentThe students will work in groups of two to three, in close contact with a tutor (ETH Prof or senior scientist). A research overview with open questions and a research grant will be developed independently by the students, with guidance from the tutor through regular mandatory meetings. The students will write both the research overview with open questions and the grant in short reports, and present them to their colleagues.
LiteratureThe identification of appropriate literature is a component of the course.
Prerequisites / NoticeThis course will be taught in English, and requires extensive independent work.
551-0364-00LFunctional Genomics
Information for UZH students:
Enrolment to this course unit only possible at ETH. No enrolment to module BIO 254 at UZH.

Please mind the ETH enrolment deadlines for UZH students: Link
W3 credits2VC. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, further lecturers
AbstractFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data.
ObjectiveFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. Such data provide the basis for systems biology efforts to elucidate the structure, dynamics and regulation of cellular networks.
ContentThe curriculum of the Functional Genomics course emphasizes an in depth understanding of new technology platforms for modern genomics and advanced genetics, including the application of functional genomics approaches such as advanced sequencing, proteomics, metabolomics, clustering and classification. Students will learn quality controls and standards (benchmarking) that apply to the generation of quantitative data and will be able to analyze and interpret these data. The training obtained in the Functional Genomics course will be immediately applicable to experimental research and design of systems biology projects.
Prerequisites / NoticeThe Functional Genomics course will be taught in English.
551-0224-00LAdvanced Proteomics Restricted registration - show details
For master students from the 2nd semester on, also doctoral candidates and post docs.
W4 credits6GP. Picotti, L. Gillet, A. Leitner, P. Pedrioli
AbstractGoal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine.
Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises.
ObjectiveTo discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology.
ContentBlock course teaching current methods for the acquisition and processing of proteomic datasets.
Prerequisites / NoticeNumber of people: Not exceeding 30.
Students from ETHZ, Uni Zurich and University of Basel
Non-ETH students must register at ETH Zurich as special students Link
701-1418-00LModelling Course in Population and Evolutionary Biology Information Restricted registration - show details
Number of participants limited to 20.

Priority is given to MSc Biology and Environmental Sciences students.
W4 credits6PS. Bonhoeffer, V. Müller
AbstractThis course provides a "hands-on" introduction into mathematical/computational modelling of biological processes with particular emphasis on evolutionary and population-biological questions. The models are developed using the Open Source software R.
ObjectiveThe aim of this course is to provide a practical introduction into the modelling of fundamental biological questions. The participants will receive guidance to develop mathematical/computational models in small teams. The participants chose two modules with different levels of difficulty from a list of projects.

