Module Guide for the Study Path - uni-luebeck.de · 2014-09-30 · Module Guide Interdisciplinary competence Ethics in Sciences / Scientific Writing (PS4610-IB, EthScWrIB) 1 Scientific

Module Guide for the Study Path

Master Infection Biology

Version from 2. July 2014

Module Guide

Interdisciplinary competence Ethics in Sciences / Scientific Writing (PS4610-IB, EthScWrIB) 1

Scientific Writing (PS4610-IB-B, SciWritIB) 2

Ethics in Sciences (PS4620-IB, EthicsIB) 3

Life Sciences Infection Biology 1 (LS4015, InfBiol1) 4

Clinical Aspects of Infection (LS4025, ClinAsp) 6

Immunology (LS4035, Immunol) 8

Diagnosis of Infectious Diseases (LS4045, DiagInfDis) 10

Practical Course 1 (LS4115, PC) 12

Infection Biology 2 (LS4145, InfBiol2) 13

Anti-microbial Therapy and Prophylaxis (LS4155, AntTherPro) 15

Anti-microbial Therapy and Prophylaxis - Therapies (LS4155-A, Therapies) 16

Anti-microbial Therapy and Prophylaxis - Vaccines (LS4155-B, Vaccines) 17

Model Systems of Infection (LS4165, ModSysInf) 18

Medical Microbiology (LS4175, MedMicro) 19

Medical Microbiology A: Molecular Virology (LS4175A, MedMicroVi) 20

Medical Microbiology B: Mechanisms of Bacterial Pathogenicity (LS4175B, MedMicroBa) 21

Medical Microbiology C: Pathogen Niches (LS4175C, MedMicroNi) 22

Medical Microbiology D: Inflammation: Methods in Immunology (LS4175D, MedMicroIn) 23

Host-Pathogen Interaction (LS4185, HostPatInt) 25

Host-Pathogen Interaction A: Principles and Analysis of Host Pathogen Interaction (LS4185A, PrinHPI) 26

Host-Pathogen Interaction B: Rational Drug Design (LS4185B, RatDruDes) 27

Master Thesis Infection Biology (LS5995, MScThesis) 28

Biology & IT Bioinformatics, Modelling, Biostatistics (CS4011, BioModEpi) 29

Bioinformatics, Modeling, Biostatistics A: Introduction to bioinformatics (CS4011A, Bioinfo) 30

Bioinformatics, Modeling, Biostatistics B: Modeling Biological Systems (CS4011B, ModBioS) 32

Bioinformatics, Modeling, Biostatistics C: Genetic Epidemiology (CS4011C, GenEpi) 33

Bioinformatics, Modeling, Biostatistics D: Microarray Data analysis (CS4011D, MicroData) 34

Structure biology Structural Biology of Infection (LS4020-IB, StrucBiol) 35

Structural Biology of Infection A: Proteinstructure / Crystallography (LS4020-IB A, ProStrCry) 36

Structural Biology of Infection B: NMR-Spectroscopy (LS4020-IB B, NMRSpr) 37

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Module Guide

Structural Biology of Infection C: Single Molecule Methods (LS4020-IB C, StrukAnaSM) 39

Structural Biology of Infection D: Microscopy, Methods and Applications (LS4020-IB D, StrBioMikr) 40

Structural Biology of Infection E: Basic Membrane Biophysics (LS4020-IB E, MemBiophy) 42

Structural Biology of Infection F: Protein-Biophysics (LS4020-IB F, ProBioPhy2) 43

Consolidation in IB Consolidating in IB: Part of the module IB1 Tuberculosis (LS5200-IB1, Tuberculos) 44

Consolidating in IB: Part of the module IB2 Virus Host Interaction (LS5200-IB2, VirHostIn) 45

Consolidating in IB: Part of the module IB3 Critical Appraisal of scientific papers (LS5200-IB3, CritApp) 46

Consolidating in IB: Part of the module IB4 Project Management (LS5200-IB4, ProjectM) 47

Consolidating in IB: Part of the module SB Biochemistry of the bacterial envelope (LS5200-SB IB, BacEnv) 48

Consolidating in IB: Part of the module SC Structure-based design and synthesis of an antiviral compound (LS5200-SC IB, antiviralc) 49

Consolidating in IB: Part of the Module SE Molecule Dynamics (LS5200-SE IB, MolDynam) 50

Consolidating in IB: Part of the module SG Structural Aspects of Protein biosynthesis (LS5200-SG IB, ProtBSynth) 51

Consolidating in IB: Part of the module SI Characterization of Protein Complexes in Structural Biology (LS5200-SI IB, ProtCompl) 52

Consolidating in IB: Part of the module SK Light up the Dark: modern fluorescence techniques in structural biology (LS5200-SK IB, ModernF) 53

Consolidating in IB: Part of the module ZB Cell Biology of the Senses (LS5200-ZB, ZellBioSen) 54

Consolidating in IB: Part of the module ZD Experimental Immunology (LS5200-ZD, ExpImmu) 55

Consolidating in IB: Part of the module ZE Advanched course in Immunology (LS5200-ZE, AdvancedIm) 56

Consolidating in IB: Part of the module ZF Gene Expression (LS5200-ZF, GenExpr) 57

Consolidating in IB: Part of the module ZK Cellular Microbiology & Inflammatory Diseases (LS5200-ZK, MicroInfDi) 58

Consolidating in IB: Part of the module ZM Molecular biology of virus infections of cytopathogenic and non-cytopathogenic viruses (LS5200-ZM, MolbioViru)59

Consolidating in IB: Part of the module ZP Inflammatory skin diseases from bench to bedside (LS5200-ZP, SkinDeas) 60

Consolidating in IB: Part of the module ZR Animal experimentation: A comprehensive introduction into laboratory mice (LS5200-ZR, AnimalExp) 61


Module Guide

PS4610-IB - Ethics in Sciences / Scientific Writing (EthScWrIB)

Duration: Turnus of offer: Credit points:

1 Semester Each summer semester 7

Course of study, specific field and term:● Master Infection Biology (compulsory), Interdisciplinary competence, 4. Term

Classes and lectures: Workload:● PS4620-IB: Ethics in Sciences (Lecture, 2 SWS)● PS4610-IB-B: Scientific Writing (Seminar, 2 SWS)

● 120 Hours Private studies● 60 Hours Presence studies

Contents of teaching:● See modules PS4620-IB and PS4610-IB-B

Qualification-goals/Competencies:● See modules PS4620-IB and PS4610-IB-B

Grading through:● Oral presentation and written report● Power-Point-Presentation● Test or Viva voce, made available by the lecturer● Participation on discussions

Responsible for this module:● Prof. Dr. rer. nat. Georg Sczakiel

Teacher:● Institute for the History of Medicine and Science Studies● Institute of Molecular Medicine

● Prof. Dr. rer. nat. Georg Sczakiel● Prof. Dr. phil. Christoph Rehmann-Sutter

Language:● English, except in case of only German-speaking participants

Notes:

The module is successfully graduated if both courses (PS4620-IB and PS4610-IB-B) are passed. The certificate will be ungraded(B-certificate).

