Search result: Catalogue data in Autumn Semester 2020
Biotechnology Master  | ||||||
 Core CoursesStudents need to acquire a total of 8 ECTS in lectures in this category. The list of core courses is a closed list, no other course can be added to this category. Students need to pass both lectures offered in this category. | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
|---|---|---|---|---|---|---|
| 636-0102-00L | Advanced Bioengineering | O | 4 credits | 3S | S. Panke, Y. Benenson, P. S. Dittrich, M. Fussenegger, A. Hierlemann, M. H. Khammash, A. Moor, D. J. Müller, M. Nash, R. Platt, J. Stelling, B. Treutlein | |
| Abstract | This course provides an overview of modern concepts of bioengineering across different levels of complexity, from single molecules to systems, microscaled reactors to production environments, and across different fields of applications | |||||
| Learning objective | Students will be able to recognize major developments in bioengineering across different organisms and levels of complexity and be able to relate it to major technological and conceptual advances in the underlying sciences. | |||||
| Content | Molecular and cellular engineering; Synthetic biology: Engineering strategies in biology; from single molecules to systems; downscaling bioengineering; Bioengineering in chemistry, pharmaceutical sciences, and diagnostics, personalized medicine. | |||||
| Lecture notes | Handouts during class | |||||
| Literature | Will be announced during the course | |||||
| Practical Training Students need to acquire a total of 14 ECTS in lab courses. All listed lab courses are mandatory. | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0201-00L | Lab Course: Methods in Cell Analysis and Laboratory Automation  | O | 2 credits | 6P | T. Horn | |
| Abstract | The course Methods in Cell Analysis and Laboratory Automation introduces students to high-end cell analysis and sample preparation methods including image analysis. Students will be taught theoretical aspects and skills in Flow Cytometry, Light Microscopy, Image Analysis, and the use of Laboratory Automation. | |||||
| Learning objective | -to understand the technical and physical principles of light microscopes and flow cytometers -to have hands-on experience in the use of these technologies to analyze/image real samples -to be able to run a basic analysis of the data and images obtained with flow cytometers and microscopes -to get introduced to liquid handling (pipetting) robotics and learn how to implement a basic workflow | |||||
| Content | The practical course will have five units at 2 days each (total 10 days): 1. Flow Cytometry: a. Introduction to Flow Cytometry b. Practical demonstration on flow cytometry analyzers and flow cytometry cell sorters c. Flow cytometry sample preparation d. Learn how to use flow cytometry equipment to analyze and sort fluorescence-labeled cells 2. Light microscopy a. Learn how to build a microscope and understand the underlying physical principles b. Learn how to use a modern automated wide field fluorescence microscope c. Use this microscope to automatically acquire images of a cell culture assay to analyze the dose-dependent effect of a drug treatment 3. Image Analysis a. Introduction to the fundamentals of image analysis b. Learn the basics of the image analysis software Fiji/ImageJ c. Use Fiji/ImageJ to analyze the images acquired during the microscopy exercise 4. Laboratory Automation a. Introduction to the basics of automated liquid handling/ lab robotics b. See examples on using lab automation for plasmid library generation and cell cultivation c. Learn how to program and execute a basic pipetting workflow including liquid handling and labware transfers on Tecan and Hamilton robotic systems 5. Presentations a. Each student will be assigned to an individual topic of the course and will have to prepare a presentation on it. b. Presentations and discussion in form of a Colloquium | |||||
| Lecture notes | You will find further information on the practical course and the equipment at: https://www.bsse.ethz.ch/scf https://www.bsse.ethz.ch/laf | |||||
| Literature | Microscopy: Murphy and Davidson, Fundamentals of Light Microscopy and Electronic Imaging, John Wiley & Sons, 2012 Flow Cytometry: Shapiro, Practical Flow Cytometry, John Wiley & Sons, 2005 Image analysis: R. C. Gonzalez, R. E. Woods, Digital Image Processing (3rd Edition), Prentice Hall Laboratory Automation: Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications (2011) J. Lab. Autom., 16(4), 292-307 | |||||
| Prerequisites / Notice | The following knowledge is required for the course: -basic laboratory methods -basic physics of optics (properties of light, refraction, lenses, fluorescence) -basic biology of cells (cell anatomy and physiology) | |||||
| 636-0203-00L | Lab Course: Microsystems and Microfluidics in Biology | O | 2 credits | 5P | P. S. Dittrich, A. Hierlemann | |
| Abstract | This practical course is an introduction to microsystems technology and microfluidics for the life sciences. It includes basic concepts of microsystem design, fabrication, and assembly into an experimental setup. Biological applications include a variety of measurements of cellular and tissue signals and subsequent analysis. | |||||
