Uwe Sauer: Catalogue data in Spring Semester 2020 |
| Name | Prof. Dr. Uwe Sauer |
| Field | Systembiologie |
| Address | Inst. f. Molekulare Systembiologie ETH Zürich, HPM H 28 Otto-Stern-Weg 3 8093 Zürich SWITZERLAND |
| Telephone | +41 44 633 36 72 |
| sauer@imsb.biol.ethz.ch | |
| Department | Biology |
| Relationship | Full Professor |
| Number | Title | ECTS | Hours | Lecturers | |
|---|---|---|---|---|---|
| 551-0001-AAL | General Biology I Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | 3 credits | 6R | U. Sauer, O. Y. Martin, A. Widmer | |
| Abstract | Organismic biology to teach the basic principles of classical and molecular genetics, evolutionary biology and phylogeny. First in a series of two lectures given over two semesters for students of agricultural and food sciences, as well as of environmental sciences. | ||||
| Learning objective | The understanding of basic principles of biology (inheritance, evolution and phylogeny) and an overview of the diversity of life. | ||||
| Content | The first semester focuses on the organismal biology aspects of genetics, evolution and diversity of life in the Campbell chapters 12-34. Week 1-7 by Alex Widmer, Chapters 12-25 12 Cell biology Mitosis 13 Genetics Sexual life cycles and meiosis 14 Genetics Mendelian genetics 15 Genetics Linkage and chromosomes 20 Genetics Evolution of genomes 21 Evolution How evolution works 22 Evolution Phylogentic reconstructions 23 Evolution Microevolution 24 Evolution Species and speciation 25 Evolution Macroevolution Week 8-14 by Oliver Martin, Chapters 26-34 26 Diversity of Life Introdution to viruses 27 Diversity of Life Prokaryotes 28 Diversity of Life Origin & evolution of eukaryotes 29 Diversity of Life Nonvascular&seedless vascular plants 30 Diversity of Life Seed plants 31 Diversity of Life Introduction to fungi 32 Diversity of Life Overview of animal diversity 33 Diversity of Life Introduction to invertebrates 34 Diversity of Life Origin & evolution of vertebrates | ||||
| Lecture notes | No script | ||||
| Literature | Campbell et al. (2018) Biology - A Global Approach. 11th Edition (Global Edition | ||||
| Prerequisites / Notice | This is a virtual self-study lecture for non-german speakers of the "Allgemeine Biology I (551-0001-00L) lecture. The exam will be written jointly with the participants of this lecture. Example exam questions will be discussed during the lectures, and old exam questions are kept by the various student organisations. If necessary, please contact Prof. Uwe Sauer (sauer@ethz.ch) for details regarding the exam. | ||||
| 551-0002-00L | General Biology II  | 4 credits | 4G | U. Sauer, K. Bomblies, O. Y. Martin | |
| Abstract | Basics of biochemistry (macromolecules, membranes, cellular structures, metabolism), molecular genetics (gene expression and its regulation; from gene to protein), and physiology of higher plants (structure, growth, development, nutrition, transport, reproduction) | ||||
| Learning objective | The understanding of basic concepts of molecular biology and physiology. | ||||
| Content | How cells function at the level of molecules and higher structures. Molecular processes during gene expression. Plant physiology. The following Campbell chapters will be covered: Week 1-5: 5 Biological macromolecules and lipids 7 Cell structure and function 8 Cell membranes 10 Respiration: introduction to metabolism 10 Cell respiration 11 Photosynthetic processes Week 6-9: 16 Nucleic acids and inheritance 17 Expression of genes 18 Control of gene expression 19 DNA Technology Week 9-13: 35 Plant Structure and Growth 36 Transport in vascular plants 37 Plant nutrition 38 Reproduction of flowering plants 39 Plants signal and behavior | ||||
| Lecture notes | No script | ||||
| Literature | Campbell, Reece et al: "Biologie" (11th global edition); Pearson 2018. | ||||
| 551-0003-AAL | General Biology I+II Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | 7 credits | 13R | U. Sauer, K. Bomblies, O. Y. Martin, A. Widmer | |
| Abstract | General Biology I: Organismic biology to teach the basic principles of classical and molecular genetics, evolutionary biology and phylogeny. General Biology II: Molecular biology approach to teach the basic principles of biochemistry, cell biology, cgenetics, evolutionary biology and form and function of vacular plants. | ||||
| Learning objective | General Biology I: The understanding of basic principles of biology (inheritance, evolution and phylogeny) and an overview of the diversity of life. General Biology II: The understanding basic concepts of biology: the hierarchy of the structural levels of biological organisation, with particular emphasis on the cell and its molecular functions, the fundamentals of metabolism and molecular genetics, as well as form and function of vascular plants. | ||||
| Content | General Biology I: General Biology I focuses on the organismal biology aspects of genetics, evolution and diversity of life in the Campbell chapters 12-34. Week 1-7 by Alex Widmer, Chapters 12-25 12 Cell biology Mitosis 13 Genetics Sexual life cycles and meiosis 14 Genetics Mendelian genetics 15 Genetics Linkage and chromosomes 20 Genetics Evolution of genomes 21 Evolution How evolution works 22 Evolution Phylogentic reconstructions 23 Evolution Microevolution 24 Evolution Species and speciation 25 Evolution Macroevolution Week 8-14 by Oliver Martin, Chapters 26-34 26 Diversity of Life Introdution to viruses 27 Diversity of Life Prokaryotes 28 Diversity of Life Origin & evolution of eukaryotes 29 Diversity of Life Nonvascular&seedless vascular plants 30 Diversity of Life Seed plants 31 Diversity of Life Introduction to fungi 32 Diversity of Life Overview of animal