Suchergebnis: Katalogdaten im Frühjahrssemester 2020

Biotechnologie Master Information
Kernfächer
Students 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.
NummerTitelTypECTSUmfangDozierende
636-0101-00LSystems GenomicsO4 KP3GN. Beerenwinkel, C. Beisel, S. Reddy
KurzbeschreibungThis lecture course is an introduction to Systems Genomics. It addresses how fundamental questions in biological systems are studied and how the resulting data is statistically analyzed in order to derive predictive mathematical models. The focus is on viewing biology from a genomic perspective, which requires high-throughput experimental methods (e.g., RNA-seq, genome-scale screening, single-cell
LernzielThe goal of this course is to learn how a detailed quantitative description of genome biology can be employed for a better understanding of molecular and cellular processes and function. Students will learn fundamental questions driving the field of Systems Genomics. They will also be introduced to traditional and advanced state-of-the-art technologies (e.g., CRISPR-Cas9 screening, droplet-microfluidic sequencing, cellular genetic barcoding) that are used to obtain quantitative data in Systems Genomics. They will learn how to use these data to develop mathematical models and efficient statistical inference algorithms to recognize patterns, molecular interrelationships, and systems behavior. Finally, students will gain a perspective of how Systems Genomics can be used for applied biological sciences (e.g., drug discovery and screening, bio-production, cell line engineering, biomarker discovery, and diagnostics).
InhaltLectures in Systems Genomics will alternate between lectures on (i) biological questions, experimental technologies, and applications, and (ii) statistical data analysis and mathematical modeling. Selected complex biological systems and the respective experimental tools for a quantitative analysis will be presented. Some specific examples are the use of RNA-sequencing to do quantitative gene expression profiling, CRISPR-Cas9 genome scale screening to identify genes responsible for drug resistance, single-cell measurements to identify novel cellular phenotypes, and genetic barcoding of cells to dissect development and lineage differentiation.

Main Topics:
-- Next-generation sequencing
-- Transcriptomics
-- Biological network analysis
-- Functional and perturbation genomics
-- Single-cell biology and analysis
-- Genomic profiling of the immune system
-- Genomic profiling of cancer
-- Evolutionary genomics
-- Genome-wide association studies

Selected genomics datasets will be analyzed by students in the tutorials using the statistical programming language R and dedicated Bioconductor packages.
SkriptThe PowerPoint presentations of the lectures as well as other course material relevant for an active participation will be made available online.
Literatur-- Do K-A, Qin ZS & Vannucci M (2013) Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data, Cambridge University Press
-- Klipp E. et al (2009) Systems Biology, Wiley-Blackwell
-- Alon U (2007) An Introduction to Systems Biology, Chapman & Hall
-- Zvelebil M & Baum JO (2008) Understanding Bioinformatics, Garland Science
Praktika
Students need to acquire a total of 14 ECTS in lab courses.
All listed lab courses are mandatory.
NummerTitelTypECTSUmfangDozierende
636-0207-00LLab Course: Cellular Engineering Stem Cells Belegung eingeschränkt - Details anzeigen
Attention: This lab course was offered in previous semesters with the number: 626-0806-00L "Laboratory Course Stem Cell Purification, Culture and Manipulation”. Students that already passed course 626-0806-00L cannot receive credits for course 636-0207-00L.
O2 KP6PT. Schroeder
KurzbeschreibungMammalian stem cells of different organs are purified, cultured, differentiated, analyzed and manipulated. Plasmids and viral vectors will be cloned, produced and transfected / transduced to manipulate stem cells. Computational and analytical molecular biology methods, FACS and imaging and lectures complement the program.
LernzielIndependent planning and conducting of experiments with mammalian stem cells including all steps from culturing different cell lines to DNA transfection / transduction and expression analysis by different analytical methods. Documenting and writing a report on conducted experiments and results.
InhaltPractical course on purification of primary mammalian stem cells, culture of primary stem cells and stem cell lines, characterization, manipulation and differentiation of stem cells. Construction of plasmids or viral vectors for gene expression, DNA transfer by transfection and transduction, analysis of gene expression by fluorescent proteins, PCR, fluorescence-activated cell sorting (FACS), imaging. Documentation of experiments in a laboratory journal, writing of a report on the experiments and results.
636-0206-00LLab Course: Cellular Engineering Mammalian Cells Belegung eingeschränkt - Details anzeigen
Attention: This lab course was offered in previous semesters with the number: 626-0802-00L "Practical Course in Mammalian Cell Biotechnology”. Students that already passed course 626-0802-00L cannot receive credits for course 636-0206-00L.
O2 KP6PM. Fussenegger, A. M. Palma Teixeira
KurzbeschreibungMammalian cells will be transfected and transduced for the production of biopharmaceuticals, for drug discovery as well as for the design of synthetic biology-inspired programmable gene circuits. A wide array of analytical techniques, lectures, and excursions to biotech companies will complement the practical part.
LernzielIndependent planning and conducting of experiments with mammalian cells including all steps from culturing different cell lines to DNA transfection/transduction and expression analysis using a wide array of analytical methods.
InhaltA practical course on characterization and cultivation of mammalian cells, DNA transfer by transfection, construction of synthetic gene networks, analysis of gene expression by enzymatic and immunological methods and fluorescent proteins, bioprocessing, mammalian cell-based assays for drug discovery and diagnostics. Excursions to Biotech/Pharma companies.
SkriptWill be distributed on first day of the practical course
636-0205-00LLab Course: Mammalian Gene Circuits Belegung eingeschränkt - Details anzeigen O2 KP5PY. Benenson
KurzbeschreibungThe students are trained in basic techniques in construction and characterization of synthetic gene circuits in mammalian cells. Experimental circuits are built with both the input and the output conjugated to fluorescent reporters, allowing characterization at the single cell level.
LernzielThe objective of the course is to construct a genetic sensor for a molecular regulatory input such as microRNA or a transcription factor and characterize the input/output relationship of this sensor with the help of fluorescent reporters, fluorescent microscopy and fluorescent-activated cell sorting. The emphasis is on single-cell characterization.
InhaltThe course will take place over 4 weeks, with 2 days per week spent on lab work. The 4 weeks will be dedicated to the following activities

