Uwe Sauer: Catalogue data in Spring Semester 2015

Name Prof. Dr. Uwe Sauer
FieldSystembiologie
Address
Inst. f. Molekulare Systembiologie
ETH Zürich, HPM H 28
Otto-Stern-Weg 3
8093 Zürich
SWITZERLAND
Telephone+41 44 633 36 72
E-mailsauer@imsb.biol.ethz.ch
DepartmentBiology
RelationshipFull Professor

NumberTitleECTSHoursLecturers
551-0001-AALGeneral Biology I
Enrolment only for MSc students who need this course as additional requirement.
3 credits6RU. Sauer, A. Widmer
AbstractBasics of structure, formation and function of cells and biomacromolecules, principles of metabolism, as well as basic classical and molecular genetics and evolutionary biology.

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.
Learning objectiveThe understanding of some basic principles of biology: the hierarchy of the structural levels of biological organisation, with particular emphasis on the cell and its functions, as well as metabolism, inheritance and evolution.
ContentThe structure and function of biomacromolecules; basics of metabolism; cell biology; membrane structure and function; basic energetics of cellular processes; respiration, photosynthesis; cell cycle, meiosis and sexual life cycles; Mendelian and molecular genetics; animal reproduction and behavior; sensory and motor mechanisms; population biology and evolution; principles of phylogeny.

We will treat the following Campbell chapters:

2 The Chemical Context of Life
3 Water and the Fitness of the Environment
4 Carbon and the Molecular Diversity of Life
5 The Structure and Function of Large Biological Molecules
6 A Tour of the Cell
7 Membrane Structure and Function
8 An Introduction to Metabolism
9 Cellular Respiration
10 Photosynthesis
13 Meiosis and Sexual Life Cycles
14 Mendel and the Gene Idea
15 The Chromosomal Basis of Inheritance
21 Genomes and their Evolution
22 Descent with Modification
23 The Evolution of Populations
24 The Origin of Species
25 The History of Life on Earth
26 Phylogeny and the Tree of Life
Lecture notesNo script
LiteratureN. A. Campbell, J. B. Reece: "Biologie" (8. aktualisierte Aufl.); Pearson Studium, München 2009. (deutsche Auflage)
oder:
J. B. Reece, L. A. Urry, M. L. Cain, S. A. Wasserman, P. V. Minorsky, R. B. Jackson: "Campbell Biology" (9th edition); Benjamin Cummings, San Francisco 2010. (English edition)
oder:
N. A. Campbell, J. B. Reece: "Biology" (8th edition); Benjamin Cummings, San Francisco 2008.
Prerequisites / NoticeThis 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-AALGeneral Biology II
Enrolment only for MSc students who need this course as additional requirement.
3 credits6RU. Sauer, R. Aebersold, H.‑M. Fischer, W. Gruissem
AbstractBasics of structure, formation and function of cells and biomacromolecules, principles of metabolism, basic molecular genetics, form and function of plants.
Learning objectiveThe understanding of some basic concepts of biology: the hierarchy of the structural levels of biological organisation, with particular emphasis on the cell and its functions, the fundamentals of metabolism and molecular genetics, as well as form and function of vascular plants.
ContentThe 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; bacteria and archaea; structure and growth of vascular plants, resource acquisition and transport, soil and plant nutrition.

The content of this lecture is identical to the "Allgemeine Biologie II" with the following Campbell chapters:

16 The Molecular Basis of Inheritance
17 From Gene to Protein
18 Regulation of Gene Expression
19 Viruses
20, 38 Biotechnology, Biosafety
27 Bacteria and Archae
28 Protists
31 Fungi
29, 30 Plant Diversity I & II
35 Plant Structure, Growth, and Development
36 Resource Acquisition and Transport
37 Soil and Plant Nutrition
38 Angiosperm Reproduction and Biotechnology
39 Plant Responses to Internal and External Signals
Lecture notesNo script
LiteratureN. A. Campbell, J. B. Reece: "Biology" (8th edition); Benjamin Cummings, San Francisco 2008.
Prerequisites / NoticeBasic general and organic chemistry
551-0002-00LGeneral Biology II3 credits3GU. Sauer, R. Aebersold, H.‑M. Fischer, W. Gruissem
AbstractBasics of molecular biology (gene expression and its regulation; from gene to protein); evolution of biological diversity (bacteria, archaea, protists, fungi, plants); basics of the physiology of higher plants (structure, growth, development, nutrition, transport, reproduction)
Learning objectiveThe understanding of basic concepts in biology: gene expression, its control and regulation; life histories of pro- and eucaryotic microorgamisms; structure, function, and reprodction of higher plants.
ContentFrom gene to protein; molecular genetics of microbial systems; structural and metabolic diversity of prokaryotes; diversity of eukaryotic microorganisms; the eukaryotic genome; regulation of gene expression; the genetic basis of the development of multicellullar organisms. Plant physiology: structure and growth, physiology of photosynthesis incl. C4 and CAM, nutrition and transport processes, reproduction and development, response to internal and external signals.

The following Campbell chapters will be covered:

16 The Molecular Basis of Inheritance
17 From Gene to Protein
18 Regulation of Gene Expression
19 Viruses
20, 38 Biotechnology, Biosafety
27 Bacteria and Archae
28 Protists
31 Fungi
29, 30 Plant Diversity I & II
35 Plant Structure, Growth, and Development
36 Resource Acquisition and Transport
37 Soil and Plant Nutrition
38 Angiosperm Reproduction and Biotechnology
39 Plant Responses to Internal and External Signals
Lecture notesno script
LiteratureN. A. Campbell, J. B. Reece: "Biology" (8th edition); Pearson, San Francisco 2008.
Prerequisites / NoticeThe lecture is the second in a series of two lectures given over two semesters for students of agricultural and food sciences, as well as of environmental sciences.
551-0324-00LSystems Biology Information 6 credits4VR. Aebersold, B. Christen, M. Claassen, E. Hafen, U. Sauer
AbstractIntroduction 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
ContentOverview 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 notesno script
LiteratureThe 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
551-0342-00LMetabolomics Information Restricted registration - show details
Number of participants limited to 10
6 credits7GN. Zamboni, U. Sauer
AbstractThe 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 objectivePerforming 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.
ContentBasics 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.
551-1174-00LSystems Biology4 credits2V + 2UU. Sauer, K. M. Borgwardt, J. Stelling, N. Zamboni
AbstractThe 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 learn to program their own analyses/models for data analysis/interpretation.
Learning objective- 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
ContentDuring 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 notesNo script
LiteratureThe 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