Search result: Catalogue data in Autumn Semester 2016

Health Sciences and Technology Master Information
Major in Molecular Health Sciences
Compulsory Courses
NumberTitleTypeECTSHoursLecturers
376-0300-00LTranslational Science for Health and Medicine Restricted registration - show details O3 credits2GJ. Goldhahn, C. Wolfrum
AbstractTranslational science is a cross disciplinary scientific research that is motivated by the need for practical applications that help people. The course should help to clarify basics of translational science, illustrate successful applications and should enable students to integrate key features into their future projects.
ObjectiveAfter completing this course, students will be able to understand:
Principles of translational science (including project planning, ethics application, basics of resource management and interdisciplinary communication)
ContentWhat is translational science and what is it not?
How to identify need?
- Disease concepts and consequences for research
- Basics about incidence, prevalence etc., and orphan indications
How to choose the appropriate research type and methodology
- Ethical considerations including ethics application
- Pros and cons of different types of research
- Coordination of complex approaches incl. timing and resources
How to measure success?
- Outcome variables
- Improving the translational process
Challenges of communication?
How independent is translational science?
- Academic boundary conditions vs. industrial influences
Positive and negative examples will be illustrated by distinguished guest speakers.
Electives
Elective Courses I
NumberTitleTypeECTSHoursLecturers
551-0309-00LConcepts in Modern GeneticsW6 credits4VY. Barral, D. Bopp, A. Hajnal, M. Stoffel, O. Voinnet
AbstractConcepts of modern genetics and genomics, including principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference.
ObjectiveThis course focuses on the concepts of classical and modern genetics and genomics.
ContentThe topics include principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference.
Lecture notesScripts and additional material will be provided during the semester.
Prerequisites / NoticeThis course is a co-production of the University of Zurich and ETH Zurich, and will be taught in English. The course takes place on Monday afternoon at ETH Hoenggerberg, and on Tuesday morning at UZH Irchel.
Elective Courses II
NumberTitleTypeECTSHoursLecturers
327-2125-00LMicroscopy Training SEM I - Introduction to SEM Restricted registration - show details
Number of participants limited to 6.
The participants will be chosen based on a short motivation letter. Please send this letter to S. Rodighiero (main lecturer) as soon as possible.
W1 credit3PS. Rodighiero, A. G. Bittermann, K. Kunze, J. Reuteler
AbstractThe introductory course on Scanning Electron Microscopy (SEM) emphasizes hands-on learning. Using 2 SEM instruments, students have the opportunity to study their own samples, or standard test samples, as well as solving exercises provided by ScopeM scientists.
Objective- Set-up, align and operate a SEM successfully and safely.
- Accomplish imaging tasks successfully and optimize microscope performances.
- Master the operation of a low-vacuum and field-emission SEM and EDX instrument.
- Perform sample preparation with corresponding techniques and equipment for imaging and analysis
- Acquire techniques in obtaining secondary electron and backscatter electron micrographs
- Perform EDX qualitative and semi-quantitative analysis
ContentDuring the course, students learn through lectures, demonstrations, and hands-on sessions how to setup and operate SEM instruments, including low-vacuum and low-voltage applications.
This course gives basic skills for students new to SEM. At the end of the course, students with no prior experience are able to align a SEM, to obtain secondary electron (SE) and backscatter electron (BSE) micrographs and to perform energy dispersive X-ray spectroscopy (EDX) qualitative and semi-quantitative analysis. The procedures to better utilize SEM to solve practical problems and to optimize SEM analysis for a wide range of materials will be emphasized.