The participant shall get a sense of the utility of modelling as a tool to investigate biological problems. The simpler modules are based mostly on examples from the earlier lecture "Ecology and evolution: populations" (script accessible at the course webpage). The advanced modules address topical research questions. Although being based on evolutionary and population biological methods and concepts, these modules also address topics from other areas of biology.
Contentsee Link
Lecture notesDetailed handouts describing both the modelling and the biological background are available to each module at the course website. In addition, the script of the earlier lecture "Ecology and evolution: populations" can also be downloaded, and contains further background information.
Prerequisites / NoticeThe course is based on the open source software R. Experience with R is useful but not required for the course. Similarly, the course 701-1708-00L Infectious Disease Dynamics is useful but not required.
551-1126-00LTechnologies in Molecular MicrobiologyW4 credits2VB. Nguyen, W.‑D. Hardt, 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, 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.
ContentImportant 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 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:
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)
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.
636-0111-00LSynthetic Biology I
Attention: This course was offered in previous semesters with the number: 636-0002-00L "Synthetic Biology I". Students that already passed course 636-0002-00L cannot receive credits for course 636-0111-00L.
W4 credits3GS. Panke, J. Stelling
AbstractTheoretical & practical introduction into the design of dynamic biological systems at different levels of abstraction, ranging from biological fundamentals of systems design (introduction to bacterial gene regulation, elements of transcriptional & translational control, advanced genetic engineering) to engineering design principles (standards, abstractions) mathematical modelling & systems desig
ObjectiveAfter the course, students will be able to theoretically master the biological and engineering fundamentals required for biological design to be able to participate in the international iGEM competition (see Link).
ContentThe overall goal of the course is to familiarize the students with the potential, the requirements and the problems of designing dynamic biological elements that are of central importance for manipulating biological systems, primarily (but not exclusively) prokaryotic systems. Next, the students will be taken through a number of successful examples of biological design, such as toggle switches, pulse generators, and oscillating systems, and apply the biological and engineering fundamentals to these examples, so that they get hands-on experience on how to integrate the various disciplines on their way to designing biological systems.
Lecture notesHandouts during classes.
LiteratureMark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press
Uri Alon, An Introduction to Systems Biology, Chapman & Hall
Prerequisites / Notice1) Though we do not place a formal requirement for previous participation in particular courses, we expect all participants to be familiar with a certain level of biology and of mathematics. Specifically, there will be material for self study available on Link as of mid January, and everybody is expected to be fully familiar with this material BEFORE THE CLASS BEGINS to be able to follow the different lectures. Please contact Link for access to material
2) The course is also thought as a preparation for the participation in the international iGEM synthetic biology summer competition (Link, Link). This competition is also the contents of the course Synthetic Biology II. Link
551-1103-00LMicrobial Biochemistry Information W4 credits2VJ. Vorholt-Zambelli, J. Piel
AbstractThe 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.
ObjectiveThe lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms.
ContentImportant 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
Microbial autotrophy
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
LiteratureWill be provided during the course.
Elective Major: Molecular and Structural Biology
Compulsory Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0307-01LMolecular and Structural Biology II: Molecular Machines and Cellular Assemblies
D-BIOL students are obliged to take part I and part II as a two-semester course.
O3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course on advanced topics in Molecular Biology and Biochemistry will cover the structure and function of cellular assemblies. General topics in basic biochemistry will be further developed with examples of the function of large cellular machines involved in DNA packaging, translation, virus architecture, RNA processing, cell-cell interactions, and the molecular basis of CRISPER systems.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
literature:
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.
Elective Compulsory Concept Courses
See D-BIOL Master Studies Guide
NumberTitleTypeECTSHoursLecturers
529-0732-00LProteins and Lipids
Note for BSc Biology students: Only one of the two concept courses 529-0731-00 Nucleic Acids and Carbohydrates (autumn semester) or 529-0732-00 Proteins and Lipids (spring semester) can be counted for the Bachelor's degree.
W6 credits3GD. Hilvert
AbstractAn overview of the relationship between protein sequence, conformation and function.
ObjectiveOverview of the relationship between protein sequence, conformation and function.
ContentProteins, structures and properties, (bio)synthesis of polypeptides, protein folding and design, protein engineering, chemical modification of proteins, proteomics.
LiteratureGeneral Literature:
- T.E. Creighton: Proteins: Structures and Molecular Properties, 2nd Edition, H.W. Freeman and Company, New York, 1993.
- C. Branden, J. Tooze , Introduction to Protein Structure, Garland Publishing, New York, 1991.
- J. M. Berg, J. L. Tymoczko, L. Stryer: Biochemistry, 5th edition, H.W. Freeman and Company, New York, 2002.
- G.A. Petsko, D. Ringe: Protein Structure and Function, New Science Press Ltd., London, 2004.

Original Literature:
Citations from the original literature relevant to the individual lectures will be assigned weekly.
551-0320-00LCellular Biochemistry (Part II)W3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
551-0314-00LMicrobiology (Part II)W3 credits2VW.‑D. Hardt, L. Eberl, J. Piel, J. Vorholt-Zambelli
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ObjectiveThis concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
551-0324-00LSystems Biology Information W6 credits4VP. Picotti, M. Claassen, U. Sauer, B. Snijder, B. Wollscheid
AbstractIntroduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects.
Objective- obtain an overview of global analytical methods
- obtain an overview of computational methods in systems biology
- understand the concepts of systems biology
ContentOverview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology.
Lecture notesno script
LiteratureThe course is not taught by a particular book, but some books are suggested for further reading:

- Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
551-1402-00LMolecular and Structural Biology VI: Biophysical Analysis of Macromolecular Mechanisms
This course is strongly recommended for the Masters Major "Biology and Biophysics".
W4 credits2VR. Glockshuber, T. Ishikawa, S. Jonas, B. Schuler, E. Weber-Ban
AbstractThe course is focussed on biophysical methods for characterising conformational transitions and reaction mechanisms of proteins and biological mecromolecules, with focus on methods that have not been covered in the Biology Bachelor Curriculum.
ObjectiveThe goal of the course is to give the students a broad overview on biopyhsical techniques available for studying conformational transitions and complex reaction mechanisms of biological macromolecules. The course is particularly suited for students enrolled in the Majors "Structural Biology and Biophysics", "Biochemistry" and "Chemical Biology" of the Biology MSc curriculum, as well as for MSc students of Chemistry and Interdisciplinary Natural Sciences".
ContentThe biophysical methods covered in the course include advanced reaction kinetics, methods for the thermodynamic and kinetic analysis of protein-ligand interactions, static and dynamic light scattering, analytical ultracentrifugation, spectroscopic techniques such as fluorescence anisotropy, fluorescence resonance energy transfer (FRET) and single molecule fluorescence spectrosopy, modern electron microscopy techniques, atomic force microscopy, and isothermal and differential scanning calorimetry.
Lecture notesCourse material from the individual lecturers wil be made available at the sharepoint website

Link
Prerequisites / NoticeFinished BSc curriculum in Biology, Chemistry or Interdisciplinary Natural Sciences. The course is also adequate for doctoral students with research projects in structural biology, biophysics, biochemistry and chemical biology.
551-0224-00LAdvanced Proteomics Restricted registration - show details
For master students from the 2nd semester on, also doctoral candidates and post docs.
W4 credits6GP. Picotti, L. Gillet, A. Leitner, P. Pedrioli
AbstractGoal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine.
Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises.
ObjectiveTo discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology.
ContentBlock course teaching current methods for the acquisition and processing of proteomic datasets.
Prerequisites / NoticeNumber of people: Not exceeding 30.
Students from ETHZ, Uni Zurich and University of Basel
Non-ETH students must register at ETH Zurich as special students Link
551-0364-00LFunctional Genomics
Information for UZH students:
Enrolment to this course unit only possible at ETH. No enrolment to module BIO 254 at UZH.

Please mind the ETH enrolment deadlines for UZH students: Link
W3 credits2VC. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, further lecturers
AbstractFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data.
ObjectiveFunctional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. Such data provide the basis for systems biology efforts to elucidate the structure, dynamics and regulation of cellular networks.
ContentThe curriculum of the Functional Genomics course emphasizes an in depth understanding of new technology platforms for modern genomics and advanced genetics, including the application of functional genomics approaches such as advanced sequencing, proteomics, metabolomics, clustering and classification. Students will learn quality controls and standards (benchmarking) that apply to the generation of quantitative data and will be able to analyze and interpret these data. The training obtained in the Functional Genomics course will be immediately applicable to experimental research and design of systems biology projects.
Prerequisites / NoticeThe Functional Genomics course will be taught in English.
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, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander, further lecturers
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 Link 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.
551-1404-00LRNA and Proteins: Post-Transcriptional Regulation of Gene Expression (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BCH252

Mind the enrolment deadlines at UZH:
Link
W3 credits2VUniversity lecturers
AbstractThe course introduces the cellular processes and molecular mechanisms involved in regulating genome expression at the post-transcriptional level.
Topics will include :
-RNA processing, and transport;
-protein synthesis and translational control, trafficking and degradation;
-RNA-guided regulation (RNA interference, microRNAs);
-molecular surveillance and quality control mechanisms
Objective-Outline the cellular processes
used by eukaryotic and prokaryotic cells
to control gene expression at the post-
transcriptional level.
-Describe the molecular mechanisms
underlying post-transcriptional gene
regulation
-Identify experimental approaches
used to study post-transcriptional gene
regulation and describe their strengths
and weaknesses.
551-1412-00LMolecular and Structural Biology IV: Visualizing Macromolecules by X-Ray Crystallography and EMW4 credits2VN. Ban, D. Böhringer, T. Ishikawa, M. A. Leibundgut, K. Locher, M. Pilhofer, K. Wüthrich, further lecturers
AbstractThis course provides an in-depth discussion of two main methods to determine the 3D structures of macromolecules and complexes at high resolution: X-ray crystallography and cryo-electron microscopy. Both techniques result in electron density maps that are interpreted by atomic models.
ObjectiveStudents will obtain the theoretical background to understand structure determination techniques employed in X-ray crystallography and electron microscopy, including diffraction theory, crystal growth and analysis, reciprocal space calculations, interpretation of electron density, structure building and refinement as well as validation. The course will also provide an introduction into the use of cryo-electron tomography to visualize complex cellular substructures at sub-nanometer resolutions, effectively bridging the resolution gap between optical microscopy and single particle cryo-electron microscopy. Lectures will be complemented with practical sessions where students will have a chance to gain hands on experience with sample preparation, data processing and structure building and refinement.
Content- History of Structural Molecular Biology