| Learning objective | The students are introduced to the basic principles of microsystems technology. They get acquainted with practical scientific work and learn the entire workflow of (a) understanding the theoretical concept, (b) planning the experiment, (c) engineering of the needed device, (d) execution of the experiment and data acquisition, (e) data evaluation and analysis, and (f) reporting and discussion of the results. | |||||
| Content | The practical course will consist of a set of 4 experiments. | |||||
| Lecture notes | Notes and guidelines will be provided at the beginning of the course. | |||||
| Literature | - S.M. Sze, "Semiconductor Devices, Physics and Technology", 2nd edition, Wiley, 2002 - W. Menz, J. Mohr, O. Paul, "Microsystem Technology", Wiley-VCH, 2001 - G. T. A. Kovacs, "Micromachined Transducers Sourcebook", McGraw-Hill, 1998 - M. J. Madou, "Fundamentals of Microfabrication", 2nd ed., CRC Press, 2002 - N.-T. Nguyen and S. Wereley, "Fundamentals and Applications of Microfluidics", Artech House, ISBN 1-580-53343-4 - O. Geschke et al., "Microsystem Engineering for Chemistry and the Life Sciences", Wiley-VCH, ISBN 3-527-30733-8 | |||||
| Prerequisites / Notice | The practical course will consist of a set of 4 experiments. For each experiment, the student will be required to - understand the theoretical concept behind the experiment - plan the experiment - engineer the devices - execute the experiments and acquire data - evaluate and analyze the data - report and discuss the results A good quality of the final report will be expected and be an important criterion. | |||||
| 636-0204-00L | Lab Course: Microbial Biotechnology | O | 2 credits | 5P | M. Held | |
| Abstract | Students will learn the foundations of monoseptic working practice and create and screen microbial libraries for identification of strains expressing different fluorescent protein (XFP) levels | |||||
| Learning objective | Students will learn the foundations of monoseptic working practice and create and screen microbial libraries for identification of strains expressing different fluorescent protein (XFP) levels | |||||
| Content | Block A: Handling and preparation and of microbial libraries D1: Introduction to microbiological cultures and monoseptic working techniques. D2: Plasmid-based expression systems and variation of XFP synthesis levels via site-directed RBS mutagenesis. Block B: Library screening D3: In vivo screening for XFP expression levels. D4: Analysis of XFP levels via SDS-PAGE analysis. RBS-sequencing. Block C: Hit recovery and validation D5: In silico analysis of RBS variants. D6: Cellular XFP content for selected variants at different culture conditions. Block D: Data analysis and presentation D7: Protein expression analysis. Q&A for reports and presentations. D8: Final presentations and wrap-up. | |||||
| Lecture notes | Material will be provided during the course. | |||||
| Literature | (1) Reetz MT, Kahakeaw D, and Lohmer R. "Addressing the numbers problem in directed evolution." ChemBioChem 2008 (2) Jeschek M, Gerngross D, and Panke S. “Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.” Nat. Commun. 2016 (3) Salis HM. “The ribosome binding site calculator.” Methods Enzymol. 2011 (4) Nienhaus G, Nienhaus K, and Wiedenmann J. "Structure–Function Relationships in Fluorescent Marker Proteins of the Green Fluorescent Protein Family." Fluorescent Proteins I. Springer Berlin Heidelberg, 2011 General introduction to microbiology: (5) Schlegel HG, and Zaborosch C. “General Microbiology.” Cambridge University Press 1993 (6) Pirt JS. “Principles of microbe and cell cultivation.” Blackwell Scientific Publications 1975 | |||||
| Advanced Courses Students need to aquire a total of 24 ECTS in this category. The list of advanced courses is a closed list, no other course can be added to this category. | ||||||
| Biomelecular-Orientated | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0103-00L | Microtechnology Attention: This course was offered in previous semesters with the number: 636-0020-00 "Microtechnology and Microelectronics". Students that already passed course 636-0020-00 cannot receive credits for course 636-0103-00. | W | 4 credits | 3G | A. Hierlemann | |
| Abstract | Students are introduced to the basics of microtechnology, cleanroom, semiconductor and silicon process technologies. They will get to know the fabrication of mostly silicon-based microdevices and -systems and all related microfabrication processes. | |||||
| Learning objective | Students are introduced to the basics of microtechnology, cleanroom, semiconductor and silicon process technologies. They will get to know the different fabrication methods for various microdevices and systems. | |||||
| Content | Introduction to microtechnology, semiconductors, and micro electro mechanical systems (MEMS) - Fundamentals of semiconductors and band model - Fundamentals of devices: transistor and diode. - Silicon processing and fabrication steps - Silicon crystal structure and manufacturing - Thermal oxidation - Doping via diffusion and ion implantation - Photolithography - Thin film deposition: dielectrics and metals - Wet etching & bulk micromachining - Dry etching & surface micromachining - Microtechnological processing and fabrication sequence - Optional: Packaging | |||||
| Lecture notes | Handouts in English | |||||