- Discussion of students' sample/interest
- Introduction and discussion on Electron Microscopy and instrumentation
- Lectures on electron sources, electron lenses and probe formation
- Lectures on beam/specimen interaction, image formation, image contrast and imaging modes.
- Lectures on sample preparation techniques for EM
- Brief description and demonstration of the SEM microscope
- Practice on beam/specimen interaction, image formation, image contrast (and image processing)
- Student participation on sample preparation techniques
- Scanning Electron Microscopy lab exercises: setup and operate the instrument under various imaging modalities
- Lecture and demonstrations on X-ray micro-analysis (theory and detection), qualitative and semi-quantitative EDX and point analysis, linescans and spectral mapping
- Practice on real-world samples and report results
Literature- Detailed course manual
- Williams, Carter: Transmission Electron Microscopy, Plenum Press, 1996
- Hawkes, Valdre: Biophysical Electron Microscopy, Academic Press, 1990
- Egerton: Physical Principles of Electron Microscopy: an introduction to TEM, SEM and AEM, Springer Verlag, 2007
Prerequisites / NoticeNo mandatory prerequisites. Please consider the prior attendance to EM Basic lectures (551- 1618-00V; 227-0390-00L; 327-0703-00L) as suggested prerequisite.
327-2126-00LMicroscopy Training TEM I - Introduction to TEM Restricted registration - show details
Does not take place this semester.
Number of participants limited to 6.

The participants will be chosen based on a short motivation letter. Please send this letter to S. Rodighiero (main lecturer).
W1 credit3P
AbstractThe introductory course on Transmission Electron Microscopy (TEM) provides theoretical and hands-on learning for new operators, utilizing lectures, demonstrations, and hands-on sessions.
Objective- Overview of TEM theory, instrumentation, operation and applications.
- Alignment and operation of a TEM, as well as acquisition and interpretation of images, diffraction patterns, accomplishing basic tasks successfully.
- Knowledge of electron imaging modes (including Scanning Transmission Electron Microscopy), magnification calibration, and image acquisition using CCD cameras.
- To set up the TEM to acquire diffraction patterns, perform camera length calibration, as well as measure and interpret diffraction patterns.
- Overview of techniques for specimen preparation.
ContentUsing two Transmission Electron Microscopes the students learn how to align a TEM, select parameters for acquisition of images in bright field (BF) and dark field (DF), perform scanning transmission electron microscopy (STEM) imaging, phase contrast imaging, and acquire electron diffraction patterns. The participants will also learn basic and advanced use of digital cameras and digital imaging methods.

- Introduction and discussion on Electron Microscopy and instrumentation.
- Lectures on electron sources, electron lenses and probe formation.
- Lectures on beam/specimen interaction, image formation, image contrast and imaging modes.
- Lectures on sample preparation techniques for EM.
- Brief description and demonstration of the TEM microscope.
- Practice on beam/specimen interaction, image formation, Image contrast (and image processing).
- Demonstration of Transmission Electron Microscopes and imaging modes (Phase contrast, BF, DF, STEM).
- Student participation on sample preparation techniques.
- Transmission Electron Microscopy lab exercises: setup and operate the instrument under various imaging modalities.
- TEM alignment, calibration, correction to improve image contrast and quality.
- Electron diffraction.
- Practice on real-world samples and report results.
Literature- Detailed course manual
- Williams, Carter: Transmission Electron Microscopy, Plenum Press, 1996
- Hawkes, Valdre: Biophysical Electron Microscopy, Academic Press, 1990
- Egerton: Physical Principles of Electron Microscopy: an introduction to TEM, SEM and AEM, Springer Verlag, 2007
Prerequisites / NoticeNo mandatory prerequisites. Please consider the prior attendance to EM Basic lectures (551- 1618-00V; 227-0390-00L; 327-0703-00L) as suggested prerequisite.
376-0815-00LWriting your Master's Thesis: Natural Sciences and Engineering C1-C2 Restricted registration - show details
Does not take place this semester.
Your course regristration is only valid with a simultaneous online registration at the language center (Link).

Number of participants limited to 15 (3 courses are available).