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Module Guide

PS4610-IB-B - Scientific Writing (SciWritIB)


1 Semester Each winter semester 7


Classes and lectures: Workload:● PS4610-IB-B: Scientific Writing (Seminar, 2 SWS) ● 120 Hours Private studies

● 60 Hours Presence studies

Contents of teaching:● Basics of ethics and moral philosophy● The ethical structure of experiments with tissue, animals and human subjects● Principles of the most important laws and guidelines regulating research● Basic issues of research ethics and cases from recent debates● Key topics of research ethics in the biomedical sciences● Introduction into categories of scientific presentations● Analysis of scientific manuscripts and rules for their presentation● Preparation and presentation of scientific posters● Preparing a project proposal

Qualification-goals/Competencies:● Understanding of basic ethical dimensions of human actions and decisions● Understanding of ethical implication of experimental scientific research● Knowledge of relevant legal regulations in Germany and internationally● Knowledge of key debates in bioethics and research ethics● Basic skills for an autonomous ethical reflection about issues in biomedical sciences● Analysis of the logical and formal structure of scientific publications. Analysis of a specific original publication. Introduction into the

´peer-review process´● Understanding the criteria underlying scientific posters. Preparation and presentation of a poster based on given experimental data● Introduction into the writing of ´grant applications´ and the funding process of research projects. Writing a grant application on the

basis of specified prior-work and scientific aims

Grading through:● Seminar work● Regular and successful participation● Test or Viva voce, made available by the lecturer

Responsible for this module:● Prof. Dr. rer. nat. Georg Sczakiel

Teacher:● Institute of Molecular Medicine

● Prof. Dr. rer. nat. Georg Sczakiel

Languages:● Offered only in English● English, except in case of only German-speaking participants

Notes:

The module is successfully graduated if both courses (PS4620-IB and PS4610-IB-B) are passed.

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Module Guide

PS4620-IB - Ethics in Sciences (EthicsIB)




Classes and lectures: Workload:● PS4620-IB: Ethics in Sciences (Lecture with exercises or seminar,

2 SWS)● 40 Hours Private studies● 30 Hours Presence studies● 20 Hours Test preparation

Contents of teaching:● Societal and ethical implications of research in biomedical sciences and technologies● Basics of philosophy and sociology of science● Good scientific practice● Basics of bioethics: duties of investigators, obligations to colleagues,● Ethics of human subjects research and animal experim. Environmental ethicsentation. Control and governance of technology. Risk

assessement● Use and implications of images in science

Qualification-goals/Competencies:● Understanding of basic ethical implications of human actions and decisions● Understanding of ethical implication of experimental scientific research● Understanding of basic dimensions of philosophy and sociology of science and technology● Knowledge of relevant legal regulations in Germany and internationally● Knowledge of key debates in bioethics and research ethics● Basic skills for an autonomous ethical reflection about issues in biomedical sciences

Grading through:● Test or Viva voce, made available by the lecturer

Responsible for this module:● Prof. Dr. phil. Christoph Rehmann-Sutter

Teacher:● Institute for the History of Medicine and Science Studies

● Prof. Dr. phil. Christoph Rehmann-Sutter

Literature:● Daniel A. Vallero: Biomedical Ethics for Engineers. Ethics and Decision Making in Biomedical and Biosystem Engineering - Amsterdam:

Elsevier 2007● Ben Mepham: Bioethics. An Introduction for the Biosciences - Oxford: Oxford University Press 2008● Sergio Sismondo: An introduction to science and technology studies - Chichester: Wiley-Blackwell 2010

Language:● Offered only in English

Notes:

The module is successfully graduated if both courses (PS4620-IB and PS4610-IB-B) are passed.

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Module Guide

LS4015 - Infection Biology 1 (InfBiol1)



Course of study, specific field and term:● Master Infection Biology (compulsory), Life Sciences, 1. Term

Classes and lectures: Workload:● Infection Biology 1 (Lecture, 4 SWS) ● 120 Hours Private studies


Contents of teaching:● Introduction into the variety of infectious diseases and their respective causative pathogens (Viruses, bacteria, parasitic protozoa and

helminths, fungi).● The lectures will cover human and animal-pathogenic viruses, bacteria and fungi as well as parasites (protozoa, helminths).● Important infectious agents and diseases will be covered in detail such as Influenza, HIV, HCV, herpes viruses, Papilloma, Pox viruses,

Cholera, typhoid fever, E.coli/EHEC, Helicobacter, MRSA, Pneumococci, Tuberculosis, Candida, Malaria, Leishmaniasis, Trypanosoma,Schistosomiasis, Filariasis, Trichinella etc.

Qualification-goals/Competencies:● The students gain comprehensive basic and advanced knowledge of the biology of important human infectious agents and their

diseases covering viruses, bacteria, fungi, parasitic protozoa and helminths, their life cycles, vectors and reservoirs, epidemiology,treatment and prophylaxis. The module provides the students with the capability to understand the complex host-pathogeninteractions during the infectious process, the capacity to integrate the pathogen's virulence functions and the hosts defensestrategies, how both evolved during co-evolution and how these interactions shape pathogenesis and disease outcome. The studentsgain the competence to employ principles of host-pathogen interactions in scientific discussions and research questions.

Grading through:● Regular and successful participation● Test or Viva voce, made available by the lecturer

Is requisite for:● Infection Biology 2 (LS4145)

Responsible for this module:● Prof. Dr. Ulrich Schaible

Teacher:● Institute for Medical Microbiology and Hygiene● Institute of Virology and Cell Biology● Abteilung Molekulare Infektiologie

● Prof. Dr. med. Werner Solbach● Prof. Tamás Laskay, Ph.D.● Prof. Dr. rer. nat Stefan Taube● Prof. Dr. Ulrich Schaible● Dr. rer. nat. Bianca Schneider

Literature:● Sebastian Suerbaum, Helmut Hahn, Gerd-Dieter Burchard, Stefan H. E. Kaufmann: Medizinische Mikrobiologie und Infektiologie - 2012● Richard Goering, Hazel Dockrell, Mark Zuckerman, Ivan Roitt von Saunders: Mims' Medical Microbiology + Student Consult Online

Access - 2012● S.J. Flint et al: Principles of Virology: Molecular Biology, Pathogenesis, and Control of Animal Viruses - American Society Microbiology,

February 2009, 3rd Ed., ISBN: 978-1-55581-443-4● S.Modrow, D. Falke, U. Truyen, H. Schätzl: Molekulare Virologie - Spektrum, Heidelberg, 3. Aufl. 2010, ISBN 978-3-8274-1833-3● Michael T. Madigan, John M. Martinko: Brock Biology of Microorganisms - Pearson International Edition, ISBN 0-13-196893-9● Mims, Nash, Stephen: Mim's Pathogenesis of Infectious Disease - 5th Edition

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Module Guide


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Module Guide

LS4025 - Clinical Aspects of Infection (ClinAsp)




Classes and lectures: Workload:● Lectures clinical aspects of infection (Lecture, 3 SWS)● Excercises clinical aspects of infection (Exercise, 1 SWS)


Contents of teaching:● Clinical background: Clinical characteristics and diagnostical approaches of the most important infectious diseases. Pathophysiological

background on the occurence of systemic and local clinical symptoms and disease-specific clinical pictures. Introduction in the mostrelevant instrumental and laboratory techniques for the diagnosis of infections. Established and novel strategies in the treatment ofinfectious diseases with respect to the emergence of multi-drug resistant pathogens.

