Search result: Catalogue data in Spring Semester 2020

Biology Master Information
Elective Major Subject Areas
Elective Major: Biochemistry
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, L. Eberl, U. F. Greber, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander
AbstractLiterature seminar for students at the masters level and PhD students. Introduction to the current research topics in infectious diseases; Introduction to key pathogens which are studied as model organisms in this field; Overview over key research groups in the field of infectious diseases in Zürich.
ObjectiveWorking with the current research literature. Getting to know the key pathogens serving as model organisms and the research technologies currently used in infection biology.
Contentfor each model pathogen (or key technology):
1. introduction to the pathogen
2. Discussion of one current research paper.
The paper will be provided by the respective supervisor. He/she will give advice (if required) and guide the respective literature discussion.
Lecture notesTeachers will provide the research papers to be discussed.
Students will prepare handouts for the rest of the group for their assigned seminar.
LiteratureTeachers will provide the research papers to be discussed.
Prerequisites / NoticeRestricted to max 22 students. Please sign up until two weeks before the beginning of the semester via e-mail to 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 credits2VH.‑M. Fischer, 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 by April 20, 2020. To apply a curriculum vitae and an application letter need to be submitted. The notification of acceptance will be given by May 22, 2020. 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, 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, 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 notesHand-outs, 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: BIO256

Mind the enrolment deadlines at UZH:
Link
W2 credits1VUniversity 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.
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