Attention: Registration is only possible from 12.9. (from 11.30h) - 15.9.2016
W2 credits2VS. Milligan
AbstractWe'll prepare you to produce your MSc thesis. You'll learn how to structure your thesis, write scientific English, and manage your writing efficiently. You'll receive detailed feedback on work in progress.
ObjectiveBy the end of the course students are able to plan, draft, and edit academic English papers and theses; structure and write clear texts in a style which is acceptable to their academic discourse community; manage the writing process efficiently; select formal vocabulary and use it in a generally accurate and correct manner; choose and use generally suitable grammatical structures, punctuation, and orthographic conventions, assess their own effectiveness as writers of academic English, and identify areas in which further development is needed.
ContentThe course covers the writing context; the writing process; structuring sentences, paragraphs, longer sections (such as introduction, methods, results, and discussion), and whole texts; presenting and integrating non-textual elements such as graphs and tables; and editing and correcting drafts and proofs. Each lesson comprises a mixture of elements, including specialist input, individual tasks, pairwork, and groupwork. Active participation is expected.
551-0223-00LImmunology III Information W4 credits2VM. Kopf, M. Bachmann, J. Kisielow, A. Lanzavecchia, S. R. Leibundgut, A. Oxenius, R. Spörri
AbstractThis course provides a detailed understanding of
- development of T and B cells
- the dynamics of a immune response during acute and chronic infection
- mechanisms of immunopathology
- modern vaccination strategies
Key experimental results will be shown to help understanding how immunological text book knowledge has evolved.
ObjectiveObtain a detailed understanding of
- the development, activation, and differentiation of different types of T cells and their effectormechanisms during immune responses,
- Recognition of pathogenic microorganisms by the host cells and molecular events thereafter,
- events and signals for maturation of naive B cells to antibody producing plasma cells and memory B cells.
- Optimization of B cell responses by intelligent design of new vaccines
Contento Development and selection of CD4 and CD8 T cells, natural killer T cells (NKT), and regulatory T cells (Treg)
o NK T cells and responses to lipid antigens
o Differentiation, characterization, and function of CD4 T cell subsets such as Th1, Th2, and Th17
o Overview of cytokines and their effector function
o Co-stimulation (signals 1-3)
o Dendritic cells
o Evolution of the "Danger" concept
o Cells expressing Pattern Recognition Receptors and their downstream signals
o T cell function and dysfunction in acute and chronic viral infections
LiteratureDocuments of the lectures are available for download at:
Link
Prerequisites / NoticeImmunology I and II recommended but not compulsory
551-0317-00LImmunology I Information W3 credits2VA. Oxenius, M. Kopf
AbstractIntroduction into structural and functional aspects of the immune system.
Basic knowledge of the mechanisms and the regulation of an immune response.
ObjectiveIntroduction into structural and functional aspects of the immune system.
Basic knowledge of the mechanisms and the regulation of an immune response.
Content- Introduction and historical background
- Innate and adaptive immunity, Cells and organs of the immune system
- B cells and antibodies
- Generation of diversity
- Antigen presentation and Major Histoincompatibility (MHC) antigens
- Thymus and T cell selection
- Autoimmunity
- Cytotoxic T cells and NK cells
- Th1 and Th2 cells, regulatory T cells
- Allergies
- Hypersensitivities
- Vaccines, immune-therapeutic interventions
Lecture notesElectronic access to the documentation will be provided. The link can be found at "Lernmaterialien"
Literature- Kuby, Immunology, 7th edition, Freemen + Co., New York, 2009
Prerequisites / NoticeImmunology I (WS) and Immunology II (SS) will be examined as one learning entity in a "Sessionsprüfung".
551-0512-00LCurrent Topics in Molecular and Cellular Neurobiology Information Restricted registration - show details
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 i.e. 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.
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%).
551-0571-00LFrom DNA to Diversity (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BIO336

Mind the enrolment deadlines at UZH:
Link
W2 credits2VA. Hajnal, D. Bopp, E. Hafen
AbstractThe evolution of the various body-plans is investigated by means of comparison of developmentally essential control genes of molecularly analysed model organisms.
ObjectiveBy the end of this module, each student should be able to
- recognize the universal principles underlying the development of
different animal body plans.
- explain how the genes encoding the molecular toolkit have evolved
to create animal diversity.
- relate changes in gene structure or function to evolutionary
changes in animal development.
Key skills:
By the end of this module, each student should be able to
- present and discuss a relevant evolutionary topic in an oral
presentation
- select and integrate key concepts in animal evolution from
primary literature
- participate in discussions on topics presented by others
551-1003-00LMethods of Biological Analysis Information W3 credits3GR. Aebersold, M. Badertscher, K. Weis
Abstract529-1042-00
Principles of the most important separation techniques and the interpretation of molecular spectra.