- X-ray diffraction from macromolecular crystals

- Data collection and statistics, phasing methods

- Crystal symmetry and space groups

- X-ray data processing

- Principle of cryo-EM for biological macromolecules I, including hardware of TEM and detectors, image formation principle (phase contrast, spherical aberration, CTF), 3D reconstruction (central-section theorem, backprojection, missing information)

- Single particle analysis, including principle (projection matching, random conical tilt, angular reconstitution)

- Tomography I, including basics and subtomogram averaging

- Tomography - recent techniques, including cryo-FIB
- EM specimen preparation (cryo, negative stain), initial EM data processing

- EM and X-ray structure building, refinement, validation and interpretation

- Model building and refinement
551-1414-00LMolecular and Structural Biology V: Studying Macromolecules by NMR and EPRW4 credits2VF. Allain, A. D. Gossert, G. Jeschke, K. Wüthrich
AbstractThe course provides an overview of experimental methods for studying function and structure of macromolecules at atomic resolution in solution. The two main methods used are Nuclear Magnetic Resonance (NMR) spectroscopy and Electron Paramagnetic Resonance (EPR) spectroscopy.
ObjectiveInsight into the methodology, areas of application and limitations of these two methods for studying biological macromolecules. Practical exercises with spectra to have hands on understanding of the methodology.
ContentPart I: Historical overview of structural biology.
Part II: Basic concepts of NMR and initial examples of applications.
2D NMR and isotope labeling for studying protein function and molecular interactions at atomic level.
Studies of dynamic processes of proteins in solution.
Approaches to study large particles.
Methods for determination of protein structures in solution.
Part III: NMR methods for structurally characterizing RNA and protein-RNA complexes.
Part IV: EPR of biomolecules
Literature1) Wüthrich, K. NMR of Proteins and Nucleic Acids, Wiley-Interscience.
2) Dominguez et al, Prog Nucl Magn Reson Spectrosc. 2011 Feb;58(1-2):1-61.
3) Duss O et al, Methods Enzymol. 2015;558:279-331.
551-1103-00LMicrobial Biochemistry Information W4 credits2VJ. Vorholt-Zambelli, J. Piel
AbstractThe 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.
ObjectiveThe lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms.
ContentImportant 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
Microbial autotrophy
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
LiteratureWill be provided during the course.
Elective Major: Biological Chemistry
Compulsory Concept Courses
NumberTitleTypeECTSHoursLecturers
529-0732-00LProteins and Lipids
Note for BSc Biology students: Only one of the two concept courses 529-0731-00 Nucleic Acids and Carbohydrates (autumn semester) or 529-0732-00 Proteins and Lipids (spring semester) can be counted for the Bachelor's degree.
O6 credits3GD. Hilvert
AbstractAn overview of the relationship between protein sequence, conformation and function.
ObjectiveOverview of the relationship between protein sequence, conformation and function.
ContentProteins, structures and properties, (bio)synthesis of polypeptides, protein folding and design, protein engineering, chemical modification of proteins, proteomics.
LiteratureGeneral Literature:
- T.E. Creighton: Proteins: Structures and Molecular Properties, 2nd Edition, H.W. Freeman and Company, New York, 1993.
- C. Branden, J. Tooze , Introduction to Protein Structure, Garland Publishing, New York, 1991.
- J. M. Berg, J. L. Tymoczko, L. Stryer: Biochemistry, 5th edition, H.W. Freeman and Company, New York, 2002.
- G.A. Petsko, D. Ringe: Protein Structure and Function, New Science Press Ltd., London, 2004.