| Literature | - S.M. Sze, "Semiconductor Devices, Physics and Technology", 2nd edition, Wiley, 2002 - R.F. Pierret, "Semiconductor Device Fundamentals", Addison Wesley, 1996 - R. C. Jaeger, "Introduction to Microelectronic Fabrication", Prentice Hall 2002 - S.A. Campbell, "The Science and Engineering of Microelectronic Fabrication", 2nd edition, Oxford University Press, 2001 - W. Menz, J. Mohr, O. Paul, "Microsystem Technology", Wiley-VCH, 2001 - G. T. A. Kovacs, "Micromachined Transducers Sourcebook", McGraw-Hill, 1998 - M. J. Madou, "Fundamentals of Microfabrication", 2nd ed., CRC Press, 2002 | |||||
| Prerequisites / Notice | Fundamentals in physics and physicochemistry (orbital models etc.) are required, a repetitorium of fundamental physics and quantum theory at the semester beginning can be offered. The information on the web can be updated until the beginning of the semester. | |||||
| 636-0104-00L | Biophysical Methods Attention: This course was offered in previous semesters with the number: 626-0010-00L "Nanomachines of the Cell (Part I): Principles". Students that already passed course 626-0010-00 cannot receive credits for course 636-0104-00. | W | 4 credits | 3G | D. J. Müller | |
| Abstract | Students will be imparted knowledge in basic and advanced biophysical methods applied to problems in molecular biotechnology. The course is fundamental to applying the methods in their daily and advanced research routines. The students will learn the physical basis of the methods as well as their limitations and possibilities to address existing and future topics in molecular biotechnology. | |||||
| Learning objective | Gain of interdisciplinary competence in experimental and theoretical research, which qualifies for academic scientific work (master's or doctoral thesis) as well as for research in a biotechnology or a pharmaceutical company. The module is of general use in courses focused on modern biomolecular technologies, systems biology and systems engineering. | |||||
| Content | The students will learn basic and advanced knowledge in applying biophysical methods to address problems and overcome challenges in biotechnology, cell biology and life sciences in general. The biological and physical possibilities and limitations of the methods will be discussed and critically evaluated. By the end of the course the students will have assimilated knowledge on a portfolio of biophysical tools widening their research capabilities and aptitude. The biophysical methods to be taught will include: • Light microscopy: Resolution limit of light microscopy, fluorescence, GFP, fluorescence microscopy, DIC, phase contrast, difference between wide-field and confocal microscopy • Super resolution optical microscopy: STED, PALM, STORM, other variations • Electron microscopy: Scanning electron microscopy, transmission electron microscopy, electron tomography, cryo-electron microscopy, single particle analysis and averaging, tomography, sectioning, negative stain • X-ray, electron and neutron diffraction • MRI Imaging • Scanning tunnelling microscopy and atomic force microscopy • Patch clamp technologies: Principles of patch clamp analysis and application. Various patch clamp approaches used in research and industry • Surface plasmon resonance-based biosensors • Molecular pore-based sensors and sequencing devices • Mechanical molecular and cellular assembly devices • Optical and magnetic tweezers • CD spectroscopy • Optogenetics • Molecular dynamics simulations | |||||
| Lecture notes | Hand out will be given to students at lecture. | |||||
| Literature | Methods in Molecular Biophysics (5th edition), Serdyuk et al., Cambridge University Press Biochemistry (5th edition), Berg, Tymoczko, Stryer; ISBN 0-7167-4684-0, Freeman Bioanalytics, Lottspeich & Engels, Wiley VCH, ISBN-10: 3527339191 Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania Methods in Modern Biophysics, Nölting, 3rd Edition, Springer, ISBN-10: 3642030211 | |||||
| Prerequisites / Notice | The module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students will prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher. | |||||
| 636-0105-00L | Introduction to Biological Computers Attention: This course was offered in previous semesters with the number: 636-0011-00L "Introduction to Biological Computers". Students that already passed course 636-0011-00L cannot receive credits for course 636-0105-00L. | W | 4 credits | 3G | Y. Benenson | |
| Abstract | Biological computers are man-made biological networks that interrogate and control cells and organisms in which they operate. Their key features, inspired by computer science, are programmability, modularity, and versatility. The course will show how to rationally design, implement and test biological computers using molecular engineering, DNA nanothechnology and synthetic biology. | |||||
| Learning objective | The course has the following objectives: * Familiarize students with parallels between theories in computer science and engineering and information-processing in live cells and organisms * Introduce basic theories of computation * Introduce approaches to creating novel biological computing systems in non-living environment and in living cells including bacteria, yeast and mammalian/human cells. The covered approaches will include - Nucleic acids engineering - DNA and RNA nanotechnology - Synthetic biology and gene circuit engineering - High-throughput genome engineering and gene circuit assembly * Equip the students with computer-aided design (CAD) tools for biocomputing circuit engineering. A number of tutorials will introduce MATLAB SimBiology toolbox for circuit design and simulations * Foster creativity, research and communication skills through semester-long "Design challenge" assignment in the broad field of biological computing and biological circuit engineering. | |||||