551-1003-00
The course will teach the basis and typical applications of methods for the analysis of nucleic acid sequences, mass spectrometric analysis of proteins and proteomes and advanced light and fluorescent imaging methods.
Objective529-1042-00
Knowledge of the necessary basics and the possibilities of application of the relevant spectroscopical and separation methods in analytical chermistry.

551-1003-00
Knowledge of the theoretical basis of the methods for nucleic acid sequence analysis, mass spectrometry based protein and proteome analysis and advanced light and fluorescent imaging methods, and an understanding of the application of these principles in experimental biology.
Content529-1042-00
Application oriented basics of instrumental analysis in organic chemistry and the empirical employment of the methods of structure elucidation (mass spectrometry, NMR-, IR-, UV/VIS spectroscopy). Basics and application of chromatographic and electrophoretic separation methods. Application of the knowledge by practising.

551-1003-00
The course will consist of lectures covering the theoretical and technical base of the respective analytical methods and of exercises where typical applications of the methods in modern experimental biology are discussed.
Lecture notes529-1042-00
A comprehensive script is available in the HCI-Shop. A summary of the part "Spektroskopie" defines the relevant material for the exam.

551-1003-00
Materials supporting the lectures and exercises will be made available via Moodle.
Literature529-1042-00
- Pretsch E., Bühlmann P., Badertscher M. Structure Determination of Organic Compounds, 5th revised and enlarged English edition, Springer-Verlag, Berlin 2009;
- Pretsch E., Bühlmann P., Badertscher M., Spektroskopische Daten zur Strukturaufklärung organischer Verbindungen, fünfte Auflage, Springer-Verlag, Berlin 2010;
- D.A. Skoog, J.J. Leary, Instrumentelle Analytik, Grundlagen, Geräte, Anwendungen, Springer, Berlin, 1996;
- K. Cammann, Instrumentelle Analytische Chemie, Verfahren, Anwendungen, Qualitätssicherung, Spektrum Akademischer Verlag, Heidelberg, 2001;
- R. Kellner, J.-M. Mermet, M. Otto, H.M. Widmer, Analytical Chemistry, Wiley-VCH Verlag, Weinheim, 1998;
- K. Robards, P.R.Haddad, P.E. Jackson, Principles and practice of modern chromatographic methods, Academic Press, London, 1994;
Prerequisites / Notice529-1042-00
Prerequisites:
- 529-1001-01 V "Allgemeine Chemie I (für Biol./Pharm.Wiss.)"
- 529-1001-00 P "Allgemeine Chemie I (für Biol./Pharm.Wiss.)"
- 529-1011-00 G "Organische Chemie I (für Biol./Pharm.Wiss.)"
551-1105-00LGlycobiologyW4 credits2VM. Aebi, T. Hennet
AbstractStructural principles, nomenclature and different classes of glycosylation. The different pathways of N- and O-linked protein glycosylation and glycolipid biosynthesis in prokaryotes and eukaryotes are discussed. Specific glycan binding proteins and their role in deciphering the glycan code are presented. The role of glycans in infectious diseases, antigen mimicry and autoimmunity are discussed.
ObjectiveDetailed knowledge in 1) the different areas of prokaryotic and eukaryotic glycobiology, in particular in the biosynthesis of glycoproteins and glycolipids, 2) the cellular machinery required for these pathways, 3) the principles of carbohydrate/protein interaction, 4) the function of lectins, 5) the role of glycans in infectious disease.
ContentStructure and linkages; analytical approaches; N-linked protein glycosylation (ER, Golgi); glycan-assisted protein folding and quality control; O-linked protein glycosylation; glucosaminoglycans; glycolipids; prokaryotic glycosylation pathways; lectins; glycans and infectious disease
Lecture noteshandouts
LiteratureIntroduction to Glycobiology; M.E.Taylor, K.Drickamer, Oxford University Press, 2003
Essentials of Glycobiology (second edition); A.Varki et al. Cold Spring Harbor Laboratory Press, 2009
Prerequisites / NoticeThe course will be in English. It will include the preparation of short essays (marked) about defined topics in Glycobiology.
551-1145-00LViral and non-Viral Vectors for Human Gene-Therapy - from Pathogens to Safe Medical Applications
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BIO708