Original Literature:
Citations from the original literature relevant to the individual lectures will be assigned weekly.
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
551-1402-00LMolecular and Structural Biology VI: Biophysical Analysis of Macromolecular Mechanisms
This course is strongly recommended for the Masters Major "Biology and Biophysics".
W4 credits2VR. Glockshuber, T. Ishikawa, S. Jonas, B. Schuler, E. Weber-Ban
AbstractThe course is focussed on biophysical methods for characterising conformational transitions and reaction mechanisms of proteins and biological mecromolecules, with focus on methods that have not been covered in the Biology Bachelor Curriculum.
ObjectiveThe goal of the course is to give the students a broad overview on biopyhsical techniques available for studying conformational transitions and complex reaction mechanisms of biological macromolecules. The course is particularly suited for students enrolled in the Majors "Structural Biology and Biophysics", "Biochemistry" and "Chemical Biology" of the Biology MSc curriculum, as well as for MSc students of Chemistry and Interdisciplinary Natural Sciences".
ContentThe biophysical methods covered in the course include advanced reaction kinetics, methods for the thermodynamic and kinetic analysis of protein-ligand interactions, static and dynamic light scattering, analytical ultracentrifugation, spectroscopic techniques such as fluorescence anisotropy, fluorescence resonance energy transfer (FRET) and single molecule fluorescence spectrosopy, modern electron microscopy techniques, atomic force microscopy, and isothermal and differential scanning calorimetry.
Lecture notesCourse material from the individual lecturers wil be made available at the sharepoint website

Link
Prerequisites / NoticeFinished BSc curriculum in Biology, Chemistry or Interdisciplinary Natural Sciences. The course is also adequate for doctoral students with research projects in structural biology, biophysics, biochemistry and chemical biology.
529-0941-00LIntroduction to Macromolecular ChemistryW4 credits3GD. Opris
AbstractBasic definitions, types of polyreactions, constitution of homo- and copolymers, networks, configurative and conformative aspects, contour length, coil formation, mobility, glass temperature, rubber elasticity, molecular weight distribution, energetics of and examples for polyreactions.
ObjectiveUnderstanding the significance of molecular size, constitution, configuration and conformation of synthetic and natural macromolecules for their specific physical and chemical properties.
ContentThis introductory course on macromolecular chemistry discusses definitions, introduces types of polyreactions, and compares chain and step-growth polymerizations. It also treats the constitution of polymers, homo- and copolymers, networks, configuration and conformation of polymers. Topics of interest are contour length, coil formation, the mobility in polymers, glass temperature, rubber elasticity, molecular weight distribution, energetics of polyreactions, and examples for polyreactions (polyadditions, polycondensations, polymerizations). Selected polymerization mechanisms and procedures are discussed whenever appropriate throughout the course. Some methods of molecular weight determination are introduced.
Lecture notesCourse materials (consisting of personal notes and distributed paper copies) are sufficient for exam preparation.
Prerequisites / NoticeThe course will be taught in English. Complicated expressions will also be given in German. Questions are welcome in English or German. The written examination will be in English, answers in German are acceptable. A basic chemistry knowledge is required.

PhD students who need recognized credit points are required to pass the written exam.
529-0242-00LSupramolecular ChemistryW6 credits3GY. Yamakoshi, B. M. Lewandowski
AbstractPrinciples of molecular recognition: cation/anion complexation and their technological applications; complexation of neutral molecules in aqueous solution; non-covalent interactions involving aromatic rings; hydrogen bonding; molecular sef-assembly - a chemical approach towards nanostructures; thermodynamics and kinetics of complexation processes; synthesis of receptors; template effects.
ObjectiveThe objective of this class is to reach an understanding of the nature and magnitude of the intermolecular interactions and solvation effects that provide the driving force for the association between molecules and/or ions induced by non-covalent bonding interactions. The lecture (2 h) is complemented by a problem solving class (1 h) which focuses on receptor syntheses and other synthetic aspects of supramolecular chemistry.
ContentPrinciples of molecular recognition: cation complexation, anion complexation, cation and anion complexation in technological applications, complexation of neutral molecules in aqueous solution, non-covalent interactions involving aromatic rings, hydrogen bonding, molecular sef-assembly - a chemical approach towards nanostructures, thermodynamics and kinetics of complexation processes, synthesis of receptors, template effects.
Lecture notesPrinted lecture notes will be available for purchase at the beginning of the class. Problem sets and answer keys will be available on-line.
LiteratureNo compulsory textbooks. Literature for further reading will be presented during the class and cited in the lecture notes.
Prerequisites / NoticeCourse prerequisite: classes in organic and physical chemistry of the first two years of studies.
551-0224-00LAdvanced Proteomics Restricted registration - show details
For master students from the 2nd semester on, also doctoral candidates and post docs.
W4 credits6GP. Picotti, L. Gillet, A. Leitner, P. Pedrioli
AbstractGoal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine.
Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises.
ObjectiveTo discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology.
ContentBlock course teaching current methods for the acquisition and processing of proteomic datasets.
Prerequisites / NoticeNumber of people: Not exceeding 30.
Students from ETHZ, Uni Zurich and University of Basel
Non-ETH students must register at ETH Zurich as special students Link
551-1412-00LMolecular and Structural Biology IV: Visualizing Macromolecules by X-Ray Crystallography and EMW4 credits2VN. Ban, D. Böhringer, T. Ishikawa, M. A. Leibundgut, K. Locher, M. Pilhofer, K. Wüthrich, further lecturers
AbstractThis course provides an in-depth discussion of two main methods to determine the 3D structures of macromolecules and complexes at high resolution: X-ray crystallography and cryo-electron microscopy. Both techniques result in electron density maps that are interpreted by atomic models.
ObjectiveStudents will obtain the theoretical background to understand structure determination techniques employed in X-ray crystallography and electron microscopy, including diffraction theory, crystal growth and analysis, reciprocal space calculations, interpretation of electron density, structure building and refinement as well as validation. The course will also provide an introduction into the use of cryo-electron tomography to visualize complex cellular substructures at sub-nanometer resolutions, effectively bridging the resolution gap between optical microscopy and single particle cryo-electron microscopy. Lectures will be complemented with practical sessions where students will have a chance to gain hands on experience with sample preparation, data processing and structure building and refinement.
Content- History of Structural Molecular Biology