Week 1: Introduction to the course; supervised construct design and detailed planning. Cloning of the constructs: part 1.
Week 2: Cloning of the constructs, purification and characterization of DNA constructs
Week 3: Cell culture transfection, microscopy and flow cytometry characterization
Week 4: Data analysis and preparation of the final report; possibility to repeat failed experiments.
SkriptPreparatory materials will be provided before the start of the course.
LiteraturWill be provided before the course
636-0202-00LLab Course: Next-Generation Sequencing Belegung eingeschränkt - Details anzeigen O2 KP5PC. Beisel, S. Reddy
KurzbeschreibungThe Lab Course will take place Monday/Tuesday 9-17h, 10 days in total, start of this lab course is on Monday, September 25 2017.
LernzielStudents shall obtain a basic understanding in NGS and its application in transcription profiling including theoretical considerations when starting an RNA-seq experiment and the practical hands-on work of library preparation and usage of bioinformatics tools for data analysis.
InhaltIntroduction to NGS technologies and applications. Design of an RNA-seq transcription profiling experiment. Specific treatment of cells (+/- signal-induction) and RNA extraction. Handling and quality control of RNA samples. Sequencing library preparation starting with total RNA. Quality control and quantification of the libraries. Setup of an NGS run and sequencing of the prepared RNA-seq libraries using the NextSeq 500 system. Analysis of the generated sequence data: sequence data QC, criteria for run performance and quality of data; pre-processing of the raw data; mapping sequence reads to a reference sequence; quantification of transcript abundance and differential gene expression.
SkriptMaterial will be provided during the course
LiteraturSara Goodwin, John D. McPherson & W. Richard McCombie. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 17, 333-351 (2016)

Zhong Wang, Mark Gerstein & Michael Snyder. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10, 57-63 (January 2009)

Fatih Ozsolak & Patrice M. Milos. RNA sequencing: advances, challenges and opportunities. Nature Reviews Genetics 12, 87-98 (February 2011)

Ana Conesa, Pedro Madrigal, Sonia Tarazona et al. A survey of best practices for RNA-seq data analysis. Genome Biology 2016 17:13.
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
636-0110-00LImmunoEngineering
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 KP3VS. Reddy
KurzbeschreibungImmunoengineering 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.
LernzielThe 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.
InhaltImmunoengineering 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.
LiteraturReading 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.
Voraussetzungen / BesonderesThis 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 KP3GA. Hierlemann
KurzbeschreibungStudents 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.
LernzielStudents 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.
InhaltIntroduction to microensors and microsystems