Mind the enrolment deadlines at UZH:
Link
W2 credits3VUniversity lecturers
AbstractBasic aspects of virology, the viral mechanisms for transfer of genetic material into cells, different vector-systems and target cells, animal models, specific applications for inborn diseases of the immune system and of metabolism, adverse effects, and new developments of vector systems will be taught.
ObjectiveKnowledge of important viral and non-viral vector systems.
Knowledge of application in human diseases.
Knowledge of limiting factors.
551-1153-00LSystems Biology of Metabolism
Number of participants limited to 15.
W4 credits2VU. Sauer, N. Zamboni, M. Zampieri
AbstractStarting from contemporary biological problems related to metabolism, the course focuses on systems biological approaches to address them. In a problem-oriented, this-is-how-it-is-done manner, we thereby teach modern methods and concepts.
ObjectiveDevelop a deeper understanding of how relevant biological problems can be solved, thereby providing advanced insights to key experimental and computational methods in systems biology.
ContentThe course will be given as a mixture of lectures, studies of original research and guided discussions that focus on current research topics. For each particular problem studied, we will work out how the various methods work and what their capabilities/limits are. The problem areas range from microbial metabolism to cancer cell metabolism and from metabolic networks to regulation networks in populations and single cells. Key methods to be covered are various modeling approaches, metabolic flux analyses, metabolomics and other omics.
Lecture notesScript and original publications will be supplied during the course.
Prerequisites / NoticeThe course extends many of the generally introduced concepts and methods of the Concept Course in Systems Biology. It requires a good knowledge of biochemistry and basics of mathematics and chemistry.
551-1171-00LImmunology: from Milestones to Current TopicsW4 credits2SB. Ludewig, J. Kisielow, M. Kopf, A. Oxenius, University lecturers
AbstractMilestones in Immunology: on old concepts and modern experiments
ObjectiveThe course will cover six grand topics in immunology (B cells, innate immunity, antigen presentation, tumor immunity, thymus and T cells, cytotoxic T cells and NK cells) and for each grand topic four hours will be allocated. During the first double hour, historical milestone papers will be presented by the supervisor providing an overview on the development of the conceptional framework and critical technological advances. The students will also prepare themselves for this double lecture by reading the historical milestone papers and contributing to the discussion. In the following lecture up to four students will present each a recent high impact research paper which emerged from the landmark achievements of the previously discussed milestone concepts.
ContentMilestones and current topics of innate immunity, antigen presentatino, B cells, thymus and T cells, cytotoxic T cells and NK cells, and tumor immunology.
Lecture notesOriginal and review articles will be distributed by the lecturer.
LiteratureLiteraturunterlagen werden vor Beginn des Kurses auf folgender website zugänglich sein: Moodle Course Link
551-1303-00LCellular Biochemistry of Health and Disease Information Restricted registration - show details
Number of participants limited to 15.
W4 credits2SP. Picotti, Y. Barral, J. Fernandes de Matos, V. Korkhov, B. Kornmann, R. Kroschewski, M. Peter, A. E. Smith, K. Weis
AbstractDuring this Masters level seminar style course, students will explore current research topics in cellular biochemistry focused on the structure, function and regulation of selected cell components, and the consequences of dysregulation for pathologies.
ObjectiveStudents will work with experts toward a critical analysis of cutting-edge research in the domain of cellular biochemistry, with emphasis on normal cellular processes and the consequences of their dysregulation. At the end of the course, students will be able to introduce, present, evaluate, critically discuss and write about recent scientific articles in the research area of cellular biochemistry.
ContentGuided by an expert in the field, students will engage in classical round-table style discussions of current literature with occasional frontal presentations. Students will alternate as discussion leaders throughout the semester, with the student leader responsible to briefly summarize key general knowledge and context of the assigned primary research paper. Together with the faculty expert, all students will participate in discussion of the primary paper, including the foundation of the biological question, specific questions addressed, key methods, key results, remaining gaps and research implications.
LiteratureThe literature will be provided during the course
Prerequisites / NoticeThe course will be taught in English.
551-1323-00LFundamentals of Biology II: Biochemistry and Molecular Biology Information W4 credits4VK. Locher, N. Ban, R. Glockshuber, E. Weber-Ban
AbstractThe course provides an introduction to Biochemistry / Molecular Biology with some emphasis on chemical and biophysical aspects.
ObjectiveTopics include the structure-function
relationship of proteins / nucleic acids, protein folding, enzymatic catalysis, cellular pathways involved in bioenergetics and the biosynthesis and breakdown of amino acids, glycans, nucleotides, fatty acids and phospholipids, and steroids. There will also be a discussion of DNA replication and repair, transcription, and translation.
Lecture notesnone
Literaturemandatory: "Biochemistry",
Autoren: Berg/Tymoczko/Stryer, 8th edition, Palgrave Macmillan, International edition (the English version will be preordered at the Polybuchhandlung)
Prerequisites / NoticeSome of the lectures are given in the English language.
