Search result: Catalogue data in Autumn Semester 2023
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 Master Studies (Programme Regulations 2023) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Major in Biochemistry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Elective Compulsory Master Courses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 551-1153-00L | Systems Biology of Metabolism Number of participants limited to 15. | W | 4 credits | 2V | U. Sauer, N. Zamboni | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Starting 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Develop a deeper understanding of how relevant biological problems can be solved, thereby providing advanced insights to key experimental and computational methods in systems biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The 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 notes | Script and original publications will be supplied during the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 636-0007-00L | Computational Systems Biology | W | 6 credits | 3V + 2U | J. Stelling | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Study of fundamental concepts, models and computational methods for the analysis of complex biological networks. Topics: Systems approaches in biology, biology and reaction network fundamentals, modeling and simulation approaches (topological, probabilistic, stoichiometric, qualitative, linear / nonlinear ODEs, stochastic), and systems analysis (complexity reduction, stability, identification). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The aim of this course is to provide an introductory overview of mathematical and computational methods for the modeling, simulation and analysis of biological networks. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Biology has witnessed an unprecedented increase in experimental data and, correspondingly, an increased need for computational methods to analyze this data. The explosion of sequenced genomes, and subsequently, of bioinformatics methods for the storage, analysis and comparison of genetic sequences provides a prominent example. Recently, however, an additional area of research, captured by the label "Systems Biology", focuses on how networks, which are more than the mere sum of their parts' properties, establish biological functions. This is essentially a task of reverse engineering. The aim of this course is to provide an introductory overview of corresponding computational methods for the modeling, simulation and analysis of biological networks. We will start with an introduction into the basic units, functions and design principles that are relevant for biology at the level of individual cells. Making extensive use of example systems, the course will then focus on methods and algorithms that allow for the investigation of biological networks with increasing detail. These include (i) graph theoretical approaches for revealing large-scale network organization, (ii) probabilistic (Bayesian) network representations, (iii) structural network analysis based on reaction stoichiometries, (iv) qualitative methods for dynamic modeling and simulation (Boolean and piece-wise linear approaches), (v) mechanistic modeling using ordinary differential equations (ODEs) and finally (vi) stochastic simulation methods. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | http://www.csb.ethz.ch/education/lectures.html | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | U. Alon, An introduction to systems biology. Chapman & Hall / CRC, 2006. Z. Szallasi et al. (eds.), System modeling in cellular biology. MIT Press, 2010. B. Ingalls, Mathematical modeling in systems biology: an introduction. MIT Press, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 401-0649-00L | Applied Statistical Regression | W | 5 credits | 2V + 1U | M. Dettling | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course offers a practically oriented introduction into regression modeling methods. The basic concepts and some mathematical background are included, with the emphasis lying in learning "good practice" that can be applied in every student's own projects and daily work life. A special focus will be laid in the use of the statistical software package R for regression analysis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The students acquire advanced practical skills in linear regression analysis and are also familiar with its extensions to generalized linear modeling. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The course starts with the basics of linear modeling, and then proceeds to parameter estimation, tests, confidence intervals, residual analysis, model choice, and prediction. More rarely touched but practically relevant topics that will be covered include variable transformations, multicollinearity problems and model interpretation, as well as general modeling strategies. The last third of the course is dedicated to an introduction to generalized linear models: this includes the generalized additive model, logistic regression for binary response variables, binomial regression for grouped data and poisson regression for count data. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | A script will be available. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Faraway (2005): Linear Models with R Faraway (2006): Extending the Linear Model with R Draper & Smith (1998): Applied Regression Analysis Fox (2008): Applied Regression Analysis and GLMs Montgomery et al. (2006): Introduction to Linear Regression Analysis | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The exercises, but also the classes will be based on procedures from the freely available, open-source statistical software package R, for which an introduction will be held. In the Mathematics Bachelor and Master programmes, the two course units 401-0649-00L "Applied Statistical Regression" and 401-3622-00L "Statistical Modelling" are mutually exclusive. Registration for the examination of one of these two course units is only allowed if you have not registered for the examination of the other course unit. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 529-0041-00L | Modern Mass Spectrometry, Hyphenated Methods, and Chemometrics | W | 6 credits | 3G | R. Zenobi, B. Hattendorf, P. Sinués Martinez-Lozano | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Modern mass spectrometry, hyphenated analytical methods, speciation, chemometrics. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Comprehensive knowledge about the analytical methods introduced in this course and their practical applications. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Hyphenation of separation with identification methods such as GC-MS, LC-MS, GC-IR, LC-IR, LC-NMR etc.; importance of speciation. Modern mass spectrometry: time-of-flight, orbitrap and ion cyclotron resonance mass spectrometry, ICP-MS. Soft ionization methods, desorption methods, spray methods. Mass spectrometry imaging. Use of statistical and computer-assisted methods for processing analytical data (chemometrics). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Lecture notes will be made available online. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Information about relevant literature will be available in the lecture & in the lecture notes. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Exercises are an integral part of the lecture. Prerequisites: 529-0051-00 "Analytische Chemie I (3. Semester)" 529-0058-00 "Analytische Chemie II (4. Semester)" (or equivalent) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 636-0108-00L | Biological Engineering and Biotechnology | W | 4 credits | 3V | M. Fussenegger | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Biological 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Biological 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | 1. 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 notes | Handout during the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-1407-00L | RNA Biology Lecture Series I: Transcription & Processing & Translation Does not take place this semester. | W | 4 credits | 2V | F. Allain, N. Ban, S. Jonas, U. Kutay, further lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course covers aspects of RNA biology related to gene expression at the posttranscriptional level. These include RNA transcription, processing, alternative splicing, editing, export and translation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The students should obtain an understanding of these processes, which are at work during gene expression. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Transcription & 3'end formation ; splicing, alternative splicing, RNA editing; the ribosome & translation, translation regulation, RNP biogenesis & nuclear export, mRNA surveillance & mRNA turnover; signal transduction & RNA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Basic knowledge of cell and molecular biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-1409-00L | RNA Biology Lecture Series II: Non-Coding RNAs: Biology and Therapeutics | W | 4 credits | 2V | J. Hall, M. Stoffel, further lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course covers aspects of RNA biology related to the functions of non-coding RNAs as well as their use as drugs to treat diseases. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The students should get familiar with the wide array of roles, which non-coding RNAs play in cellular functions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Micro RNAs; computational approaches to miRNAs; micro RNA function in metabolism; viruses and viral RNAs; nucleic acid-based drugs; ncRNA-mediated genome regulation; epigenetic programming of genome remodelling in ciliates; telomerase and telomeres; tRNA biology. http://www.nccr-rna-and-disease.ch/tiki-index.php?page=LectureSeries | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Basic knowledge of cell and molecular biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 227-0939-00L | Cell Biophysics | W | 6 credits | 4G | T. Zambelli | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Applying two fundamental principles of thermodynamics (entropy maximization and Gibbs energy minimization), an analytical model is derived for a variety of biological phenomena at the molecular as well as cellular level, and critically compared with the corresponding experimental data in the literature. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Engineering uses the laws of physics to predict the behavior of a system. Biological systems are so diverse and complex prompting the question whether we can apply unifying concepts of theoretical physics coping with the multiplicity of life’s mechanisms. Objective of this course is to show that biological phenomena despite their variety can be analytically described using only two principles from statistical mechanics: maximization of the entropy and minimization of the Gibbs free energy. Starting point of the course is the probability theory, which enables to derive step-by-step the two pillars of thermodynamics from the perspective of statistical mechanics: the maximization of entropy according to the Boltzmann’s law as well as the minimization of the Gibbs free energy. Then, an assortment of biological phenomena at the molecular and cellular level (e.g. cytoskeletal polymerization, action potential, photosynthesis, gene regulation, morphogen patterning) will be examined at the light of these two principles with the aim to derive a quantitative expression describing their behavior. Each analytical model is finally validated by comparing it with the corresponding experimental results from the literature. By the end of the course, students will also learn to critically evaluate the concepts of making an assumption and making an approximation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | • Basics of theory of probability • Boltzmann's law • Entropy maximization and Gibbs free energy minimization • Ligand-receptor: two-state systems and the MWC model • Random walks, diffusion, crowding • Electrostatics for salty solutions • Elasticity: fibers and membranes • Molecular motors • Action potential: Hodgkin-Huxley model • Photosynthesis and vision • Gene regulation • Development: Turing patterns Theory and corresponding exercises are merged together during the classes. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | No lecture notes because the two proposed textbooks are more than exhaustive! An extra hour (Mon 17.00 o'clock - 18.00) will be proposed via ZOOM to solve together the exercises of the previous week. !!!!! I am using OneNote. All lectures and exercises will be broadcast via ZOOM (the link of the recordings will be available in Moodle on Fri, 22 Dec after the last lesson) !!!!! | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | • (Statistical Mechanics) K. Dill, S. Bromberg, "Molecular Driving Forces", 2nd Edition, Garland Science, 2010. • (Biophysics) R. Phillips, J. Kondev, J. Theriot, H. Garcia, "Physical Biology of the Cell", 2nd Edition, Garland Science, 2012. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Participants need a good command of • differentiation and integration of a function with one or more variables (basics of Analysis), • Newton's and Coulomb's laws (basics of Mechanics and Electrostatics). Notions of vectors in 2D and 3D are beneficial. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 551-0357-00L | Cellular Matters: Properties, Functions and Applications of Biomolecular Condensates The number of participants is limited to 30 and will only take place with a minimum of 6 participants. The first lecture will serve to form groups of students and assign papers. | W | 4 credits | 2S | T. Michaels, F. Allain, P. Arosio, Y. Barral, D. Hilvert, M. Jagannathan, R. Mezzenga, G. Neurohr, R. Riek, A. E. Smith, K. Weis, H. Wennemers, further lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This Master level course delves into the emerging field of biomolecular condensates - membrane-less organelles in cells. Using interdisciplinary concepts from biology, chemistry, biophysics, and soft matter, we will explore the biological properties of these condensates, their functions in health and disease, and their potentiol as new biomimetic materials for various applications. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | In the last decade, a novel type of cell compartments called biomolecular condensates have been discovered. This discovery is radically changing our understanding of the cell, its organization, and dynamics. The emerging picture is that the cytoplasm and nucleoplasm are highly complex fluids that can (meta)stably segregate into membrane-less compartments, similary to emulsions. This interdisciplinary course encompasses milestone works and cutting-edge research questions in the young field of biomolecular condensates, including their properties, functions, and applications. The course begins with a lecture series that introduces the topic of condensates to an interdisciplinary audience and provides a theoretical foundation for understanding current research questions in the field. the lecturesprovide a base for student presentations of recent publications in the field, and for research seminars given by course lecturers, who are all active researchers with diverse expertise. Through this exciting interdisciplinary understanding of biomolecular condensates, bridging biology, chemistry, biophysics, and soft matter. Students will not only learn how to critically read and evaluate scientific literature but will also gain valuable experience in giving scientific presentations to an interdisciplinary audience. Each presentation will require an introduction, critical analysis of the results, and a discussion of their significance, allowing student to substantiate their statements with a critical mindset that considers the pros and cons of chosen approaches and methods, as well as any limitations or possible follow-up experiments. This process will enable student to ask relevant querions and actively participate in class discussions, further enhancing their scientific skills. In preparing the presentations, the students will have the unique opportunity to interact closely with each other and with the lecturers, who are all internationally well-established experts, and receive guidance in selectin a topic for the final presentaton and supporting literature. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The topic of biomolecular condensates goes beyond the boundaries of traditional disciplines and requires a multi-disciplinary approach that leverages and cross-fertilizes biology, physical chemistry, biophysics, and soft matter. This course will explore the properties, functions and potentioal applicatons of biomolecular condensates, including their role in neurodegenerative diseases such as Alzheimer's and Parkinson's, as well as their use as smart biomimetic materials. This course is divided into two parts. The fist part will introduce the basic concepts essentialto the study of biomolecular condensates and phase separation. Topics include: fundamental units and scales in soft matter, phase transitions in biology, biopolymers and molecular self-assembly, introduction to active matter. This will establish a foundation for the second part, which will explore milestone works and current research in the field of biomolecular condensates. Each lecture of this second part will consist of: 1) a short literature seminar, where student groups will present and discuss a milestone paper assigned in advance and 2) a research seminar, where one of the course lecturers will present their own state-of-the art research in the field, building upon the milestone literature. At the beginning of the course, student groups will be formed and assigned the milestone papers. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Lecture slides and some scripts will be provided. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | No compulsory textbooks. Literature will be provided during the course | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 529-0733-02L | Chemical Biology and Synthetic Biochemistry | W | 6 credits | 3G | K. Lang, M. Fottner | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Overview of modern chemical biology and synthetic biochemistry techniques, focussed on protein modification and labeling and on methods to endow proteins with novel functionalities. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | After taking this course, students should be capable of the following: A) Recall different possibilities for modifying proteins in vitro and in vivo and their applications in a biological context, B) Understand the chemical and biochemical consequences of modifications and assess the different reaction possibilities in the context of in vivo - in vitro, C) Critically analyze and assess current chemical biology articles D) Question the approaches learned and apply them to new biological problems. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | principles of protein labeling and protein modification (fluorescent proteins, enzyme-mediated labeling, bioorthogonal chemistries) advanced genetic code expansion methods (amber suppression, orthogonal ribosomes, unnatural base pairs, genome engineering and genome editing) directed evolution and protein engineering chemical biology of ubiquitin and targeted protein degradation | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | A script will not be handed out. Handouts to the lecture will be provided through moodle. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Citations from the original literature relevant to the individual lectures will be assigned during the lectures. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Knowledge provided in the bachelor lectures 'Nucleic Acids and Carbohydrates' and 'Proteins and Lipids' is assumed for this lecture. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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