diversity 33 Diversity of Life Introduction to invertebrates 34 Diversity of Life Origin & evolution of vertebrates General Biology II: The structure and function of biomacromolecules; basics of metabolism; tour of the cell; membrane structure and function; basic energetics of cellular processes; respiration, photosynthesis; cell cycle, from gene to protein; structure and growth of vascular plants, resource acquisition and transport, soil and plant nutrition. Specifically the following Campbell chapters will be covered: 3 Biochemistry Chemistry of water 4 Biochemistry Carbon: the basis of molecular diversity 5 Biochemistry Biological macromolecules and lipids 7 Cell biology Cell structure and function 8 Cell biology Cell membranes 10 Cell biology Respiration: introduction to metabolism 10 Cell biology Cell respiration 11 Cell biology Photosynthetic processes 16 Genetics Nucleic acids and inheritance 17 Genetics Expression of genes 18 Genetics Control of gene expression 19 Genetics DNA Technology 35 Plant structure&function Plant Structure and Growth 36 Plant structure&function Transport in vascular plants 37 Plant structure&function Plant nutrition 38 Plant structure&function Reproduction of flowering plants 39 Plant structure&function Plants signal and behavior | ||||
| Lecture notes | No script | ||||
| Literature | Campbell et al. (2018) Biology - A Global Approach. 11th Edition (Global Edition) | ||||
| Prerequisites / Notice | Basic general and organic chemistry This is a virtual self-study lecture for non-German speakers of the "Allgemeine Biology I (551-0001-00L) and "Allgemeine Biology II (551-0002-00L) lectures. The exam will be written jointly with the participants of this lecture. | ||||
| 551-0324-00L | Systems Biology  | 6 credits | 4V | P. Picotti, M. Claassen, U. Sauer, B. Snijder, B. Wollscheid | |
| Abstract | Introduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects. | ||||
| Learning objective | - obtain an overview of global analytical methods - obtain an overview of computational methods in systems biology - understand the concepts of systems biology | ||||
| Content | Overview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology. | ||||
| Lecture notes | no script | ||||
| Literature | The course is not taught by a particular book, but some books are suggested for further reading: - Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005 | ||||
| 551-0342-00L | Metabolomics Number of participants limited to 15. The enrolment is done by the D-BIOL study administration. | 6 credits | 7G | N. Zamboni, U. Sauer | |
| Abstract | The course covers all basic aspects of metabolome measurements, from sample sampling to mass spectrometry and data analysis. Participants work in groups and independently perform and interpret metabolomic experiments. | ||||
| Learning objective | Performing and reporting a metabolomic experiment, understanding pro and cons of mass spectrometry based metabolomics. Knowledge of workflows and tools to assist experiment interpretation, and metabolite identification. | ||||
| Content | Basics of metabolomics: workflows, sample preparation, targeted and untargeted mass spectrometry, instrumentation, separation techniques (GC, LC, CE), metabolite identification, data interpretation and integration, normalization, QCs, maintenance. Soft skills to be trained: project planning, presentation, reporting, independent working style, team work. | ||||
| 551-1174-00L | Systems Biology | 4 credits | 2V + 2U | U. Sauer, K. M. Borgwardt, J. Stelling, N. Zamboni | |
| Abstract | The course teaches computational methods and first hands-on applications by starting from biological problems/phenomena that students in the 4th semester are somewhat familiar with. During the exercises, students will obtain first experience with programming their own analyses/models for data analysis/interpretation. | ||||
| Learning objective | We will teach little if any novel biological knowledge or analysis methods, but focus on training the ability of use existing knowledge (for example from enzyme kinetics, regulatory mechanisms or analytical methods) to understand biological problems that arise when considering molecular elements in their context and to translate some of these problems into a form that can be solved by computational methods. Specific goals are: - understand the limitations of intuitive reasoning - obtain a first overview of computational approaches in systems biology - train ability to translate biological problems into computational problems - solve practical problems by programming with MATLAB - make first experiences in computational interpretation of biological data - understand typical abstractions in modeling molecular systems | ||||
| Content | During the first 7 weeks, the will focus on mechanistic modeling. Starting from simple enzyme kinetics, we will move through the dynamics of small pathways that also include regulation and end with flux balance analysis of a medium size metabolic network. During the second 7 weeks, the focus will shift to the analysis of larger data sets, such as metabolomics and transcriptomics that are often generated in biology. Here we will go through multivariate statistical methods that include clustering and principal component analysis, ending with first methods to learn networks from data. | ||||
| Lecture notes | Scripts to prepare the lectures will be provided via Moodle | ||||
| Literature | The course is not taught by a particular book, but two books are suggested for further reading: - Systems Biology (Klipp, Herwig, Kowald, Wierling und Lehrach) Wiley-VCH 2009 - A First Course in Systems Biology (Eberhardt O. Voight) Garland Science 2012 | ||||