● Modern therapeutic approaches● Clinical epidemiology: Introduction into epidemiology; What is normal? Diagnosis; Frequencies; Survey, registers and data sources;

Geographical epidemiology; Study designs (RCT, cohort study, case control study, cross sectional study); Effect measures; Causality;Chance, bias and confounding; Control of errors.

● Assessment of scientific articles on the basis of clinical epidemiology

Qualification-goals/Competencies:● Basic knowledge on clinical aspects of infectious diseases● Knowledge of basic concepts in epidemiology with focus on clinical epidemiology● Qualification to appraise data, results, methods and literature in the context of medicine and epidemiology● Understanding the links between clinic - infection medicine for diagnosis, patient management and therapy


Responsible for this module:● Prof. Dr. med. Jan Rupp

Teacher:● Research Center Borstel● Institute for Social Medicine and Epidemiology● Institute for Medical Microbiology and Hygiene

● Prof. Dr. med. Jan Rupp● Prof. Dr. med. Alexander Katalinic● Prof. Dr. med. Johannes Knobloch● Prof. Dr. Christoph Lange● Dr. rer. nat. Annika Waldmann● Dr.Dr. Joachim Hübner● Dr. phil. Janine Simons● Dr. rer. hum. biol. Maike Schnoor● Dipl.-Inf. Heiner Fauteck● Dipl.-Stat. Nora Eisemann● Dipl.-Inf. Anke Richter● Dipl.-Geogr. Dr. rer. nat. Ron Pritzkuleit● Dr. med. Gunar Günther● Dr. med. Claudia Jafari● PD Dr. med. Christian Sina● Dr. med. Barbara Kalsdorf● Dr. med. Jochen Krajewski● Dr. med. Jan Heyckendorf

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Module Guide

Literature:● Mims, Nash, Stephen: Mims' Pathogenesis of Infectious Disease - 5th edition● Fletcher. Fletcher & Fletcher: Clincal Epidemiology� The Essentials. 5th edition


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Module Guide

LS4035 - Immunology (Immunol)




Classes and lectures: Workload:● Lectures (Lecture, 4 SWS) ● 120 Hours Private studies


Contents of teaching:● History of Immunology.● Hematopoiesis and hematopoietic stem cells.● Cells of the innate immune system.● Immune sensing by cell-bound pattern recognition systems.● Immune sensing by soluble pattern recognition systems.● B cells, gene rearrangement and antibodies.● MHC, antigen presentation and T cell activation.● T cell subsets, functions and regulation.● Cytokine receptors and signaling.● Soluble mediators and cell trafficking.● Mucosal immunity.● The immune response in allergy.● The immune response in autoimmune diseases.● Introduction: Basic mechanisms of immune defense against pathogens.● The impact of the microbiome on innate and adaptive immune responses.● Immune mechanisms in infection with extracellular bacteria.● Immune mechanisms in infection with intracellular bacteria.● Immune mechanisms in infection with pathogenic protozoa, nematodes, trematodes and cestodes.● Immune mechanisms in infection with DNA and RNA viruses.● The Sepsis syndrome.● Vaccination strategies to prevent infections.● Immune mechanisms related to fungal infections.

Qualification-goals/Competencies:● Understanding the basics in Immunology● Understanding the immune mechanisms in infection● Employing principles of immunology for studies in infection-immunology

Grading through:● Regular and successful participation● Viva Voce● Test or Viva voce, made available by the lecturer

Responsible for this module:● Prof. Dr. rer. nat. Marc Ehlers

Teacher:● ● Institute of Anatomy● Abteilung Molekulare Infektiologie ● Institute for Medical Microbiology and Hygiene● Institute for Systemic Inflammation Research (ISEF)

● Prof. Dr. rer. nat. Marc Ehlers● Prof. Dr. med. Jörg Köhl● Prof. Dr. rer. nat. Rudolf Manz

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http://www.isef.uni-luebeck.de/

Module Guide

● Prof. Tamás Laskay, Ph.D.● Dr. rer. nat. Christoph Hölscher● PD Dr. rer. nat. Norbert Reiling● Dr. rer. nat. Kathrin Kalies● Prof. Dr. med. Jan Rupp● Prof. Dr. med. Werner Solbach● Dr. Christian Karsten● Prof. Dr. med. Jörg Köhl● Dr.rer.nat. Yves Laumonnier● Ph.D. Kensuke Shima● Dr. rer. nat. Inga Kaufhold

Literature:● Kenneth Murphy: Janeway's Immunobiology


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Module Guide

LS4045 - Diagnosis of Infectious Diseases (DiagInfDis)




Classes and lectures: Workload:● Lectures (Lecture, 2 SWS)● Practical course (practical course, 2 SWS)● Seminars (Seminar, 1 SWS)

● 75 Hours Presence studies● 50 Hours Private studies

Contents of teaching:● Lecture: Molecular biology-based diagnostic methods; Serological techniques for the diagnosis of infectious diseases; Diagnosis of viral

and bacterial infections; Diagnosis of tuberculosis; Infection of the skin and diagnosis; Infection of the heart and diagnosis● Seminar: Selected topics concerning the diagnosis of infectious diseases (i.e. diagnostics of bacterial and viral infections, molecular

diagnostics, resistance testing of bacteria and viruses, biomarkers as novel tools to detect infections, mass spectrometry in clinicalmicrobiology, and application of next generation genome sequencing for infection diagnostics)

● Practical course: Basic laboratory rules and instructions for handling infectious organisms and materials; Techniques of bacteriology:Culture, media, preparation of slides, staining techniques; Characterization and identification of microbes (bacteria, fungi, protozoa,helminiths) by macroscopic and microscopic growth characteristics and morphology; Biochemical characterization of bacteria;Diagnostic immunology/serology: agglutination, precipitation, immunofluorescence; Diagnosis by the novel technique-MALDI-TOF/MS;Analysis of antibiotic susceptibility

Qualification-goals/Competencies:● Detailed knowledge of methods for the diagnosis of infectious diseases. Application of diagnostic principles for the identification of

pathogenic bacteria, fungi, virus, protozoa and helminits in infectious diseases. Identification of unknown pathogens from suspectedinfectious materials of respiratory, intestinal, urinary tract and blood infections by various diagnostic techniques

Grading through:● Regular and successful participation in practical course● Presentation● Protocols ● Test or Viva voce, made available by the lecturer

Is requisite for:● Infection Biology 2 (LS4145)

Responsible for this module:● Prof. Dr. med. Werner Solbach

Teacher:● LADR GmbH Geesthacht● Medical Clinic II● Institute for Systemic Inflammation Research (ISEF) ● Berhard Nocht Institute, Hamburg ● Department of Dermatology, Allergology and Venerology● Institute of Virology and Cell Biology● Research Center Borstel● Institute of Molecular Medicine● Institute for Medical Microbiology and Hygiene