# Brief introduction to semiconductors
# Silicon and glass micromachining
# Plastic materials and their micromachining
# Fundamentals of different transducers
# Mechanical sensors
# Thermal sensors
# Magnetic sensors
# Optical devices
# Chemical and biosensors
# Microfluidics
# BioMEMS
SkriptHandouts in English
Literatur- 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
Voraussetzungen / BesonderesParts of the course rely on knowledge of the fall semester class "Microtechnology" (636-0103-00L).
Lab URL: Link
636-0113-00LGenome Engineering
No longer accepting registrations. Course is fully booked.
W4 KP3VR. Platt
KurzbeschreibungThis course is both an introduction to genome engineering and also a highly interactive practical training on effectively reading, writing, and presenting in an academic context.
LernzielThe objective of this course is to learn how gene editing technologies function at the molecular and cellular level and how they are applied in research and clinical settings. 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. This content will be explored by critically examining and discussing current literature in the field and devising a technology development plan.
InhaltThe course content is comprised of lectures, discussions, 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. Primary research articles will be assigned each week, which will be followed by an in-class lecture and discussion. The course 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 molecular recording devices
--Gene editing tools as diagnostics and therapeutics
SkriptMade available through the course website.
LiteraturAssigned each week. Made available through the course website.
636-0022-00LDesign of ExperimentsW4 KP3GH.‑M. Kaltenbach
KurzbeschreibungThe 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.
LernzielStudents 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.
InhaltThe 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.
SkriptCourse material will be made available at: Link
LiteraturMain 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 KP3GS. Panke, W. Minas
KurzbeschreibungThe course covers the fundamentals of implementing biotechnological reactions and cultivations into reactors and major methods of product purification.
LernzielThe 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.
InhaltEnzyme kinetics – mass transfer in heterogeneous systems – enzyme reactors – residence time distributions - upstream processing of fermentation processes – ideal reactors – macrokinetics - gas transfer – membrane processes – chromatography
SkriptHandouts and text book references will be provided over the course.
LiteraturEg 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 KP3GP. S. Dittrich
KurzbeschreibungAnalytical 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
LernzielStudents will learn the basic principles, potential and limitations of analytical methods and lab-on-chip technology.
InhaltAnalytical 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
SkriptHandouts 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 KP3GS. Panke, J. Stelling
KurzbeschreibungTheoretical & 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
LernzielAfter 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).
InhaltThe 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.
SkriptHandouts during classes.
LiteraturMark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press
Uri Alon, An Introduction to Systems Biology, Chapman & Hall
Voraussetzungen / Besonderes1) 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
Findet dieses Semester nicht statt.
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 KP3GD. J. Müller
KurzbeschreibungThe lecture "Nanomachines of the Cell" introduces the concept of using functional biomolecular units of the cell as nanoscopic machines and to assemble them to nanoscopic factories. The specific aim is to be able to use these machines and factories in more complex biotechnological processes as nanoscale functional elements or to control cellular systems and health
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.
Inhalt- What 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? 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. Energy landscape concept to describe protein folding, stabilization, destabilization, and unfolding. Mechanisms of protein stabilization, destabilization and aggregation in health and disease. Mechanisms of protein (de-)stabilization in biomaterials science, bioengineering, and in biotechnological and pharmacological applications. 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. 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. Structural and functional characterization of membrane proteins. Bionanotechnological tools to handle and manipulate single membrane proteins.
- Membrane proteins as a toolbox to assemble nanoscopic functional vesicles. 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 to use the pumps and to 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. Tuning the adsorption spectra of a light-driven ion pump.
- Structure, function, engineering and application of F-ATP synthases. Engineering artificial vesicular systems 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.
- Engineering light-activated channels for cellular control: Optogenetics.
- Assembly and employing fibrillar structures.
- DNA origami. Using DNA to build artificial three-dimensional structures at nanometer precision.
- Microtubuli. Occurrence, structure, function, and properties. Designing 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. Translational motors, rotary motors, chemical driven motors, light-driven motors, unidirectional and bidirectional motors, reversibility, molecular ratchets, future visions. 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.
SkriptWill be provided as needed.
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 / BesonderesStudents 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.
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.
636-0121-00LSingle Cell TechnologiesW+4 KP3GB. Treutlein
KurzbeschreibungSingle-cell sequencing and imaging technologies are being applied to primary human organs and to engineered cells and tissues to understand cell states that emerge in these systems at unparalleled resolution. These technologies require sophisticated experimental and computational methods, which we will discuss in practical detail in this course.
LernzielTo understand the history and current state of the art of single-cell sequencing and imaging methods, gain experimental experience in the implementation of these methods, and to learn data analytical techniques to extract biological insight from the high-information content data.
InhaltThis course will include lecture sessions and paper discussion seminars, along with wet lab single-cell genomic experiments, followed by computational data analysis sessions based in R. In the lecture, I will cover the molecular biology and technical aspects underlying popular single-cell sequencing methods, as well as methods to spatially localize cell states within tissues or other multi-cellular systems. We will also cover the experimental aspects of light sheet microscopy and other microscopy methods as a tool to analyze cellular dynamics within complex tissues. We will read recent, seminal manuscripts in the single-cell genomics field and discuss the papers in detail as a group.