| Content | Note: the exact subjects can change, the details below should only serve for general orientation Lecture 1. Introduction: what is molecular computation (part I)? * What is computing in general? * What is computing in the biological context (examples from development, chemotaxis and gene regulation) * The difference between natural computing and engineered biocomputing systems Lecture 2: What is molecular computation (part II) + State machines 1st hour * Detailed definition of an engineered biocomputing system * Basics of characterization * Design challenge presentation 2nd hour * Theories of computation: state machines (finite automata and Turing machines) Lecture 3: Additional models of computation * Logic circuits * Analog circuits * RAM machines Basic approaches to computer science notions relevant to molecular computation. (i) State machines; (ii) Boolean networks; (iii) analog computing; (iv) distributed computing. Design Challenge presentation. Lecture 4. Classical DNA computing * Adleman experiment * Maximal clique problem * SAT problem Lecture 5: Molecular State machines through self-assembly * Tiling implementation of state machine * DNA-based tiling system * DNA/RNA origami as a spin-off of self-assembling state machines Lecture 6: Molecular State machines that use DNA-encoded tapes * Early theoretical work * Tape extension system * DNA and enzyme-based finite automata for diagnostic applications Lecture 7: Introduction to cell-based logic and analog circuits * Computing with (bio)chemical reaction networks * Tuning computation with ultrasensitivity and cooperativity * Specific examples Lecture 8: Transcriptional circuits I * Introducing transcription-based circuits * General features and considerations * Guidelines for large circuit construction Lecture 9: Transcriptional circuits II * Large-scale distributed logic circuits in bacteria * Toward large-scale circuits in mammalian cells Lecture 10: RNA circuits I * General principles of RNA-centered circuit design * Riboswitches and sRNA regulation in bacteria * Riboswitches in yeast and mammalian cells * General approach to RNAi-based computing Lecture 11: RNA circuits II * RNAi logic circuits * RNAi-based cell type classifiers * Hybrid transcriptional/posttranscriptional approaches Lecture 12: In vitro DNA-based logic circuits * DNAzyme circuits playing tic-tac-toe against human opponents * DNA brain Lecture 13: Advanced topics * Engineered cellular memory * Counting and sequential logic * The role of evolution * Fail-safe design principles Lecture 14: Design challenge presentation | |||||
| Lecture notes | Lecture notes will be available online | |||||
| Literature | As a way of general introduction, the following two review papers could be useful: Benenson, Y. RNA-based computation in live cells. Current Opinion in Biotechnology 2009, 20:471:478 Benenson, Y. Biocomputers: from test tubes to live cells. Molecular Biosystems 2009, 5:675:685 Benenson, Y. Biomolecular computing systems: principles, progress and potential (Review). Nature Reviews Genetics 13, 445-468 (2012). | |||||
| Prerequisites / Notice | Basic knowledge of molecular biology is assumed. | |||||
| 636-0108-00L | Biological 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. | 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. | |||||
| 636-0107-00L | Microbial Biotechnology | W | 4 credits | 3G | S. Panke, M. Jeschek | |
| Abstract | Students of this course know and can evaluate modern methods of microbial biotechnology and enzyme technology and understand their relation to modern applications of microbial biotechnology. | |||||
| Learning objective | Students of this course know and can evaluate modern methods of microbial biotechnology and enzyme technology and understand their relation to modern applications of microbial biotechnology. | |||||
| Content | The course will cover in its main part selected fundamental and advanced topics and methodologies in microbial molecular biotechnology. Major topics include I) Microbial physiology of microbes (prokaryotes and selected fungi), II) Applications of Microbial Biotechnology, III) Enzymes - advanced kinetics and engineering, IV) Principles of in vivo directed evolution, V) System approaches to cell engineering/metabolic engineering, and VI) Trends in Microbial Biotechnology. The course is a mix of lectures and different exercise formats. | |||||
| Lecture notes | Notes will be provided in the forms of handouts. | |||||
| Literature | The course will use selected parts of textbooks and then original scientific publications and reviews. | |||||
| 636-0018-00L | Data Mining I | W | 6 credits | 3G + 2A | K. M. Borgwardt | |
| Abstract | Data Mining, the search for statistical dependencies in large databases, is of utmost important in modern society, in particular in biological and medical research. This course provides an introduction to the key problems, concepts, and algorithms in data mining, and the applications of data mining in computational biology. | |||||