● Prof. Dr. med. Werner Solbach● Prof. Dr. med. Johannes Knobloch● Prof. Dr. rer. nat. Tobias Restle● PD. Dr. rer. nat. Stefan Niemann● Dr. rer. nat. Alessandra Mescalchin● Prof. Dr. rer. nat. Georg Sczakiel

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Module Guide

● Dr. rer. nat. Martina Behnen-Haerer● Ph.D. Kensuke Shima● Prof. Dr. rer. nat Stefan Taube● Prof. Dr. rer. nat. Norbert Tautz● Prof. Dr. rer. nat. Marc Ehlers● Prof. Dr. Stephan Günther● Priv.-Doz. Dr. rer. nat. Elvira Richter● PD Dr. med. Kai Mortensen● Dr. med. Waltraud Anemüller● Dr. med. Detlef Kramer


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Module Guide

LS4115 - Practical Course 1 (PC)




Classes and lectures: Workload:● Practical Courses (practical course, 24 SWS) ● 360 Hours Presence studies

● 120 Hours Private studies

Contents of teaching:● In two practical courses in each case 2 of the different skills, described below, have to be acquired. At least one practical course must

have a duration of 3 months (12 weeks) full time. The second one can last 8 to 12 weeks.● Molecular microbiology:M 1: Genomics/ transcriptomicsM 2: Proteomics/ lipidomicsM 3: Structure analytics of macromoleculesM 4:

Protein expression and -purificationM 5: Membrane biophysicsM 6: RNA/ siRNA-TechnologiesM 7: Molecular Genetics ofmicrobes/pathogens

● Cellular microbiology: C 1: Tissue culture/ Cell cultureC 2: Microbe-infected cell/ tissue modelsC 3: In vivo infection modelsC 4: Celltracing/ Cell sorting/ Cellular biochemistryC 5: ImmunologyC 6: Microscopic Techniques/ Ultrastructure

● Medical Microbiology Me1: Diagnostic tools in microbiology and serologyMe2: Tropical medicineMe3: Infection-epidemiology

Qualification-goals/Competencies:● Extension and application of the theoretically gained experience to the experimental work in two fields of Cellular- and Molecular

microbiology (called competences) in each course;absorbing knowledge in documentation and presentation of scientific data(presentation with defense)ability to work in a team;getting lab experiences by working on real research projects

● Live long learning competence

Grading through:● Regular and successful participation in practical course● Presentation● Poster

Requires:● Infection Biology 2 (LS4145)

Teacher:● All institutes of the University of Lübeck●

● MitarbeiterInnen des Instituts


Notes:

All practical courses must be approved by Prof. Schaible 4 weeks in time before.

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Module Guide

LS4145 - Infection Biology 2 (InfBiol2)




Classes and lectures: Workload:● Infection Biology Lectures (Lecture, 2 SWS)● Practical course (practical course, 3 SWS)

● 75 Hours Presence studies● 50 Hours Private studies

Contents of teaching:● Cellular and molecular mechanisms of infections● Interaction of pathogens with cellular signalling pathways● Extracellular pathogens; biofilms● Intracellular pathogens, molecular mechanisms of intracellular survival, type II-V secretion systems, host cell death and its

consequenses● Immune therapy and DNA vaccines● Immune deficiencies, immunosuppressive chemotherapy and its consequences, retroviruses, HIV-AIDS● Infections and environment● Experimental techniques in the infection biology, in vitro and ex vivo methods, experimental animal models of infectious diseases,

gene knock-out mice, genetically manipulated infectious agents

Qualification-goals/Competencies:● Detailed knowledge of infectious agents, infectious diseases and their pathomechanisms● Detailed understanding of antimicrobial defence mechanisms at the cellular and molecular level.● Understanding the mechanisms of vaccination and immune deficiencies.● Knowledge and practical skills in laboratory techniques of infection biology.

Grading through:● Certificates and protocols● Regular and successful participation● Protocols ● Test or Viva voce, made available by the lecturer

Is requisite for:● Practical Course 1 (LS4115)

Requires:● Diagnosis of Infectious Diseases (LS4045)● Infection Biology 1 (LS4015)

Responsible for this module:● Prof. Tamás Laskay, Ph.D.

Teacher:● Institute of Virology and Cell Biology● Research Center Borstel

● Prof. Dr. Ulrich Schaible● Prof. Tamás Laskay, Ph.D.● Prof. Dr. rer. nat. Marc Ehlers● PD Dr. rer. nat. Norbert Reiling● Dr. rer. nat. Christoph Hölscher● Prof. Dr. rer. nat. Rudolf Manz● Prof. Dr. rer. nat Stefan Taube

Literature:

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Module Guide

● : - Textbooks, original and review articles


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Module Guide

LS4155 - Anti-microbial Therapy and Prophylaxis (AntTherPro)




Classes and lectures: Workload:● A) Therapies (Lecture, 2 SWS)● B) Vaccination Strategies (Seminar, 2 SWS)


Contents of teaching:● see:Anti-microbial Therapy and Prophylaxis - Therapies- Vaccines

Qualification-goals/Competencies:● Detailed knowledge on general concepts of anti-microbial therapies and prophylaxis● Competences in presenting and discussing scientific results

Grading through:● Presentation● Viva Voce● Test or Viva voce, made available by the lecturer

Responsible for this module:● Prof. Dr. rer. nat. Tobias Restle

Teacher:● Institute of Biochemistry● Research Center Borstel● Institute of Molecular Medicine

● Prof. Dr. rer. nat. Tobias Restle● Prof. Dr. rer. nat. Rolf Hilgenfeld● Prof. Dr. Ulrich Schaible● Dr. rer. nat. Alessandra Mescalchin● MitarbeiterInnen des Instituts

Literature:● : Recent review articles


Notes:

*more details see LS4155A and B

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Module Guide

LS4155-A - Anti-microbial Therapy and Prophylaxis - Therapies (Therapies)




Classes and lectures: Workload:● A) Therapies (Lecture, 2 SWS) ● 60 Hours Private studies


Contents of teaching:●

● General concepts of anti-microbial therapies; potentials and limitations, Concepts in drug design, Alternative strategies, The problem ofdrug resistance, Future challenges, Selected examples: antibacterial (antibiotics), antiviral (e.g. polymerase and protease inhibitors ofHIV, Herpes), antifungal (e.g. antimycotics and Candida albicans), antiprotozoal (e.g. chloroquine and Malaria) and drugs againstmulticellular eukaryotes (e.g. anthelmintics and fox-tapeworm).