Seminar topics will include: Single-cell RNA/DNA/Epigenome sequencing, Lineage tracing, Perturbation screens, Trajectory reconstruction, Light sheet microscopy, Tissue clearing

In the lab, we will select an exciting biological phenomena to explore using single-cell sequencing and each student will get hands on experience in designing and executing the experiment, going through the steps of tissue dissociation, isolating cells, capturing and labeling nucleic acid, generating and sequencing libraries. We will then go through each step of sequencing read processing and quality control analysis, followed by sessions on data exploration (cell composition, marker gene detection, trajectory reconstruction, differential gene expression analysis, etc.)
System-Orientierung
NummerTitelTypECTSUmfangDozierende
636-0110-00LImmunoEngineering
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 KP3VS. Reddy
KurzbeschreibungImmunoengineering 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.
LernzielThe 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.
InhaltImmunoengineering 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.
LiteraturReading 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.
Voraussetzungen / BesonderesThis 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 KP3GA. Hierlemann
KurzbeschreibungStudents 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.
LernzielStudents 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.
InhaltIntroduction to microensors and microsystems

# Brief introduction to semiconductors
# Silicon and glass micromachining
# Plastic materials and their micromachining
# Fundamentals of different transducers
# Mechanical sensors
# Thermal sensors
# Magnetic sensors
# Optical devices
# Chemical and biosensors
# Microfluidics
# BioMEMS
SkriptHandouts in English
Literatur- 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
Voraussetzungen / BesonderesParts of the course rely on knowledge of the fall semester class "Microtechnology" (636-0103-00L).
Lab URL: Link
636-0113-00LGenome Engineering
No longer accepting registrations. Course is fully booked.
W4 KP3VR. Platt
KurzbeschreibungThis course is both an introduction to genome engineering and also a highly interactive practical training on effectively reading, writing, and presenting in an academic context.
LernzielThe objective of this course is to learn how gene editing technologies function at the molecular and cellular level and how they are applied in research and clinical settings. 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. This content will be explored by critically examining and discussing current literature in the field and devising a technology development plan.
InhaltThe course content is comprised of lectures, discussions, 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. Primary research articles will be assigned each week, which will be followed by an in-class lecture and discussion. The course 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 molecular recording devices
--Gene editing tools as diagnostics and therapeutics
SkriptMade available through the course website.
LiteraturAssigned each week. Made available through the course website.
636-0022-00LDesign of ExperimentsW4 KP3GH.‑M. Kaltenbach
KurzbeschreibungThe 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.
LernzielStudents 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.
InhaltThe 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.
SkriptCourse material will be made available at: Link
LiteraturMain 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 KP3GS. Panke, W. Minas
KurzbeschreibungThe course covers the fundamentals of implementing biotechnological reactions and cultivations into reactors and major methods of product purification.
LernzielThe 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.
InhaltEnzyme kinetics – mass transfer in heterogeneous systems – enzyme reactors – residence time distributions - upstream processing of fermentation processes – ideal reactors – macrokinetics - gas transfer – membrane processes – chromatography
SkriptHandouts and text book references will be provided over the course.
LiteraturEg Pauline Doran, Bioprocess Engineering, Clark & Blanch, Biochemical Engineering, Harrison and Todd, Bioseparation Science and Engineering
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