Search result: Catalogue data in Autumn Semester 2017

Health Sciences and Technology Master Information
Major in Molecular Health Sciences
Electives
Elective Courses II
NumberTitleTypeECTSHoursLecturers
327-2125-00LMicroscopy Training SEM I - Introduction to SEM Restricted registration - show details
Number of participants limited to 9.

Master students will have priority over PhD students. PhD students may still enrol, but will be asked for a fee (http://www.scopem.ethz.ch/education/MTP.html).
W2 credits3PS. Rodighiero, A. G. Bittermann, L. Grafulha Morales, 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
Number of participants limited to 6.

Master students will have priority over PhD students. PhD students may still enrol, but will be asked for a fee (http://www.scopem.ethz.ch/education/MTP.html).
W2 credits3PS. Rodighiero, E. J. Barthazy Meier, A. G. Bittermann, F. Gramm
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.
376-0121-00LMultiscale Bone Biomechanics Restricted registration - show details
Number of participants limited to 25.
W6 credits4SR. Müller
AbstractThe seminar provides state-of-the-art insight to the biomechanical function of bone from molecules, to cells, tissue and up to the organ. Multiscale imaging and simulation allows linking different levels of hierarchy, where systems biology helps understanding the mechanobiological response of bone to loading and injury in scenarios relevant for personalized health and translational medicine.
ObjectiveThe learning objectives include 1. advanced knowledge of the state-of-the-are in multiscale bone biomechanics; 2. basic understanding of the biological principles governing bone in health, disease and treatment from molecules, to cells, tissue and up to the organ; 3. good understanding of the prevalent biomechanical testing and imaging techniques on the various levels of bone hierarchy; 4. practical implementation of state-of-the-art multiscale simulation techniques; 5. improved programing skills through the use of 4th generation scripting language; 6. hands on experience in designing solutions for clinical and industrial problems; 7. encouragement of critical thinking and creating an environment for independent and self-directed studying.
ContentBone is one of the most investigated biological materials due to its primary function of providing skeletal stability. Bone is susceptible to different local stimuli including mechanical forces and has great capabilities in adapting its mechanical properties to the changes in its environment. Nevertheless, aging or hormonal changes can make bone lose its ability to remodel appropriately, with loss of strength and increased fracture risk as a result, leading to devastating diseases such as osteoporosis. To better understand the biomechanical function of bone, one has to understand the hierarchical organization of this fascinating material down from the molecules, to the cells, tissue and up to the organ. Multiscale imaging and simulation allows to link these different levels of hierarchy. Incorporating systems biology approaches, not only biomechanical strength of the material can be assessed but also the mechanobiological response of the bone triggered by loading and injury in scenarios relevant for personalized health and translational medicine. Watching cells working together to build and repair bone in a coordinated fashion is a spectacle, which will need dynamic image content and deep discussions in the lecture room to probe the imagination of the individual student interested in the topic.