Grading through:● Viva Voce● Test or Viva voce, made available by the lecturer


Teacher:● Institute of Molecular Medicine● Institute of Biochemistry

● Prof. Dr. rer. nat. Rolf Hilgenfeld● Dr. rer. nat. Alessandra Mescalchin● MitarbeiterInnen des Instituts


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Module Guide

LS4155-B - Anti-microbial Therapy and Prophylaxis - Vaccines (Vaccines)




Classes and lectures: Workload:● B) Vaccination Strategies (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Pathogen niches and immunity, Determine vaccine types, Vaccine types (live attenuated, killed, subunit, recombinant live and

examples), Epitopes, Vaccine carriers, Adjuvants

Grading through:● Attendance, min. 90%● Presentation


Teacher:● Research Center Borstel

● Prof. Dr. Ulrich Schaible


Notes:

* graded talk

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Module Guide

LS4165 - Model Systems of Infection (ModSysInf)




Classes and lectures: Workload:● Lectures In vivo Models (Lecture, 3 SWS)● Excercises In vivo Models (Exercise, 2 SWS)● Practical course In vivo Models (practical course, 2 SWS)


Contents of teaching:● (1) Animal experimentation and biological safetyLecture:- animal protection laws, animal experimentation application, documentation

of animal experiments- anatomy and physiology of mouse and rat, breeding methods and nomenclature, transgenic mice- anesthetics,analgesia, methods of anesthesia, criteria for animal burden and experiment abortion- ethics, alternative and additional methods-biological and gene technological safety

● Practicals:- biology and handling of mouse and rat- handling and behaviour of mouse, health and gender controling- applicationmethods, blood sampling and animal protection apporpriate sacrifice, sectioning mouse- working under biological safety levels,transgenic technology

● (2) Clinic-near model systems in infection biology- principles of animal experimentation in infection biology- infections of the skin(leishmaniasis), lung (tuberculosis, influenza), intestinal (helminths, salmonella), intracerebral (toxoplasmosis) and systemic infections(trypanosomis, malaria, sepsis)- humanized animal experimental models- comparison of scientific results from animal experimentationand the situation in humans

Qualification-goals/Competencies:● Basic knowledge of laws regulating animal experimentaion; theoretical and practical basics in handling of experimental animals; basic

knowledge on aspects of biological and gene technological safety; basic knowledge on the generation of transgenic animals● Basic knowledge based on experimental examples; consolidation of knowledge in seminar● Knowing how to handle the model systemsCompetence in protocol writing


Responsible for this module:● Dr. rer. nat. Christoph Hölscher

Teacher:● Institute for Medical Microbiology and Hygiene● Research Center Borstel

● Dr. rer. nat. Christoph Hölscher● Prof. Tamás Laskay, Ph.D.● Prof. Dr. rer. nat Stefan Taube● Dr. rer.nat. Hanna Erdmann● PD Dr. rer. nat. Norbert Reiling● Dr. rer. nat. Bianca Schneider● Prof. Dr. Guntram Grassl Grassl● Dr. Kerstin Walter● Dr.rer.nat. Christian Karsten● Dr. rer. nat. Jochen Behrends


Notes:

*attendance in lecture and practical course min. 90%

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Module Guide

LS4175 - Medical Microbiology (MedMicro)




Classes and lectures: Workload:● A Molecular Virology (Seminar, 2 SWS)● B Bacterial Virulence Factors (Seminar, 2 SWS)● C Pathogen Niches (Seminar, 2 SWS)● D Methods in Immunology (Seminar, 2 SWS)


Contents of teaching:● See LS4175 module parts A to D

Qualification-goals/Competencies:● Competence in critical reading, discussing and preseting of research articles.More details see LS4175 module parts A to D

Grading through:● Attendance, min. 90%● Presentation● Contributions to the discussion

Responsible for this module:● Prof. Dr. rer. nat Stefan Taube

Teacher:● Institute for Systemic Inflammation Research (ISEF) ● Research Center Borstel● Institute for Medical Microbiology and Hygiene● Institute of Virology and Cell Biology

● Prof. Dr. rer. nat Stefan Taube● Prof. Dr. med. Jan Rupp● Prof. Dr. rer. nat. Otto Holst● Dr. rer. nat. Bianca Schneider● Prof. Dr. rer. nat. Marc Ehlers● Prof. Dr. med. Jörg Köhl● Prof. Dr. rer. nat. Rudolf Manz● PD Dr. med. Peter König


Notes:

Choice of two of LS 4175 A to D; * graded talk; * min. 4 students/ seminar; If one participate in more than two of the required seminars and talks are given, the two best grades aretaken into account. The additional program achievement will be added non-graded in the transcript of records.

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Module Guide

LS4175A - Medical Microbiology A: Molecular Virology (MedMicroVi)



Course of study, specific field and term:● Master Infection Biology (Optional Subject), Life Sciences, 2. Term

Classes and lectures: Workload:● A Molecular Virology (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Viral and cellular receptors for virus-cell interaction as well as their inhibition by inhibitors● Detailed molecular mechanisms of genome replication from selected virus families (focussed on RNA viruses)● Host factors and their function in viral genome replication on the basis of selected examples● Structural biology of viruses and its application for anti-viral therapy● Basics of viral pathogenesis● Viral strategies against the innate immune system

Qualification-goals/Competencies:● Detailed knowledge on the interaction between viruses and their host cells● Detail knowledge on virus structure and replication mechanisms as well as on derived anti-viral strategies● Knowledge of and applicable understanding pathogenic processes and virus-host interactions in virus infections



Teacher:● Institute of Virology and Cell Biology

● Prof. Dr. rer. nat Stefan Taube


Notes:

* graded talk* min. 4 students/ seminar

20



Module Guide

LS4175B - Medical Microbiology B: Mechanisms of Bacterial Pathogenicity (MedMicroBa)




Classes and lectures: Workload:● B Mechanisms of Bacterial Pathogenicity (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Historical background: Milestones in the discovery of the factors involved in microbial virulence● Invasiveness, toxigenesis, colonization, specific adherence● Structure of bacterial cell membrane, cell wall and cell surface: Gram-positive and Gram-negative bacteria, mycobacteria, virulence

factors● Structure and biosynthesis of lipopolysacharides● Structure and biosynthesis of lipoarabinomannan● Structure, biosynthesis and functions of mycobacterial lipids● Recognition of microbial virulence factors by pattern recognition receptors● Recognition of lipids by immune cells, the role of CD1 presentation● Microbial toxins (e.g., leucocidin, hemolysin, botulinum toxin, diphtheria toxin, anthrax toxin, tetanus toxin, pertussis toxin, cholera

enterotoxin, adenylate cyclase, Staphylococcus aureus enterotoxin, TSST, superantigen, shiga toxin, Escherichia coli LT toxin, ST toxin)

Qualification-goals/Competencies:● Detailed knowledge of the structures and biosynthetic pathways of microbial constituents responsible for microbial virulence.● Understanding of the virulence mechanisms of pathogenic microorganisms.




● Prof. Dr. rer. nat. Otto Holst● Priv.-Doz. Dr. rer. nat. Sven Müller-Loennies

Literature:● Actual textbooks, original and review articles:


Notes:


21



Module Guide

LS4175C - Medical Microbiology C: Pathogen Niches (MedMicroNi)




Classes and lectures: Workload:● C Pathogen Niches (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Intracellular vs. extracellular pathogens and their nichesBlood vs. tissue, extracellular matrix● Metabolic adaptations of pathogenic microbes and competition with host● Immunopriviledged tissue/organ sitesNiches for immune escape of pathogens● The physiology and cell biology of intracellular microbes● Erythrocytes as host cellsPhagocytes and non-phagocytes as host cells● Microbial biofilms and consortiaNiches formed by immunity and toxins

Qualification-goals/Competencies:● Students should gain knowledge on the niches pathogens occupy in the host and how they influence immunity and therapy.● They should learned and understand the mechanisms how the pathogens can (ab)use thses niches.● They should understand the physiological benefits for the pathogens.


