Suchergebnis: Katalogdaten im Herbstsemester 2017

Biotechnologie Master Information
Master-Studium (Studienreglement 2017)
Vertiefungsfächer
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.
Biomolekulare Orientierung
NummerTitelTypECTSUmfangDozierende
636-0103-00LMicrotechnology
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.
W4 KP3GA. Hierlemann
KurzbeschreibungStudents 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.
LernzielStudents 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.
InhaltIntroduction 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
SkriptHandouts in English
Literatur- 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
Voraussetzungen / BesonderesFundamentals 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.
636-0104-00LNanomachines of the Cell
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.
W4 KP3GD. J. Müller
KurzbeschreibungMolecular biotechnology students will combine basic knowledge in molecular cell biology, biochemistry, proteomics, biophysics, bioinformatics, bionanotechnology and engineering to learn how the nanomachines of the cell works and to use this knowledge to address future molecular biotechnological and bionanotechnological questions. Particularly it will be addressed how biomolecular units can be char
LernzielGain of an interdisciplinary research and development competence, which qualifies for scientific work (master's or doctoral thesis) as well as for work in the research and development department of a biotechnological company. The module is of general use in nano- and biotechnological courses of study focusing modern biomolecular technologies.
InhaltWhat are nanomachines of the cell? Understanding the cell as a complex factory. Are there engineering principles of the cell and if so what can we learn? Introducing new ways to understand and to apply engineering principles of cellular nanomachines in biotechnology and nanotechnology.
Introduction into factors and mechanisms that determine protein folding and stability. Inter- and intramolecular interactions. Understanding the concept of an energy landscape to describe protein folding, stabilization, destabilization, and unfolding. Mechanisms of protein stabilization, destabilization and aggregation in health and disease. Are there methods and ways to prevent protein destabilization and aggregation? Mechanisms of protein destabilization in biomaterials science, bioengineering, and in biotechnological and pharmacological applications. Protein stability in biotechnology. Biophysical methods that allow quantifying protein stability. Methods to prevent protein destabilization in biotechnological applications. Ways to adjust and manipulate the protein stability in biotechnology and medicine. Designing molecular compounds that stabilize specific proteins. Designing molecular compounds that lead to protein destabilization, misfolding and denaturation.
Biological and artificial membranes. Principles of membrane assembly, properties, stability and durability. Vesicles as containers for cargo. Engineering vesicles from native and synthetic components. Engineering ultrastable synthetic vesicles. Applying vesicles in biotechnology and medicine. Functionalizing vesicular membranes with proteins. Principles of membrane proteins. Structure and function relationship of membrane proteins. Importance of membrane proteins in pharmacology and biotechnology. Ways to structurally and functionally characterize membrane proteins. Bionanotechnological tools to handle and manipulate single membrane proteins. Membrane proteins as a toolbox to assemble nanoscopic functional vesicles. Designing multifunctional synthetic vesicles: Vesicles for drug delivery, vesicles for active transport, vesicles converting energy, vesicles switching their affinity, function, stability, and other properties.
Energy currencies of the cell. Energy conversion. Storable and transient forms of energy. Nature created a variety of light-driven ion pumps. How can we use this pumps, how can we modify them to our purpose? Employing light-driven ion pumps in biotechnology. Employing light-driven proton pumps adsorbing different wavelengths to boost the membrane gradient. How to create a synthetic membrane that allows no diffusion of ions. Transforming a proton into a chloride pump. Tuning the adsorption spectra of a light-driven ion pump. Engineering proton pumps as safety standards for credit cards and ID cards. Engineering proton pumps for holographic devices. Native and artificial light-activated ion channels. Engineering light-activated channels for their use in neuroscience: Optogenetics. ATP synthases convert transient into storable energies. Experimental approaches to explore the nanoscopic rotary machinery of single ATP synthases. Are there ways to engineer and to exchange the building blocks of the ATP synthase? Ways to change to gear of ATP synthases and to 'tune' its fuel consumption. Engineering an artificial vesicular system to convert light into ion gradients to synthesize ATP. Engineering ATP synthases as nanopropellers to move vesicles. Engineering a light-frequency tuned proton pumps to control the speed of nanopropelled vesicles. Engineering light-driven ion pumps to power the synthetic ATP propellers and to steer vesicles. Engineering and employing ATP synthases as molecular mixing devices.