| Learning objective | The goal of this course is that the participants gain an understanding of data mining problems and algorithms to solve these problems, in particular in biological and medical applications. | |||||
| Content | The goal of the field of data mining is to find patterns and statistical dependencies in large databases, to gain an understanding of the underlying system from which the data were obtained. In computational biology, data mining contributes to the analysis of vast experimental data generated by high-throughput technologies, and thereby enables the generation of new hypotheses. In this course, we will present the algorithmic foundations of data mining and its applications in computational biology. The course will feature an introduction to popular data mining problems and algorithms, reaching from classification via clustering to feature selection. This course is intended for both students who are interested in applying data mining algorithms and students who would like to gain an understanding of the key algorithmic concepts in data mining. Tentative list of topics: 1. Distance functions 2. Classification 3. Clustering 4. Feature Selection | |||||
| Lecture notes | Course material will be provided in form of slides. | |||||
| Literature | Will be provided during the course. | |||||
| Prerequisites / Notice | Basic understanding of mathematics, as taught in basic mathematics courses at the Bachelor's level. | |||||
| 636-0550-00L | Biomolecular Nanotechnology | W | 4 credits | 2V + 1U | M. Nash | |
| Abstract | Biomolecular nanotechnology is a broad field that focuses on the study and science of biological materials including DNA, RNA and proteins at length scales below 10 nm. This is a broad overview of the topic with a focus on current research themes. | |||||
| Learning objective | The objective is to familiarise the students with a broad range of topics related to biotechnology, nanotechnology, and biophysics with a focus on current research and reading of scientific literature. | |||||
| Content | Introduction to biomacromolecules; Measurement techniques for characterisation of biomacromolecules; Fundamentals of molecular recognition; Recombinant DNA; Protein engineering; Directed evolution; Protein folding; Polymers; Elastin-like polypeptides; Intelligent materials; Spatially localized hydrogels; Mechanical properties of proteins and macromolecules; Single-molecule force spectroscopy | |||||
| Literature | Representative literature: (1) Alberts, Molecular Biology (Ch.2 Cellular chemistry). (2) Ratner, Biomaterials Science (Ch. 2.3, 2.4 Polymers & hydrogels). (3) Walsh, Protein Biochemistry, (Ch. 2, Protein Structure). (4) Nath et. al. Analytical chemistry, 74(3): 504-509, 2002. (5) DeMonte, D., et. al. Proteins DOI: 10.1002/prot.24320, 2013. (6) Feldhaus, M.J., et al. Nature Biotechnology 21 (2): 163–70, 2003. (7) Link, A.J., et al. PNAS 103 (27): 10180–85, 2006. (8) Chen, I. et al. PNAS 108 (28): 11399–404, 2011. (9) Marín-Navarro, J., et. al. PloS One 10 (12). journals.plos.org: e0144289, 2015. (10) Christensen, T. et al. Biomacromolecules 14 (5): 1514–19, 2013. (11) Shimoboji, T., et al. PNAS. 99(26): 16592-16596, 2002. (12) Puchner, E.M. et al. PNAS. 105(36): 13385–13390, 2008. (13) Dietz, H., et al. PNAS 103 (5): 1244–47, 2006. | |||||
| 636-0117-00L | Mathematical Modelling for Bioengineering and Systems Biology | W | 4 credits | 3G | D. Iber | |
| Abstract | Basic concepts and mathematical tools to explore biochemical reaction kinetics and biological network dynamics. | |||||
| Learning objective | The course enables students to formulate, analyse, and simulate mathematical models of biochemical networks. To this end, the course covers basic mathematical concepts and tools to explore biochemical reaction dynamics as well as basic concepts from dynamical systems theory. The exercises serve to deepen the understanding of the presented concepts and the mathematical methods, and to train students to numerically solve and simulate mathematical models. | |||||
| Content | Biochemical Reaction Modelling Basic Concepts from Linear Algebra & Differential Equations Mathematical Methods: Linear Stability Analysis, Phase Plane Analysis, Bifurcation Analysis Dynamical Systems: Switches, Oscillators, Adaptation Signal Propagation in Signalling Networks Parameter Estimation | |||||
| 636-0118-00L | Introduction to Dynamical Systems with Applications to Biology | W | 4 credits | 3G | M. H. Khammash, A. Gupta | |
| Abstract | Many physical systems are dynamic and are characterized by internal variables that change with time. Describing the quantitative and qualitative features of this change is the topic of dynamical systems theory. Dynamical systems arise naturally in virtually all scientific disciplines including physics, biology, chemistry and engineering. This course is a broad introduction to the topic dynamical s | |||||
| Learning objective | The goal of this course is to introduce the student to dynamical systems and to develop a solid understanding of their fundamental properties. The theory will be developed systematically, focusing on analytical methods for low dimensional systems, geometric intuition, and application examples from biology. Computer simulations using matlab will be used to demonstrate various concepts | |||||