Requires:● Biology of Infections (LS4120)


Teacher:● Research Center Borstel● Berhard Nocht Institute, Hamburg

● Dr. rer. nat. Bianca Schneider● Dr.rer.nat. Monica Hagedorn

Literature:● Ulrich E. Schaible, Albert Haas: Intracellular Niches of Microbes: A Pathogens Guide Through the Host Cell - Wiley-VCH 2009● Pascale Cossart, Patrice Boquet, Staffan Normark: Cellular Microbiology - Asm Pr


Notes:


22




Module Guide

LS4175D - Medical Microbiology D: Inflammation: Methods in Immunology (MedMicroIn)




Classes and lectures: Workload:● D Methods in Immunology (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Phage display● Flow Cytometry (FACS, MACS, FACS-sort)● Recombinant antibodies● Experimental and therapeutic● Biologica● Conventional and confocal Microscopy● 2-Photon-Microscopy● Signaltransduction analysis● Migration Assays● Generation of transgenic mice● Generation of knock-out mice● Generation of knock-in mice● SNPs Analysis● Microbiome Analysis● Animal models in Life Science

Qualification-goals/Competencies:● Competence in methods and their applications in immunology.



Teacher:● Department of Dermatology, Allergology and Venerology● Institute of Anatomy● Institute for Systemic Inflammation Research (ISEF)

● Prof. Dr. rer. nat. Marc Ehlers● Prof. Dr. med. Jörg Köhl● Prof. Dr. rer. nat. Rudolf Manz● PD Dr. med. Peter König● Dr.rer.nat. Christian Karsten● Prof. Dr. med. Saleh Ibrahim● Dr.rer.nat. Yves Laumonnier


Notes:


23





Module Guide

24


Module Guide

LS4185 - Host-Pathogen Interaction (HostPatInt)




Classes and lectures: Workload:● A Principles and Analysis of Host-Pathogen Interaction

(Lecture, 2 SWS)● A Principles and Analysis of Host-Pathogen (practical course, 1

SWS)● B Rational Drug Design (Lecture, 3 SWS)


Contents of teaching:● See LS4185 module parts A or B

Qualification-goals/Competencies:● More details see LS4185 module parts A or B


Responsible for this module:● PD Dr. med. Peter König

Teacher:● Ernst-Moritz-Arndt-University of Greifswald● Berhard Nocht Institute, Hamburg ● Research Center Borstel● Institute of Biochemistry● Institute of Chemistry● Institute of Anatomy


Notes:

Choice of one course of LS4185A or B

* more details see LS4185A or B

25


http://www.medizin.uni-greifswald.de/funkgenom/index.html




http://www.chemie.uni-luebeck.de/


Module Guide

LS4185A - Host-Pathogen Interaction A: Principles and Analysis of Host Pathogen Interaction (PrinHPI)




Classes and lectures: Workload:● Principles and Analysis of Host-Pathogen Interaction (Lecture, 2

SWS)● Principles and Analysis of Host-Pathogen Interaction (practical

course, 1 SWS)


Contents of teaching:● Host-pathogen interaction using different examples● Importance of commensal colonization for infection● Methods for the analysis of host-pathogen interaction with focus on imaging and omics methods to analyze genes, proteins and lipids

Qualification-goals/Competencies:● Understanding of different ways how host and pathogen can interact and its impact on disease● Knowledge of in vivo and in vitro methods to analyze pathogen-host interaction● Insight into experimental design and data analysis of imaging and omics experiments

Grading through:● Presentation● Protocols

Responsible for this module:● PD Dr. med. Peter König

Teacher:● Institute of Anatomy● Research Center Borstel● Ernst-Moritz-Arndt-University of Greifswald● Berhard Nocht Institute, Hamburg

● PD Dr. med. Peter König● Prof. Dr. Ulrich Schaible● Dr. Frank Schmidt● Dr.rer.nat. Monica Hagedorn● PD. Dr. rer. nat. Stefan Niemann● Prof. Dr. rer. nat. Dominik Schwudke● Dr. Silke Feuerriegel ● Dr. Susanne Homolka


26




http://www.medizin.uni-greifswald.de/funkgenom/index.html


Module Guide

LS4185B - Host-Pathogen Interaction B: Rational Drug Design (RatDruDes)




Classes and lectures: Workload:● B Rational Drug Design (Lecture, 3 SWS) ● 60 Hours Private studies


Contents of teaching:● Drug development � an overview● Target identification and validation● Role of x-ray crystallography in drug development● Structure-based drug design � Principles and methods● Case studies of structure-based drug development● Combinatorial approach for nucleic acid therapeutics identification● Oligomeric nucleic acid therapeutics● Cellular applications of nucleic acid therapeutics via non-viral carrier systems

Qualification-goals/Competencies:● Basic strategies of drug design● The path from the discovery of an active principle to a marketable product. Rational drug design● NMR and crystallography as fundamental tools for finding and optimizing active agents● Structure and effect relationships will be demonstrated using examples, techniques used for theoretical prediction and experimental

proof will be introduced, especially the complementary approach using crystallographic methods and NMR experiments● Students will critically evaluate these methods and perceive their limits


Responsible for this module:● Prof. Dr. rer. nat. Thomas Peters

Teacher:● Institute of Biochemistry● Institute of Chemistry

● Prof. Dr. rer. nat. Thomas Peters● Prof. Dr. rer. nat. Rolf Hilgenfeld● Dr. rer. nat. Alessandra Mescalchin● Prof. Dr. rer. nat. Tobias Restle● PD Dr. phil. nat. Thomas Weimar● Dr. phil. nat. Hannelore Peters


27




Module Guide

LS5995 - Master Thesis Infection Biology (MScThesis)


1 Semester Each semester 30

Course of study, specific field and term:● Master Infection Biology (compulsory), Life Sciences, 3. and 4. term

Classes and lectures: Workload:● Practical work (practical course, 2,4 SWS)● Authoring of the Master Thesis (Self-dependent practical

research , 0,6 SWS)


Contents of teaching:● Scientific project in the field of infection biology

Qualification-goals/Competencies:● Competence and ability to solve a preformulated more complex scientific problem in a defined period of time and to document with

respect to good scientific practice and present and critically defend the experimental results.

Grading through:● Written examination, oral presentation and defence of the experiment´s results

Responsible for this module:● Alle prüfungsberechtigten DozentInnen des Studienganges

Teacher:●

● Alle prüfungsberechtigten DozentInnen des Studienganges● Prüfungsausschussvorsitzender


Notes:

Prerequisites: Minimum of 77 ECTS.If the Master thesis is done externally (outside our university) the student has to choose a licensed lecturer (see PO) of our university as asecond instructor who will be First Examiner in the examination.