Principles of signal transduction. The family of G-protein coupled receptors (GPCRs). Structure and function of GPCRs. Engineering (and other) possibilities to manipulate the functional state of GPCRs.
SkriptHand out will be given to students at lecture.
LiteraturAlberts et al: Molecular Biology of the cell
Biochemistry (5th edition), Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; ISBN 0-7167-4684-0, Freeman
Principles of Biochemistry, Nelson & Cox; ISBN: 1-57259-153-6, Worth Publishers, New York
Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania
Intermolecular & Surface Forces, Israelachvili; ISBN: 0-12-375181-0, Academic Press, London
Proteins: Biochemistry and Biotechnolgy, Walsh; ISBN: 0-471-899070, Wiley & Sons, New York
Textbook of Biochemistry with Clinical Correlations, Devlin; ISBN: 0-471-411361, Wiley & Sons, New York
Molecular Virology, Modrow et al.; ISBN: 3-8274-1086-X, Spektrum Verlag, Heidelberg
Voraussetzungen / BesonderesThe module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher.
636-0105-00LIntroduction 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.
W4 KP3GY. Benenson
KurzbeschreibungBiological 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.
LernzielThe 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.
InhaltNote: 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
SkriptLecture notes will be available online
LiteraturAs 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).
Voraussetzungen / BesonderesBasic knowledge of molecular biology is assumed.
636-0106-00LAdvanced Imaging Technologies
Attention: This course was offered in previous semesters with the number: 636-0014-00L "Imaging in Systems Biology". Students that already passed course 636-0014-00 cannot receive credits for course 636-0106-00.
W4 KP3GP. Pantazis
KurzbeschreibungImaging in systems biology offers the unique advantage of observing complex biological processes with high spatiotemporal resolution in whole organisms, offering a path to more refined, quantitative dynamic models. The course highlights the recent introduction of advanced imaging tools and automated instrumentation that will enable researchers to apply imaging for both research and analysis.
LernzielThe aim of the present teaching activity is to introduce the power of imaging to play a vital role in systems biology with an emphasis on addressing developmental biology processes in various animal models. The participant is expected to appreciate imaging as a particularly valuable tool in the pursuit of dissecting dynamic processes in complex biological systems.
InhaltThis lecture course will give an in-depth view into modern microscopy covering emerging imaging techniques (e.g. volumetric imaging), applications of quantitative fluorescence microscopy (e.g. FRAP, FDAP, FCS), and digital image analysis (e.g. image processing, image visualization). The goal is to enable the participant to appreciate the potential of available imaging methodologies to address questions in biology and to interpret experimental imaging data. Given the introduction into model organisms covering fruitfly (Drosophila melanogaster), zebrafish (Danio rerio), and mice (Mus musculus), emphasis will be given to imaging applications in developmental biology processes.
SkriptSlides of the lecture will be available online.
636-0108-00LBiological Engineering and Biotechnology
Attention: This course was offered in previous semesters with the number: 636-0003-00L "Biological Engineering and Biotechnology". Students that already passed course 636-0003-00L cannot receive credits for course 636-0108-00L.
W4 KP3VM. Fussenegger
KurzbeschreibungBiological 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.
LernzielBiological 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.
Inhalt1. 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.
SkriptHandout during the course.
636-0107-00LMicrobial BiotechnologyW4 KP3GS. Panke, M. Jeschek
KurzbeschreibungStudents 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.
LernzielStudents 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.
InhaltThe 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.
SkriptNotes will be provided in the forms of handouts.
LiteraturThe course will use selected parts of textbooks and then original scientific publications and reviews.
636-0018-00LData Mining IW6 KP3G + 2AK. M. Borgwardt
KurzbeschreibungData 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.
LernzielThe 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.
InhaltThe 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
SkriptCourse material will be provided in form of slides.
LiteraturWill be provided during the course.
Voraussetzungen / BesonderesBasic understanding of mathematics, as taught in basic mathematics courses at the Bachelor's level.
636-0550-00LBiomolecular NanotechnologyW3 KP2VM. Nash
Kurzbeschreibung
Lernziel
  •  Seite  1  von  1