- X-ray diffraction from macromolecular crystals

- Data collection and statistics, phasing methods

- Crystal symmetry and space groups

- X-ray data processing

- Principle of cryo-EM for biological macromolecules I, including hardware of TEM and detectors, image formation principle (phase contrast, spherical aberration, CTF), 3D reconstruction (central-section theorem, backprojection, missing information)

- Single particle analysis, including principle (projection matching, random conical tilt, angular reconstitution)

- Tomography I, including basics and subtomogram averaging

- Tomography - recent techniques, including cryo-FIB
- EM specimen preparation (cryo, negative stain), initial EM data processing

- EM and X-ray structure building, refinement, validation and interpretation

- Model building and refinement
551-1414-00LMolecular and Structural Biology V: Studying Macromolecules by NMR and EPRW4 credits2VF. Allain, A. D. Gossert, G. Jeschke, K. Wüthrich
AbstractThe course provides an overview of experimental methods for studying function and structure of macromolecules at atomic resolution in solution. The two main methods used are Nuclear Magnetic Resonance (NMR) spectroscopy and Electron Paramagnetic Resonance (EPR) spectroscopy.
ObjectiveInsight into the methodology, areas of application and limitations of these two methods for studying biological macromolecules. Practical exercises with spectra to have hands on understanding of the methodology.
ContentPart I: Historical overview of structural biology.
Part II: Basic concepts of NMR and initial examples of applications.
2D NMR and isotope labeling for studying protein function and molecular interactions at atomic level.
Studies of dynamic processes of proteins in solution.
Approaches to study large particles.
Methods for determination of protein structures in solution.
Part III: NMR methods for structurally characterizing RNA and protein-RNA complexes.
Part IV: EPR of biomolecules
Literature1) Wüthrich, K. NMR of Proteins and Nucleic Acids, Wiley-Interscience.
2) Dominguez et al, Prog Nucl Magn Reson Spectrosc. 2011 Feb;58(1-2):1-61.
3) Duss O et al, Methods Enzymol. 2015;558:279-331.
Elective Concept Courses
NumberTitleTypeECTSHoursLecturers
551-0320-00LCellular Biochemistry (Part II)W3 credits2VY. Barral, R. Kroschewski, A. E. Smith
AbstractThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
ObjectiveThe full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry.
The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
ContentSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteratureRecommended supplementary literature may be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
551-0307-01LMolecular and Structural Biology II: Molecular Machines and Cellular Assemblies
D-BIOL students are obliged to take part I and part II as a two-semester course.
W3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course on advanced topics in Molecular Biology and Biochemistry will cover the structure and function of cellular assemblies. General topics in basic biochemistry will be further developed with examples of the function of large cellular machines involved in DNA packaging, translation, virus architecture, RNA processing, cell-cell interactions, and the molecular basis of CRISPER systems.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
literature:
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.