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Module Guide

CS4011 - Bioinformatics, Modelling, Biostatistics (BioModEpi)



Course of study, specific field and term:● Master Infection Biology (compulsory), Biology & IT, 1. Term

Classes and lectures: Workload:● Lectures Module Part A: Introduction to Bioinformatics

(Lecture, 2 SWS)● Excercises Module Part A: Introduction to Bioinformatics

(Exercise, 1 SWS)● Lectures Module Part B: Modelling of Biological Systems

(Lecture, 2 SWS)● Excercises Module Part B: Modelling of Biological Systems

(Exercise, 2 SWS)● Lectures Module Part C: Genetic Epidemiology (Lecture, 1 SWS)● Excercises Module Part C: Genetic Epidemiology (Exercise, 1

SWS)● Chatroom Module Part C: Genetic Epidemiology (E-Learning, 1

SWS)● Lectures Module Part D: Microarray Data analysis (Lecture, 2

SWS)● Excercises Module Part D: Microarray Data analysis (Seminar, 1

SWS)


Contents of teaching:● See possible module parts CS4011A-D

Qualification-goals/Competencies:● See possible module parts CS4011A-D

Grading through:● Exercises● Test or Viva voce, made available by the lecturer

Responsible for this module:● Prof. Dr. rer. nat. Thomas Martinetz

Teacher:● Research Center Borstel● Institute of Medical Biometry and Statistics● Institute for Mathematics● Institute for Neuro- and Bioinformatics

● Prof. Dr. rer. nat. Thomas Martinetz● Prof. Dr. Karsten Keller● Prof. Dr. rer. nat. Andreas Ziegler● Prof. Dr. rer. biol. hum. Inke R. König● Dr. rer. nat. Kurt Fellenberg

Language:●

Notes:

You must choose exactly one (1 out of four) of the module parts.

29


http://www.inb.uni-luebeck.de/index.php?id=107


http://www.imbs-luebeck.de/imbs/de

http://www.math.uni-luebeck.de/

http://www.inb.uni-luebeck.de/


Module Guide

CS4011A - Bioinformatics, Modeling, Biostatistics A: Introduction to bioinformatics (Bioinfo)



Course of study, specific field and term:● Master Infection Biology (Optional Subject), Biology & IT, 1. Term

Classes and lectures: Workload:● Introduction to bioinformatics (Lecture, 2 SWS)● Introduction to bioinformatics (Exercise, 1 SWS)

● 55 Hours Private studies● 45 Hours Presence studies● 20 Hours Test preparation

Contents of teaching:● Life, genes & gene evolution● Structure of the human DNA● Sequence assembly - Industrial reading of genetic information● DNA sequence models & hidden markov models● Sequence alignment & dynamic programming● DNA microarrays & GeneChip technologies● Introduction into systems biology● The human brain● Neural networks / multilayer perzeptrons● Supervised & unsupervised learning

Qualification-goals/Competencies:● Basic understanding of DNA and the coding of genetic information● Principles of probabilistic modeling● Application of basic algorithms for the analysis of genetic sequences● Basic techniques and methods for the processing of genetic information● Introduction to bioinformatic databases● Basic understanding of Microarrays and GeneChip-Technologies● Understanding the challenges of systems biology● Principles of information processing in nervous systems● Building a bridge between machine and biological (Hebbian) learning


Responsible for this module:● Prof. Dr. rer. nat. Amir Madany Mamlouk● Prof. Dr. rer. nat. Thomas Martinetz

Teacher:● Institute for Neuro- and Bioinformatics

● Prof. Dr. rer. nat. Amir Madany Mamlouk

Literature:● H. Lodish, A. Berk, S. L. Zipursky and J. Darnell: Molekulare Zellbiologie - Spektrum Akademischer Verlag, 4. Auflage, 2001, ISBN-13:

978-3827410771● A. M. Lesk: Introduction to Bioinformatics - Oxford University Press, 3. Auflage, 2008, ISBN-13: 978-0199208043● R. Merkl and S. Waack: Bioinformatik Interaktiv: Grundlagen, Algorithmen, Anwendungen - Wiley-VCH Verlag, 2. Auflage, 2009, ISBN-13:

978-3527325948● M. S. Waterman: Introduction to Computational Biology - Chapman and Hall, 1995● S. Haykin: Neural Networks - London: Prentice Hall, 1999● H. Ritter, T. Martinetz, K. Schulten: Neuronale Netze: Eine Einführung in die Neuroinformatik selbstorganisierender Netzwerke - Bonn:

Addison Wesley, 1991

30



http://www.inb.uni-luebeck.de/

Module Guide

Language:● Offered only in German

Notes:

also named: CS1400 Einführung in die Bioinformatik

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Module Guide

CS4011B - Bioinformatics, Modeling, Biostatistics B: Modeling Biological Systems (ModBioS)




Classes and lectures: Workload:● Modeling Biological Systems (Lecture, 2 SWS)● Modeling Biological Systems (Exercise, 1 SWS)

● 65 Hours Self studies and exercises● 45 Hours Presence studies● 10 Hours Test preparation

Contents of teaching:● Elementary time-discrete deterministic models● Structured time-discrete population dynamics● Generating functions, Galton-Watson-processes● Markov chains with applications● Modeling of data and data analysis

Qualification-goals/Competencies:● Knowledge of elementary time-discrete models for modeling biological processes● Development of skills in connecting ideas from different fields of mathematics● Competencies in data analysis and modelling● Interdisciplinary competencies


Responsible for this module:● Prof. Dr. Karsten Keller

Teacher:● Institute for Mathematics

● Prof. Dr. Karsten Keller

Literature:● F. Braer, C. Castillo-Chavez: Mathematical Models in Population Biology and Epidemiology - New York: Springer 2000● H. Caswell: Matrix Population Modells - Sunderland: Sinauer Associates 2001● S. N. Elaydi: An Introduction to Difference Equations - New York: Springer 1999● B. Huppert: Angewandte Lineare Algebra - Berlin: de Gruyter 1990● U. Krengel: Einführung in die Wahrscheinlichkeitstheorie und Statistik - Wiesbaden: Vieweg 2002● E. Seneta: Non-negative Matrices and Markov Chains - New York: Springer 1981

Language:● Offered only in German

Notes:

also named: MA4450 - Modeling Biological Systems (MoBS)

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http://www.math.uni-luebeck.de/

Module Guide

CS4011C - Bioinformatics, Modeling, Biostatistics C: Genetic Epidemiology (GenEpi)


1 Semester Every second year 4


Classes and lectures: Workload:● Genetic Epidemiology (Lecture, 2 SWS)● Genetic Epidemiology (Exercise, 1 SWS)


Contents of teaching:● Fundamentals in molecular genetics: Genetic information, transmission and variation of genetic information, genotyping methods● Fundamentals in formal genetics: Mendelian laws, segregation patterns, Hardy-Weinberg-equilibrium● Genetic markers● Data quality: Errors in the data, methods of error detection● Association studies: Study designs, tests, estimates, linkage disequilibrium, bias in the data● Haplotype-based association: Estimation of haplotypes, tests, haplotype blocks● Genome-wide association: Study designs, study conduct, specific problems● Family-based association: Transmission-disequilibrium and other tests, estimates, sample size estimation

