Search result: Catalogue data in Spring Semester 2018

Biotechnology Master Information
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Master Studies (Programme Regulations 2017)
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.
636-0109-00LStem 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.
W4 credits3GT. Schroeder
AbstractStem 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.
ObjectiveUnderstanding of current knowledge, and lack thereof, in stem cell biology, regenerative medicine and required technologies. Theoretical preparation for practical laboratory experimentation with stem cells.
ContentWe 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
Attention: This course was offered in previous semesters with the number: 636-0010-00L "Biomolecular Engineering and Immunotechnology". Students that already passed course 636-0010-00L cannot receive credits for course 636-0110-00L.
W4 credits3VS. Reddy
AbstractImmunoengineering is an emerging area of research that uses technology and engineering principles to understand and manipulate the immune system. This is a highly interdisciplinary field and thus the instructor will present an integrated view that will include basic immunology, systems immunology, and synthetic immunology.
ObjectiveThe objective of this course is to introduce the students to the basic principles and applications of Immunoengineering. There will be an emphasis directed towards applications directly relevant in immunotherapy and biotechnology. This course requires prerequisite knowledge of molecular biology, biochemistry, cell biology, and genetics; these subjects will only be reviewed briefly during the course.
ContentImmunoengineering will be divided into three primary sections: i) basic principles in immunology; ii) systems immunology; iii) synthetic immunology.

I. Basic principles in immunology will cover the foundational concepts of innate and adaptive immunity. Topics include immunogenetics, pattern recognition receptors, lymphocyte receptors, humoral and T cell responses.

II. Systems immunology uses quantitative multiscale measurements and computational biology to describe and understand the complexity of the immune system. In this section we will cover high-throughput methods that are used to understand and profile immune responses.

III. Synthetic immunology is based on using methods in molecular and cellular engineering to control immune cell function and behavior. In this section students will learn about how immune receptors and cells are being engineered for applications such as cancer immunotherapy and precision and personalized medicine.
LiteratureReading material from Janeway's Immunobiology will be distributed, so students do not need to worry about purchasing or obtaining it. Supporting reading material from research articles will be provided to students.
Prerequisites / NoticeThis course requires prerequisite knowledge of molecular biology, biochemistry, cell biology, and genetics; these subjects will only be reviewed briefly during the course.
636-0114-00LMicrosensors and Microsystems
Attention: This course was offered in previous semesters with the number: 636-0004-00 "Microsensors and Microsystems". Students that already passed course 636-0004-00 cannot receive credits for course 636-0114-00.
Prerequisites: Physics I and Physics II highly recommended. This class builds on the contents of course 636-0103-00L, "Microtechnology", which are assumed to be known
W4 credits3GA. Hierlemann
AbstractStudents are introduced to microsensor and microsystem technology, the different materials and associated micromachining and fabrication techniques. They become acquainted with fundamentals of different transducers and their applications.
ObjectiveStudents are introduced to microsensor and microsystem technology. The students will get to know the different materials (silicon, glass, plastics) and the respective micromachining and fabrication techniques. They will become acquainted with the fundamentals of the different transducers including mechanical, thermal, magnetic, chemical, optical, and biosensors. They also will get to know strategies to integrate components into microsystems.
ContentIntroduction to microensors and microsystems