| Content | A dynamical view of the world; the importance of nonlinearity; solutions of differential equations; solving equations on the computer; the phase plane; fixed points and stability; linear stability analysis; classifications of linear systems; Liapunov functions and nonlinear stability; cycles and oscillations; bifurcations and bifurcation diagrams. Many biological examples will be used through the course to demonstrate the concepts | |||||
| Lecture notes | Will be provided as needed. | |||||
| Literature | Strogatz, S. H. (2018). Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering. CRC Press. Segel, L. A., & Edelstein-Keshet, L. (2013). A Primer in Mathematical Models in Biology (Vol. 129). SIAM. | |||||
| Prerequisites / Notice | Prerequisites: Calculus; a first course in differential equations; basic linear algebra (eigenvalues and eigenvectors). Matlab programming. | |||||
| 636-0109-00L | Stem Cells: Biology and Therapeutic Manipulation Attention: This course was offered in previous semesters with the number: 636-0013-00L "Stem Cells: Biology and Therapeutic Manipulation". Students that already passed course 636-0013-00L cannot receive credits for course 636-0109-00L. | W | 4 credits | 3G | T. Schroeder | |
| Abstract | Stem cells are central in tissue regeneration and repair, and hold great potential for therapy. We will discuss the role of stem cells in health and disease, and possibilities to manipulate their behavior for therapeutic application. Basic molecular and cell biology, engineering and novel technologies relevant for stem cell research and therapy will be discussed. | |||||
| Learning objective | Understanding of current knowledge, and lack thereof, in stem cell biology, regenerative medicine and required technologies. Theoretical preparation for practical laboratory experimentation with stem cells. | |||||
| Content | We will use different diseases to discuss how to potentially model, diagnose or heal them by stem cell based therapies. This will be used as a guiding framework to discuss relevant concepts and technologies in cell and molecular biology, engineering, imaging, bioinformatics, tissue engineering, that are required to manipulate stem cells for therapeutic application. Topics will include: - Embryonic and adult stem cells and their niches - Induced stem cells by directed reprogramming - Relevant basic cell biology and developmental biology - Relevant molecular biology - Cell culture systems - Cell fates and their molecular control by transcription factors and signalling pathways - Cell reprogramming - Disease modelling - Tissue engineering - Bioimaging, Bioinformatics - Single cell technologies | |||||
| System-Orientated | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0103-00L | Microtechnology Attention: This course was offered in previous semesters with the number: 636-0020-00 "Microtechnology and Microelectronics". Students that already passed course 636-0020-00 cannot receive credits for course 636-0103-00. | W | 4 credits | 3G | A. Hierlemann | |
| Abstract | Students are introduced to the basics of microtechnology, cleanroom, semiconductor and silicon process technologies. They will get to know the fabrication of mostly silicon-based microdevices and -systems and all related microfabrication processes. | |||||
| Learning objective | Students are introduced to the basics of microtechnology, cleanroom, semiconductor and silicon process technologies. They will get to know the different fabrication methods for various microdevices and systems. | |||||
| Content | Introduction to microtechnology, semiconductors, and micro electro mechanical systems (MEMS) - Fundamentals of semiconductors and band model - Fundamentals of devices: transistor and diode. - Silicon processing and fabrication steps - Silicon crystal structure and manufacturing - Thermal oxidation - Doping via diffusion and ion implantation - Photolithography - Thin film deposition: dielectrics and metals - Wet etching & bulk micromachining - Dry etching & surface micromachining - Microtechnological processing and fabrication sequence - Optional: Packaging | |||||
| Lecture notes | Handouts in English | |||||
| Literature | - S.M. Sze, "Semiconductor Devices, Physics and Technology", 2nd edition, Wiley, 2002 - R.F. Pierret, "Semiconductor Device Fundamentals", Addison Wesley, 1996 - R. C. Jaeger, "Introduction to Microelectronic Fabrication", Prentice Hall 2002 - S.A. Campbell, "The Science and Engineering of Microelectronic Fabrication", 2nd edition, Oxford University Press, 2001 - W. Menz, J. Mohr, O. Paul, "Microsystem Technology", Wiley-VCH, 2001 - G. T. A. Kovacs, "Micromachined Transducers Sourcebook", McGraw-Hill, 1998 - M. J. Madou, "Fundamentals of Microfabrication", 2nd ed., CRC Press, 2002 | |||||
| Prerequisites / Notice | Fundamentals in physics and physicochemistry (orbital models etc.) are required, a repetitorium of fundamental physics and quantum theory at the semester beginning can be offered. The information on the web can be updated until the beginning of the semester. | |||||
| 636-0104-00L | Biophysical Methods Attention: This course was offered in previous semesters with the number: 626-0010-00L "Nanomachines of the Cell (Part I): Principles". Students that already passed course 626-0010-00 cannot receive credits for course 636-0104-00. | W | 4 credits | 3G | D. J. Müller | |