For the seminar, concepts of video lectures will be used in a flipped class room setup, where students can study the basic biology, engineering and mathematical concepts in video tutorials online. All videos and animations will be incorporated in an eSkript (eskript.ethz.ch) allowing studying and eventually even interactive course participation online. It is anticipated that the students need to prepare 2x45 minutes for the study of the actual lecture material. The Friday morning time slots will be used for students, who want to complete these assignments in a classroom setting. The student will have to study independently or in groups, but lecturer will be available for questions and answers during that time. In the Friday afternoon time slots, short clips with video/animation content will be used to introduce problems and discuss specific scientific findings using multiscale imaging and simulation technology. The students will have to form small groups to try to solve such problems and to present their solutions for advanced multiscale investigation of bone ranging from basic science to personalized health and onto translational medicine.
Lecture notesMaterial will be provided in Moodle and eScript (eskript.ethz.ch).
Prerequisites / NoticeSeminar will be held in English.
376-1151-00LTranslation of Basic Research Findings from Genetics and Molecular Mechanisms of Aging Restricted registration - show details
Number of participants limited to 30.
W3 credits2VC. Ewald
AbstractRecently, several start-up companies are aiming to translate basic molecular findings into new drugs/therapeutic interventions to slow aging or post-pone age-related diseases (e.g., Google founded Calico or Craig Venter's Human Longevity, Inc.). This course will teach students the basic skill sets to formulate their own ideas, design experiments to test them and explains the next steps to translat
ObjectiveThe overall goal of this course is to be able to analyse current therapeutic interventions to identify an unmet need in molecular biology of aging and apply scientific thinking to discover new mechanisms that could be used as a novel therapeutic intervention.
Learning objectives include:
1. Evaluate the current problem of our aging population, the impact of age-dependent diseases and current strategies to prevent these age-dependent diseases.
2. Analyse/compare current molecular/genetic strategies that address these aging problems.
3. Analyse case studies about biotech companies in the aging sector. Apply the scientific methods to formulate basic research questions to address these problems.
4. Generate own hypotheses (educated guess/idea), design experiments to test them, and map out the next steps to translate them.
ContentOverview of aging and age-related diseases. Key discoveries in molecular biology of aging. Case studies of biotech companies addressing age-related complications. Brief introduction from bench to bedside with focus on start-up companies.
Prerequisites / NoticeNo compulsory prerequisites, but student should have basic knowledge about genetics and molecular biology.
376-1622-00LPractical Methods in Tissue Engineering Restricted registration - show details
Number of participants limited to 16
W5 credits4PK. Würtz-Kozak, O. Krupkova, M. Zenobi-Wong
AbstractThe goal of this course is to teach MSc students the necessary skills for doing research in the fields of tissue engineering and regenerative medicine.
ObjectivePractical exercises and demonstrations on topics including sterile cell culture, light microscopy and histology, protein and gene expression analysis, and viability assays are covered. The advantages of 3D cell cultures will be discussed and practical work on manufacturing and evaluating hydrogels and scaffolds for tissue engineering will be performed in small groups. In addition to practical lab work, the course will teach skills in data acquisition/analysis.
551-0223-00LImmunology III Information W4 credits2VM. Kopf, M. Bachmann, S. B. Freigang, J. Kisielow, 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:
https://moodle-app2.let.ethz.ch/course/view.php?id=2581¬ifyeditingon=1
Prerequisites / NoticeImmunology I and II recommended but not compulsory
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:
https://www.uzh.ch/cmsssl/en/studies/application/mobilitaet.html
W2 credits2VA. Hajnal, D. Bopp
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
Does not take place this semester.
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:
https://www.uzh.ch/cmsssl/en/studies/application/mobilitaet.html
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 https://moodle-app2.let.ethz.ch/course/view.php?id=3450
551-1303-00LCellular Biochemistry of Health and Disease Information Restricted registration - show details
Number of participants limited to 20.
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.
636-0017-00LComputational Biology Information W6 credits3G + 2AC. Magnus, T. Stadler, T. Vaughan
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 this data 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 for direct alignment analysis using approaches such as BLAST and GWAS. 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. Lastly, we introduce the field of phylodynamics. The aim of phylodynamics 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 notesLecture slides will be available on moodle.
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. Programming in R will be required for the "Central Element". We provide an R tutorial and help sessions during the first two weeks of class to learn the required skills.
636-0108-00LBiological Engineering and Biotechnology
Attention: This course was offered in previous semesters with the number: 636-0003-00L "Biological Engineering and Biotechnology". Students that already passed course 636-0003-00L cannot receive credits for course 636-0108-00L.
W4 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.
ObjectiveBiological 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.
Content1. 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 notesHandout during the course.
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 (www.igem.org).
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 (< 20 minutes) introductory lecture, before students independently research the primary literature and develop discussion points and questions, followed by interactive discussion in class.
LiteratureThe focus is on primary literature, but for some parts the following text books provide good background information:

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.
752-3105-00LPhysiology Guided Food Structure and Process DesignW3 credits2VE. J. Windhab, B. Le Révérend, T. Wooster
AbstractA “cook-and look” approach to process design is no longer applicable in the current environmental, nutritional and competitive constraints. The modern R&D chemical/food engineer should have a clear focus on the desired structure that needs to be achieved to design a process line or a processing equipment, coupled with in depth knowledge of the processed materials.
ObjectiveThe objective of this course is to highlight the intimate links between human physiology and product sensory and nutritional functions. To optimize these functions, an understanding of the physiological functions that interact and encode the actions of those product structures must be well understood.

Therefore the objective of this course is for students to be equipped with a skill set that will encompass basic digestion and sensory physiology knowledge and food structures.

The students will be exposed to this interplay all along the GI tract, including taste, aroma and texture perception, swallowing mechanics and gastro intestinal digestion with an engineering or physical sciences angle.
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