# Brief introduction to semiconductors
# Silicon and glass micromachining
# Wafer bonding
# Plastic materials and their micromachining
# Fundamentals of different transducers
# Mechanical sensors
# Thermal sensors
# Magnetic sensors
# Optical devices
# Chemical and biosensors
# Microfluidics
Lecture notesHandouts in English
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
- S.A. Campbell, "The Science and Engineering of Microelectronic Fabrication", 2nd edition, Oxford University Press, 2001
Prerequisites / NoticeLab URL: Link
636-0113-00LGenome EngineeringW4 credits3VR. Platt
AbstractThis course is an introduction to genome engineering and an examination of recent advancements and future challenges. It covers the discovery and development of gene editing technologies and their applications in basic and applied research. The focus is on gaining an in-depth molecular and cellular understanding of the technologies and also insight into how these tools can be used and further deve
ObjectiveThe objective of this course is to learn how gene editing technologies function at the molecular and cellular level, and how they are leveraged to understand the role of genetic elements in biological processes. Students will be introduced to the history and motivation behind the discovery and development of transformative genome engineering technologies, and also gain insight into the ethical, safety, and regulatory facets shaping the field.
ContentThe course content is comprised of lectures, discussions of important literature in the field, and a project. Lectures in Genome Engineering will be technology-focused and incorporate: 1) historical context to motivate the need for developing the technology, 2) development of the technology from concept to robust tool, 3) methods to discover, characterize, and evaluate the technology, and 4) applications of the technology in basic and applied research. Discussions of important literature in the field will be conducted in class, one course meeting following a lecture covering the topic material and assignment of the reading. The project will be team-based and entail devising a solution to a critical need in the field.

Main topics:
--Discovery and development of genome editing technologies
--The prokaryotic adaptive immune system CRISPR-Cas
--Genome engineering methods for generating genetically engineered model systems
--Genotype-phenotype linkage via genetic screens
--Massively paralleled perturbation and phenotyping
--Gene editing tools as genetic recording devices
--Gene editing tools as diagnostics and therapeutics
--Ethics, safety, and regulatory facets of genome engineering
Lecture notesHandout during the course.
LiteraturePeer-reviewed scientific publications will be assigned to complement lecture content.
636-0022-00LDesign of ExperimentsW4 credits3GH.‑M. Kaltenbach
AbstractThe course introduces 'classical' statistical design of experiments, particularly designs for blocking, full and fractional factorial designs with confounding, and response surface methods. Topics covered include (restricted) randomization and blocking, sample size and power calculations, confounding, and basics of analysis-of-variance methods for analysis including random effects and nesting.
ObjectiveStudents will learn about the statistical basics of designing and analyzing experiments with multiple qualitative and/or quantitative variables. Students will be able to construct designs for efficiently identifying important influence factors in their experiments, use sequential designs for optimizing experimental conditions, and correctly handle analyses with nested sampling or involving multiple comparisons.
ContentThe course introduces the basics of statistical design of experiments. We will start by discussing the role of randomization for the validity of inferences, see how replication (i.e., sample size) affects the precision of estimates that can be made, how we deal with nested replication (for example, taking several measurements on the same animal), and how we correctly handle multiple comparisons based on the same data.

We will then discuss how restrictions of randomization lead to blocked designs, which serve to improve precision of comparisons between experimental conditions. Such designs are also important to avoid confounding of the experimental effect of interest with other effects of no interest, e.g., to handle batch effects that are common in biological experimentation.

Next, we learn how to design efficient experiments with multiple factors of interest. In contrast to a one-variable-at-a time approach, factorial designs allow investigation of multiple factors simultaneously, and under some assumptions on the interplay of the factors, we may even get away with only a fraction of all possible factor combinations while still getting all the information we need.

We then discuss optimizing the combination of factors with respect to some response function, such as optimizing the composition of a medium solution to achieve maximum growth rate. Response surface methods offer an efficient and systematic way of finding optimal conditions with low effort through sequential experimentation; they are also common in industrial (engineering) applications.

Throughout the course, we will touch on several additional topics without getting into much detail, such as designs that are 'optimal' for either inference or prediction, and designs where experimental conditions are nested (e.g., split-plot designs).