| Abstract | Students will be imparted knowledge in basic and advanced biophysical methods applied to problems in molecular biotechnology. The course is fundamental to applying the methods in their daily and advanced research routines. The students will learn the physical basis of the methods as well as their limitations and possibilities to address existing and future topics in molecular biotechnology. | |||||
| Learning objective | Gain of interdisciplinary competence in experimental and theoretical research, which qualifies for academic scientific work (master's or doctoral thesis) as well as for research in a biotechnology or a pharmaceutical company. The module is of general use in courses focused on modern biomolecular technologies, systems biology and systems engineering. | |||||
| Content | The students will learn basic and advanced knowledge in applying biophysical methods to address problems and overcome challenges in biotechnology, cell biology and life sciences in general. The biological and physical possibilities and limitations of the methods will be discussed and critically evaluated. By the end of the course the students will have assimilated knowledge on a portfolio of biophysical tools widening their research capabilities and aptitude. The biophysical methods to be taught will include: • Light microscopy: Resolution limit of light microscopy, fluorescence, GFP, fluorescence microscopy, DIC, phase contrast, difference between wide-field and confocal microscopy • Super resolution optical microscopy: STED, PALM, STORM, other variations • Electron microscopy: Scanning electron microscopy, transmission electron microscopy, electron tomography, cryo-electron microscopy, single particle analysis and averaging, tomography, sectioning, negative stain • X-ray, electron and neutron diffraction • MRI Imaging • Scanning tunnelling microscopy and atomic force microscopy • Patch clamp technologies: Principles of patch clamp analysis and application. Various patch clamp approaches used in research and industry • Surface plasmon resonance-based biosensors • Molecular pore-based sensors and sequencing devices • Mechanical molecular and cellular assembly devices • Optical and magnetic tweezers • CD spectroscopy • Optogenetics • Molecular dynamics simulations | |||||
| Lecture notes | Hand out will be given to students at lecture. | |||||
| Literature | Methods in Molecular Biophysics (5th edition), Serdyuk et al., Cambridge University Press Biochemistry (5th edition), Berg, Tymoczko, Stryer; ISBN 0-7167-4684-0, Freeman Bioanalytics, Lottspeich & Engels, Wiley VCH, ISBN-10: 3527339191 Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania Methods in Modern Biophysics, Nölting, 3rd Edition, Springer, ISBN-10: 3642030211 | |||||
| Prerequisites / Notice | The module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students will prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher. | |||||
| 636-0105-00L | Introduction to Biological Computers Attention: This course was offered in previous semesters with the number: 636-0011-00L "Introduction to Biological Computers". Students that already passed course 636-0011-00L cannot receive credits for course 636-0105-00L. | W | 4 credits | 3G | Y. Benenson | |
| Abstract | Biological computers are man-made biological networks that interrogate and control cells and organisms in which they operate. Their key features, inspired by computer science, are programmability, modularity, and versatility. The course will show how to rationally design, implement and test biological computers using molecular engineering, DNA nanothechnology and synthetic biology. | |||||
| Learning objective | The course has the following objectives: * Familiarize students with parallels between theories in computer science and engineering and information-processing in live cells and organisms * Introduce basic theories of computation * Introduce approaches to creating novel biological computing systems in non-living environment and in living cells including bacteria, yeast and mammalian/human cells. The covered approaches will include - Nucleic acids engineering - DNA and RNA nanotechnology - Synthetic biology and gene circuit engineering - High-throughput genome engineering and gene circuit assembly * Equip the students with computer-aided design (CAD) tools for biocomputing circuit engineering. A number of tutorials will introduce MATLAB SimBiology toolbox for circuit design and simulations * Foster creativity, research and communication skills through semester-long "Design challenge" assignment in the broad field of biological computing and biological circuit engineering. | |||||
| Content | Note: the exact subjects can change, the details below should only serve for general orientation Lecture 1. Introduction: what is molecular computation (part I)? * What is computing in general? * What is computing in the biological context (examples from development, chemotaxis and gene regulation) * The difference between natural computing and engineered biocomputing systems Lecture 2: What is molecular computation (part II) + State machines 1st hour * Detailed definition of an engineered biocomputing system * Basics of characterization * Design challenge presentation 2nd hour * Theories of computation: state machines (finite automata and Turing machines) Lecture 3: Additional models of computation * Logic circuits * Analog circuits * RAM machines Basic approaches to computer science notions relevant to molecular computation. (i) State machines; (ii) Boolean