636-0003-00LBiological Engineering and BiotechnologyW6 credits3VM. Fussenegger
AbstractBiological Engineering and Biotechnology will cover the latest biotechnological advances as well as their industrial implementation to engineer mammalian cells for use in human therapy. This lecture will provide forefront insights into key scientific aspects and the main points in industrial decision-making to bring a therapeutic from target to market.
Objective1. Insight Into The Mammalian Cell Cycle. Cycling, The Balance Between Proliferation and Cancer - Implications For Biopharmaceutical Manufacturing. 2. The Licence To Kill. Apoptosis Regulatory Networks - Engineering of Survival Pathways To Increase Robustness of Production Cell Lines. 3. Everything Under Control I. Regulated Transgene Expression in Mammalian Cells - Facts and Future. 4. Secretion Engineering. The Traffic Jam getting out of the Cell. 5. From Target To Market. An Antibody's Journey From Cell Culture to The Clinics. 6. Biology and Malign Applications. Do Life Sciences Enable the Development of Biological Weapons? 7. Functional Food. Enjoy your Meal! 8. Industrial Genomics. Getting a Systems View on Nutrition and Health - An Industrial Perspective. 9. IP Management - Food Technology. Protecting Your Knowledge For Business. 10. Biopharmaceutical Manufacturing I. Introduction to Process Development. 11. Biopharmaceutical Manufacturing II. Up- stream Development. 12. Biopharmaceutical Manufacturing III. Downstream Development. 13. Biopharmaceutical Manufacturing IV. Pharma Development.
Lecture notesHandsout during the course.
636-0017-00LComputational Biology Information W4 credits3GT. Stadler, C. Magnus
AbstractThe aim of the course is to provide up-to-date knowledge on how we can study biological processes using genetic sequencing data. Computational algorithms extracting biological information from genetic sequence data are discussed, and statistical tools to understand this information in detail are introduced.
ObjectiveAttendees will learn which information is contained in genetic sequencing data and how to extract information from them using computational tools. The main concepts introduced are:
* stochastic models in molecular evolution
* phylogenetic & phylodynamic inference
* maximum likelihood and Bayesian statistics
Attendees will apply these concepts to a number of applications yielding biological insight into:
* epidemiology
* pathogen evolution
* macroevolution of species
ContentThe course consists of four parts. We first introduce modern genetic sequencing technology, and algorithms to obtain sequence alignments from the output of the sequencers. We then present methods to directly analyze this alignment (such as BLAST algorithm, GWAS approaches). Second, we introduce mechanisms and concepts of molecular evolution, i.e. we discuss how genetic sequences change over time. Third, we employ evolutionary concepts to infer ancestral relationships between organisms based on their genetic sequences, i.e. we discuss methods to infer genealogies and phylogenies. We finally introduce the field of phylodynamics. The aim of that field is to understand and quantify the population dynamic processes (such as transmission in epidemiology or speciation & extinction in macroevolution) based on a phylogeny. Throughout the class, the models and methods are illustrated on different datasets giving insight into the epidemiology and evolution of a range of infectious diseases (e.g. HIV, HCV, influenza, Ebola). Applications of the methods to the field of macroevolution provide insight into the evolution and ecology of different species clades. Students will be trained in the algorithms and their application both on paper and in silico as part of the exercises.
Lecture notesSlides of the lecture will be available online.
Link
LiteratureThe course is not based on any of the textbooks below, but they are excellent choices as accompanying material:
* Yang, Z. 2006. Computational Molecular Evolution.
* Felsenstein, J. 2004. Inferring Phylogenies.
* Semple, C. & Steel, M. 2003. Phylogenetics.
* Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST
Prerequisites / NoticeBasic knowledge in linear algebra, analysis, and statistics will be helpful. Some programming experience will be useful for the exercises, but is not required. Programming skills will not be tested in the examination.
636-0507-00LSynthetic Biology II Restricted registration - show details W4 credits4AS. Panke, Y. Benenson, J. Stelling
Abstract7 months biological design project, during which the students are required to give presentations on advanced topics in synthetic biology (specifically genetic circuit design) and then select their own biological system to design. The system is subsequently modeled, analyzed, and experimentally implemented. Results are presented at an international student competition at the MIT (Cambridge).
ObjectiveThe students are supposed to acquire a deep understanding of the process of biological design including model representation of a biological system, its thorough analysis, and the subsequent experimental implementation of the system and the related problems.
ContentPresentations on advanced synthetic biology topics (eg genetic circuit design, adaptation of systems dynamics, analytical concepts, large scale de novo DNA synthesis), project selection, modeling of selected biological system, design space exploration, sensitivity analysis, conversion into DNA sequence, (DNA synthesis external,) implementation and analysis of design, summary of results in form of scientific presentation and poster, presentation of results at the iGEM international student competition (Link).
Lecture notesHandouts during course
Prerequisites / NoticeThe final presentation of the project is typically at the MIT (Cambridge, US). Other competing schools include regularly Imperial College, Cambridge University, Harvard University, UC Berkeley, Princeton Universtiy, CalTech, etc.