The course assumes familiarity with the content of a typical introductory course in statistics: distributions and random variables, estimators and confidence intervals, hypothesis testing using p-values and false positives/negatives, and basics of linear regression or analysis of variance.
Lecture notesCourse material will be made available at: Link
LiteratureMain text:
Gary W. Oehlert: A first course in design and analysis of experiments, Freeman (Link)
Additional texts:
D. R. Cox: Planning of Experiments, Wiley
G. Casella: Statistical Design, Springer
H. R. Lindman: Analysis of variance in complex experimental designs, Freeman (now Springer)
636-0115-00LBiochemical EngineeringW4 credits3GS. Panke, W. Minas
AbstractThe course covers the fundamentals of implementing biotechnological reactions and cultivations into reactors and major methods of product purification.
ObjectiveThe objective is to instruct students in the key concepts that are required for efficient application of biotechnological systems (enzymes and cells) for the production of chemicals and proteins.
ContentEnzyme kinetics – mass transfer in heterogeneous systems – enzyme reactors – residence time distributions - upstream processing of fermentation processes – ideal reactors – macrokinetics - gas transfer – membrane processes – chromatography
Lecture notesHandouts and text book references will be provided over the course.
LiteratureEg Pauline Doran, Bioprocess Engineering, Clark & Blanch, Biochemical Engineering, Harrison and Todd, Bioseparation Science and Engineering
636-0112-00LAnalytical Methods and Lab-on-Chip Technology for Biology and Molecular DiagnosticsW4 credits3GP. S. Dittrich
AbstractAnalytical methods are the key for a comprehensive understanding of biological systems. This course introduces modern bioanalytical concepts and methods that are applied in the life sciences. Techniques for sample preparation, fluid handling, and detection, including microfluidics, microarray technology, immunological methods, sensors and biosensors, and various spectroscopic detection techniques
ObjectiveStudents will learn the basic principles, potential and limitations of analytical methods and lab-on-chip technology.
ContentAnalytical methods are the key for a comprehensive understanding of biological systems. This course introduces into modern bioanalytical concepts and methods that are applied in the life sciences. The lecture includes discussions of highly topical studies.

