Shinichi Sunagawa: Catalogue data in Spring Semester 2021

Name Prof. Dr. Shinichi Sunagawa
FieldMicrobiome Research
Institut für Mikrobiologie
ETH Zürich, HCI F 417
Vladimir-Prelog-Weg 1-5/10
8093 Zürich
Telephone+41 44 633 61 55
RelationshipAssociate Professor

551-0104-00LFundamentals of Biology II Information Restricted registration - show details
Registrations via myStudies until 29.1.2021 at the latest. Subsequent registrations will not be considered.

General safety regulations:
-Whenever possible the distance rules have to be respected.
-All students have to wear masks throughout the course. Please keep reserve masks ready. Surgical masks (IIR) or medical grade masks (FFP2) without a valve are permitted. Community masks (fabric masks) are not allowed.
-The installation and activation of the Swiss Covid-App is highly encouraged.
-Any additional rules for individual courses have to be respected.
-Students showing any COVID-19 symptoms are not allowed to enter ETH buildings and have to inform the course responsible.
8 credits8PM. Gstaiger, E. Dultz, W. Kovacs, H. Stocker, S. Sunagawa, U. Suter, S. Werner
AbstractThis introductory Laboratory course introduces the student to the entire range of classical and modern molecular biosciences. In the second year (Praktikum GL Bio II) the students will perform three praktikum days in:
- Bioinformatics
- Plant Physiology
- Genetics and
- Cell Biology II.

(total of 12 experiments)

Each experiment takes one full day.
ObjectiveIntroduction to theoretical and experimental biology
Moodle www-link for general Praktikum-information and course material: Moodle

The general Praktikum information (Assignment list, Instructions and Schedule & Performance Sheet) will also be sent to the students directly (E-mail).
ContentThe class is divided into four blocks: Cell Biology II, Genetics, Bioinformatics and Plant Physiology. One block lasts three weeks.

- Cells: Cell types & staining methods, cell fusion & cell motility,
- Tissue and development: histology of mice embryos & embryogenesis
- Repair mechanisms: DNA repair & wound healing,

- Yeast genetics
- Drosophila genetics
- Human genetics

- the command line interface (UNIX/LINUX)
- reinforce programming skills in R
- programmatic, analytical and statistical principles

- Plants and light
- Phytohormones and other growth factors
- Molecular biology of systemic gene silencing
- Literature and presentations

The students will also prepare short presentations (approx. 10 min) of the various topics within this course.
Lecture notesLaboratory manuals

- The protocols can be downloaded from: Moodle

- The protocols can be found from: Moodle

- The protocols can be found from: Moodle

- The protocols can be found from: Moodle
Prerequisites / NoticeTHE PRAKTIKUM RULES:

Your attendance is obligatory and you have to attend all 12 Praktikum days. Absences are only acceptable if you are able to provide a Doctor’s certificate. The original Dr's certificate has to be given to Dr. M. Gstaiger (HPM F43) within five days of the absence of the Praktikum day.

If there will be any exceptional or important situations then you should directly contact the Director of Studies of D-Biol, who will decide if you are allowed to miss a Praktikum day or not.


1. Due to the increased number of students, the official Praktikum registration has to be done, using myStudies, preferably at the end of HS20 but not later than Wednesday January 29, 2021.

2. Later registration is NOT possible and can NOT be accepted!

3. The course registration for FS21 is usually possible at the end of HS20 and you will obtain an E-mail from the Rectorate when the course registration using myStudies is possible.

Students can register for a practice group via myStudies. As soon as the course unit is registered in myStudies, a text box appears indicating that a group can be selected. Accordingly, students can select a group in the next step. If more than 180 students register, the surplus students will be placed on a waiting list and then allocated by the course responsible.

The Praktikum GL BioII FS21 will take place during the following days and therefore, you have to make sure already now that you do not have any other activities & commitments during these days:


26.02.; 05.03.; 12.03.; 19.03.; 26.03.; 16.04.; 23.04.; 30.04.; 07.05.; 21.05.; 28.05.; 04.06.