networks; (iii) analog computing; (iv) distributed computing. Design Challenge presentation. Lecture 4. Classical DNA computing * Adleman experiment * Maximal clique problem * SAT problem Lecture 5: Molecular State machines through self-assembly * Tiling implementation of state machine * DNA-based tiling system * DNA/RNA origami as a spin-off of self-assembling state machines Lecture 6: Molecular State machines that use DNA-encoded tapes * Early theoretical work * Tape extension system * DNA and enzyme-based finite automata for diagnostic applications Lecture 7: Introduction to cell-based logic and analog circuits * Computing with (bio)chemical reaction networks * Tuning computation with ultrasensitivity and cooperativity * Specific examples Lecture 8: Transcriptional circuits I * Introducing transcription-based circuits * General features and considerations * Guidelines for large circuit construction Lecture 9: Transcriptional circuits II * Large-scale distributed logic circuits in bacteria * Toward large-scale circuits in mammalian cells Lecture 10: RNA circuits I * General principles of RNA-centered circuit design * Riboswitches and sRNA regulation in bacteria * Riboswitches in yeast and mammalian cells * General approach to RNAi-based computing Lecture 11: RNA circuits II * RNAi logic circuits * RNAi-based cell type classifiers * Hybrid transcriptional/posttranscriptional approaches Lecture 12: In vitro DNA-based logic circuits * DNAzyme circuits playing tic-tac-toe against human opponents * DNA brain Lecture 13: Advanced topics * Engineered cellular memory * Counting and sequential logic * The role of evolution * Fail-safe design principles Lecture 14: Design challenge presentation | |||||
| Lecture notes | Lecture notes will be available online | |||||
| Literature | As a way of general introduction, the following two review papers could be useful: Benenson, Y. RNA-based computation in live cells. Current Opinion in Biotechnology 2009, 20:471:478 Benenson, Y. Biocomputers: from test tubes to live cells. Molecular Biosystems 2009, 5:675:685 Benenson, Y. Biomolecular computing systems: principles, progress and potential (Review). Nature Reviews Genetics 13, 445-468 (2012). | |||||
| Prerequisites / Notice | Basic knowledge of molecular biology is assumed. | |||||
| 636-0108-00L | Biological 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. | 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. | |||||
| 636-0018-00L | Data Mining I | W | 6 credits | 3G + 2A | K. M. Borgwardt | |
| Abstract | Data Mining, the search for statistical dependencies in large databases, is of utmost important in modern society, in particular in biological and medical research. This course provides an introduction to the key problems, concepts, and algorithms in data mining, and the applications of data mining in computational biology. | |||||
| Learning objective | The goal of this course is that the participants gain an understanding of data mining problems and algorithms to solve these problems, in particular in biological and medical applications. | |||||
| Content | The goal of the field of data mining is to find patterns and statistical dependencies in large databases, to gain an understanding of the underlying system from which the data were obtained. In computational biology, data mining contributes to the analysis of vast experimental data generated by high-throughput technologies, and thereby enables the generation of new hypotheses. In this course, we will present the algorithmic foundations of data mining and its applications in computational biology. The course will feature an introduction to popular data mining problems and algorithms, reaching from classification via clustering to feature selection. This course is intended for both students who are interested in applying data mining algorithms and students who would like to gain an understanding of the key algorithmic concepts in data mining. Tentative list of topics: 1. Distance functions 2. Classification 3. Clustering 4. Feature Selection | |||||
| Lecture notes | Course material will be provided in form of slides. | |||||
| Literature | Will be provided during the course. | |||||
| Prerequisites / Notice | Basic understanding of mathematics, as taught in basic mathematics courses at the Bachelor's level. | |||||
| 636-0117-00L | Mathematical Modelling for Bioengineering and Systems Biology | W | 4 credits | 3G | D. Iber | |
| Abstract | Basic concepts and mathematical tools to explore biochemical reaction kinetics and biological network dynamics. | |||||
| Learning objective | The course enables students to formulate, analyse, and simulate mathematical models of biochemical networks. To this end, the course covers basic mathematical concepts and tools to explore biochemical reaction dynamics as well as basic concepts from dynamical systems theory. The exercises serve to deepen the understanding of the presented concepts and the mathematical methods, and to train students to numerically solve and simulate mathematical models. | |||||
| Content | Biochemical Reaction Modelling Basic Concepts from Linear Algebra & Differential Equations Mathematical Methods: Linear Stability Analysis, Phase Plane Analysis, Bifurcation Analysis Dynamical Systems: Switches, Oscillators, Adaptation Signal Propagation in Signalling Networks Parameter Estimation | |||||
Page
1
of
3
All