Topics will include:
Targets: Biomolecules, biomarkers, signalling factors – what and where to measure
Detection: Fluorescence spectroscopy, related techniques and label-free detection methods
Basic principles of microfluidics/lab-on-chip technology
Applied microfluidics: Single-cell analysis, medical applications and point-of-care diagnostic
Microarray technology
Immunological methods
Sensors and biosensors
Lecture notesHandouts during the course .
636-0111-00LSynthetic Biology I
Attention: This course was offered in previous semesters with the number: 636-0002-00L "Synthetic Biology I". Students that already passed course 636-0002-00L cannot receive credits for course 636-0111-00L.
W4 credits3GS. Panke, J. Stelling
AbstractTheoretical & practical introduction into the design of dynamic biological systems at different levels of abstraction, ranging from biological fundamentals of systems design (introduction to bacterial gene regulation, elements of transcriptional & translational control, advanced genetic engineering) to engineering design principles (standards, abstractions) mathematical modelling & systems desig
ObjectiveAfter the course, students will be able to theoretically master the biological and engineering fundamentals required for biological design to be able to participate in the international iGEM competition (see Link).
ContentThe overall goal of the course is to familiarize the students with the potential, the requirements and the problems of designing dynamic biological elements that are of central importance for manipulating biological systems, primarily (but not exclusively) prokaryotic systems. Next, the students will be taken through a number of successful examples of biological design, such as toggle switches, pulse generators, and oscillating systems, and apply the biological and engineering fundamentals to these examples, so that they get hands-on experience on how to integrate the various disciplines on their way to designing biological systems.
Lecture notesHandouts during classes.
LiteratureMark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press
Uri Alon, An Introduction to Systems Biology, Chapman & Hall
Prerequisites / Notice1) Though we do not place a formal requirement for previous participation in particular courses, we expect all participants to be familiar with a certain level of biology and of mathematics. Specifically, there will be material for self study available on Link as of mid January, and everybody is expected to be fully familiar with this material BEFORE THE CLASS BEGINS to be able to follow the different lectures. Please contact Link for access to material
2) The course is also thought as a preparation for the participation in the international iGEM synthetic biology summer competition (Link, Link). This competition is also the contents of the course Synthetic Biology II. Link
636-0116-00LNanomachines of the Cell (Part II): Engineering and Application
Attention: This course was offered in previous semesters with the number: 636-0008-00L "Nanomachines of the Cell II". Students that already passed course 636-0008-00 cannot receive credits for course 636-0116-00.
Prerequisites: Students should have an interdisciplinary background (bachelor) in molecular biotechnology, biochemistry, cell biology, physics, bioinformatics or molecular bioengineering.
W4 credits3GD. J. Müller
AbstractThis second part of the lecture series "Nanomachines of the Cell" extends what has been learned in the first module. "Engineering and application" will be thus a consolidation of the concepts of functional biomolecular units of the cell as nanoscopic machines. The specific aim is to be able to use these cellular machines in more complex biotechnological processes as nanoscale functional elements.
ObjectiveGain 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.
ContentAssembly of fibrillar structures. Filamentous structures inside and outside the cell. Principles of polymerisation dynamics: Nucleation, polarity, equilibrium and non-equilibrium driven polymerization, treadmilling, energy consumption, asymmetric building blocks, ... Self-assembly processes in polymer chemistry and physics. Self-assembly processes into two- and three-dimensions. Filaments of the cell: F-actin, intermediate filaments, microtubuli, and collagen. Filaments of the cell fulfil several functions: Structural integrity and functionalization of the environment. How does the cell control these functions? Example: The collagen family. Molecular and supramolecular structure of collagens. On the importance of motifs on the molecular packing mechanism of collagen. Occurrence of collagens and functional roles. Diseases related to collagen malfunction. Properties of collagen: Flexibility, elasticity, strength, persistence length, conformations, binding sites, signal transduction, ... Proteins that functionalize collagens. Can we use these proteins as a biomolecular toolbox to build up three-dimensional functional scaffolds? Directing and controlling the self-assembly of collagen type I. Learning which factors determine the supramolecular structure of self-assembled collagen. Using this knowledge to guide the self-assembly of collagen into nanoscopic scaffolds. Creating intelligent collagen scaffolds to guide cellular functions. Ways to functionalize collagen matrices for their use in biotechnology and tissue engineering. The great challenges: How can we create three-dimensional collagen scaffolds?
DNA origami. Using DNA to build artificial three-dimensional structures at nanometer precision. From smilies to mechanical building blocks to three-dimensional containers almost every three-dimensional structure can be build. Self-assembly process of DNA. 'Programming the DNA': How to engineer the DNA sequence to promote it's self-assembly into a three-dimensional structure. How to engineer the DNA sequence to promote the self-assembly of the DNA into a precise three-dimensional nanoscopic arrangement. Engineering lessons: How to functionalize three-dimensional DNA containers so that they have a different fluorescent protein on each corner? How to functionalize a functionalize three-dimensional DNA container so that it frees its cargo on response to an external stimuli? How to functionalize a three-dimensional DNA container so that a cell can opens it and extract the cargo? Where may DNA origami be in 10 years? Comparative approaches using peptides to design origami.
Microtubuli. Occurrence, structure, function, and properties. Cell mechanics, motility and dynamic. Mitosis. Cargo transport by motor proteins. Assembly mechanisms, tubulin subunits, nucleation, polarity, kinetics, concentration dependent growth, GTP dependency, dynamic instability, capping, ..). Designing three-dimensional structures using microtubuli. Creating a racing track: Motility assays. Designing and microstructuring of supports as circuits for molecular shuttles. Biofunctionalization of the circuits. Transporting molecular cargo along circuits. Engineering molecular devices to switch the transport 'on' and 'off'.
Motor proteins. Introduction: Translational motors, rotary motors, chemical driven motors, light-driven motors, unidirectional and bidirectional motors, reversibility, molecular ratchets, future visions. Example of rotary motors: F-ATP synthase and flagella motor. F-ATP synthase was introduced in (Nanomachines of the cell Part I). Common and different engineering principles of the F-ATP synthase and the flagella motor. Structure, function, energy source, and rotational modes. Controlled assembly of a complex machinery such as the flagella motor. Are there ways to exchange the building blocks of the motor and to 'tune' it?
Motor proteins of the cytoskeleton.
Prediction, design und engineering of cellular machines.
Lecture notesHand out will be given to students at lecture.
Literaturelberts 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
Prerequisites / NoticeStudents should have an interdisciplinary background (bachelor) in molecular biotechnology, biochemistry, cell biology, physics, bioinformatics or molecular bioengineering.

The 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.
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