This project takes place between end of Spring Semester and beginning of Autumn Semester. Registration in April.

Please note that the number of ECTS credits and the actual work load are disconnected.
701-1703-00LEvolutionary Medicine for Infectious DiseasesW3 credits2GA. Hall
AbstractThis course explores infectious disease from both the host and pathogen perspective. Through short lectures, reading and active discussion, students will identify areas where evolutionary thinking can improve our understanding of infectious diseases and, ultimately, our ability to treat them effectively.
ObjectiveStudents will learn to (i) identify evolutionary explanations for the origins and characteristics of infectious diseases in a range of organisms and (ii) evaluate ways of integrating evolutionary thinking into improved strategies for treating infections of humans and animals. This will incorporate principles that apply across any host-pathogen interaction, as well as system-specific mechanistic information, with particular emphasis on bacteria and viruses.
ContentWe will cover several topics where evolutionary thinking is relevant to understanding or treating infectious diseases. This includes: (i) determinants of pathogen host range and virulence, (ii) dynamics of host-parasite coevolution, (iii) pathogen adaptation to evade or suppress immune responses, (iv) antimicrobial resistance, (v) evolution-proof medicine. For each topic there will be a short (< 30 minutes) introductory lecture, before students independently research the primary literature and develop half a page of discussion points and questions, followed by interactive discussion in class.
LiteratureStudents will read the primary literature on each topic, and in places we will use the following books:

Schmid Hempel 2011 Evolutionary Parasitology
Stearns & Medzhitov 2016 Evolutionary Medicine
Prerequisites / NoticeA basic understanding of evolutionary biology, microbiology or parasitology will be advantageous but is not essential.
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