No Praktikum during the Easter break: 02.04-09.04.
551-1109-00LSeminars in Microbiology Information 0 credits2KW.‑D. Hardt, M. Künzler, J. Piel, S. Sunagawa, J. Vorholt-Zambelli
AbstractSeminars by invited speakers covering selected microbiology themes.
ObjectiveDiscussion of selected microbiology themes presented by invited speakers.
551-1298-00LGenetics, Genomics, Bioinformatics Information 4 credits2V + 2UE. Hafen, C. Beyer, B. Christen, U. K. Genick, J. Piel, R. Schlapbach, G. Schwank, S. Sunagawa, K. Weis, A. Wutz
AbstractThe course provides the basis of modern genetics, genomics and bioinformatics. A special focus is placed on the use of these tools for the understanding of biological processes in bacteria, model organisms and humans. The unit uses the principle of blended learning consisting of self-study modules in Moodle, tasks and input lectures by experts from the department.
ObjectiveAt the end of this course you know the most important genetic tools in different organisms. You can use the essential methods in bioinformatics by using online tools. You know the advantages and disadvantages of various model organisms to understand biological processes. You know the various mutagenesis methods and other tools to disrupt gene function and can discuss their merits and drawbacks. You are aware of the difficulties in choosing a phenotype for selection in a mutagenesis experiment. Finally, you can describe how you would study a specific biological process by choosing a model organism and the appropriate genetic or genomic tools.
ContentThe appearance and function of an organism (phenotype) is determined by the interplay between its genome (genotype) and the environment: Genotype + environment = phenotype. Understanding these interactions to the point where we can ultimately predict the phenotype from knowledge of the genotype and environmental factors is one oft the great challenges of biology.

In the course Bio IA you learnt about the composition and function of the genome and how it is inherited. The goal of this course is that you learn how genetic, genomic and bioinformatics methods are used to understand biological processes (the connection between genotype and phenotype).

You will start by refreshing and deepening your knowledge of the basic principles of genetics and genomics in an interactive learning modules on the Moodle platform. This is followed by an introduction of the basic tools of bioinformatics and genomic analysis.

After you have mastered the basic principles you will learn how to study biological processes either by inactivating specific genes or by randomly mutagenizing the entire genome. You will be introduced to different model organisms (bacteria, yeast, Drosophila) and humans.

At the end of this first part of the course, you will test your knowledge by working with a group of fellow students to design your own genetic study.

Conventional genetic methods rely on the alteration of the function of single genes and on the observation of the effect on the organism (phenotype). Based on the observed phenotype one deduces the normal function of the gene. However, this is a strong simplification. Even if environmental factors are controlled, phenotypes are very rarely controlled by a single gene. It is therefore important to understand the influence of the entire genome in conjunction with environmental factors on a given phenotype (e.g. human disease). Modern methods in genomics now permit first approaches in this direction. Therefore, the focus of the second part of the unit is on genomics methods. You learn, how the influence of the entire genome on a specific phenotype is detected and what challenges are involved in the analysis and the interpretation of the results. We will examine these methods in model organisms and humans. You will also learn how the genome of cancer cells changes under the constant selection for these cells to survive and how this genome analysis provides new insights into diagnosis and therapy.

This course is based on active learning. Each week consists of a learning unit with clearly defined learning goals. In the first two hours you will learn the basics from texts, videos and questionnaires on the Moodle platform. In the third lecture an expert on the topic of the week (e.g. genetic screens in yeast) from the department will give an input lecture that builds on the basic knowledge that you acquired. In the fourth lecture you will discuss the tests and topics of the week with the expert. During the semester you will have access to assistants and lecturers via the Moodle online forum.
Lecture notesThe learning material and slides of the input lectures are available on Moodle. There you will also find further information (articles, links, videos).
LiteratureAll texts and references will be available on Moodle. To follow the most recent developments in this rapidly evolving field follow the following experts on Twitter:
und/oder @ehafen
Prerequisites / NoticeThe course builds on the course Bio IA, in particular on that course's content regarding genetics and genomics. The course is based on self-learning units on Moodle, input lectures by experts from D-BIOL and exercises.