Qualification-goals/Competencies:● FK: Understand the generation of genetic data, its error sources and methods to detect errors● FK: Master the most important approaches for genetic epidemiological association studies on the level of single markers and

haplotypes● FK: Apply basic test procedures manually and more complex test procedures using the computer● SK: Be competent for large-scale tasks that need to be solved cost- and time-efficiently. Organize the own work and collaborators

involved in the project● SK: With limited resources (time, personnel etc.) develop solutions that comply with general quality criteria and are accepted by all

project partners● SK: Present ideas and solutions in written and oral form, identify discrepant positions from others and integrate them in an appropriate

solution


Responsible for this module:● Prof. Dr. rer. biol. hum. Inke R. König

Teacher:● Institute of Medical Biometry and Statistics

● Prof. Dr. rer. biol. hum. Inke R. König● MitarbeiterInnen des Instituts

Literature:● Ziegler A, König IR.: A statistical approach to genetic epidemiology. Concepts and applications. - 2010. ISBN: 978-3-527-32389-0


Notes:

also named: MA3200 - Genetic Epidemiology 1

33


http://www.imbs-luebeck.de/imbs/de

Module Guide

CS4011D - Bioinformatics, Modeling, Biostatistics D: Microarray Data analysis (MicroData)


1 Semester Every second year 4


Classes and lectures: Workload:● Microarray Data analysis (Lecture, 2 SWS)● Microarray Data analysis (Exercise, 1 SWS)


Contents of teaching:● Motivation of high-troughput data acquiry in context of systems biology● Regulatory levels, according molecules to quantify and available platforms● Past, present and future of microarray platforms● Workflow in the laboratory● Imaging (systematic errors dealt with here)● Normalization algorithms (systematic errors adjusted)● QC of normalization● Planar projection (ordination) methods● Clustering methods● Picking a distance metric● Gene and experiment annotations● Sytematically partitioning the total variance

Qualification-goals/Competencies:● Overview over most widely used microarray platforms ..● .. and their (typical) systematic errors - Avoiding pitfalls in projecting microarray studies (experimental design)● Basic understanding of selected preprocessing methods (when to apply which)● Principles of machine learning● Basic understanding and application of selected unsupervised learning methods● Assessing (also scoring) results● Introduction into the interpretation of very large datasets

Grading through:● Exercises and project tasks● Test or Viva voce, made available by the lecturer

Responsible for this module:● Prof. Dr. rer. nat. Thomas Martinetz


● Dr. rer. nat. Kurt Fellenberg


34




Module Guide

LS4020-IB - Structural Biology of Infection (StrucBiol)



Course of study, specific field and term:● Master Infection Biology (compulsory), Structure biology, 1. Term

Classes and lectures: Workload:● A Protein Structure/Crystallography (Lecture, 2 SWS)● B NMR Spectroscopy (Lecture, 2 SWS)● C Protein Biophysics/Single Molecule Methods (Lecture, 2 SWS)● D Microscopy, Methods and Application (Lecture, 2 SWS)● E Membrane Biophyics (Lecture, 2 SWS)● F Protein-Biophysics (Lecture, 2 SWS)


Contents of teaching:● See Modul parts LS4020-IB A - F

Qualification-goals/Competencies:● See Modul parts LS4020-IB A - F


Responsible for this module:● Prof. Dr. rer. nat. Christian Hübner

Teacher:● Institute for Biology● Research Center Borstel● Institute of Physics● Institute of Biochemistry● Institute of Chemistry

● Prof. Dr. rer. nat. Thomas Peters● Prof. Dr. rer. nat. Rolf Hilgenfeld● Prof. Dr. rer. nat. Christian Hübner● Prof. Dr. rer. nat. Thomas Gutsmann● PD Dr. rer. nat. Andra Schromm● Prof. Dr. rer nat. Rainer Duden● PD Dr. rer. nat. Hauke Paulsen


Notes:

Choice of two courses LS 4020 IB A-F

If more than two of the required exams passed, the two best grades are taken into account. The additional program achievement willbe added non-graded in the transcript of records.

35


http://www.bioweb.uni-luebeck.de/


http://www.physik.uni-luebeck.de/



Module Guide

LS4020-IB A - Structural Biology of Infection A: Proteinstructure / Crystallography (ProStrCry)



Course of study, specific field and term:● Master Infection Biology (Optional Subject), Structure biology, 1. Term

Classes and lectures: Workload:● Crystallography (Lecture, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Crystal growth, precipitant and phase diagram, crystal morphology, symmetry and space groups, crystallogenesis● X-rays, X-ray sources, X-ray diffraction, Bragg's law, reciprocal lattice and Ewald-sphere construction● X-ray diffraction by electrons, Fourier analysis and synthesis● Protein structure determination by X-ray diffraction, crystallographic phase problem, Patterson map, molecular replacement (MR),

multiple isomorphous replacement (MIR), multi-wavelength anomalous diffraction (MAD)● Crystallography and the drug discovery process: studying protein-ligand interactions● Practical exercises at the X-ray generator and at the computer● Site visit at the Synchrotron DESY (Hamburg)

Qualification-goals/Competencies:● Understanding and application of fundamental techniques and methodologies in macromolecular crystallography for unraveling

infection biology relevant subjects● Expand basic knowledge in general structural biology● Understand and perform calculation, display and correct interpretation of macromolecules (PDB files) and electron density maps● Appreciate and apply X-ray crystallography as a central tool in the modern structure based drug design process● To advance the general scientific awareness for challenges concerning structure and infection biology



Teacher:● Institute of Biochemistry

● Prof. Dr. rer. nat. Rolf Hilgenfeld● Dr. math. et dis. nat. Jeroen Mesters

Literature:● Jan Drenth: Principles of Protein X-ray Crystallography - Science+Business Media, LLC, New York


Notes:


36



Module Guide

LS4020-IB B - Structural Biology of Infection B: NMR-Spectroscopy (NMRSpr)




Classes and lectures: Workload:● NMR-Spectroscopy (Lecture, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Interpretation and assigment of NMR spectra using amino acids as examples● Description of NOESY experiments using the vector model● Parameters important for NOESY experiment● Analysis and interpretation of NOESY experiments● Transfer-NOEs● Assigning NMR spectra to enzyme substrates● Identification of spin systems using the example fo amino acids● Introduction into product operator formalism by using the example fo COSY experiment● Assigning of a natural product● Exercises in POF● Determination of the bioactive conformation of an enzyme substrate● Description of HSQC experimentssuing POF● Prediction of a NMR spectrum from the chemical structure● Analysis of NMR spectra of a compound● Description of HSQC experiments using POF (II)● Quantification using NMR● Analysing "molecular movement" through relaxation experiments● Identification of natural products using NMR, mass spectrometry and analytical procedures● Analysis of "molecular movements" through relaxation experimnets (II)● Identification of natural products using NMR, mass spectrometry and analytical procedures (II)● Applied aspects of NMR in basic research

Qualification-goals/Competencies:● Practical aspects:Detailed knowledge on NMR spectra interpretation● Competence in determination of the bioactive conformation of an enzyme substrate● Theoretical knowledge:Product operator formalism (POF) for description of pulse sequences● Application of POF for simple NMR experiments (COSY, HSQC)● Competence in analysing the dynamics of biological macromolecules through ralaxation experiments

Grading through:● Test


Teacher:● Institute of Chemistry

● Prof. Dr. rer. nat. Thomas Peters● PD Dr. phil. nat. Thomas Weimar● Prof. Dr. rer. nat. Karsten Seeger

Literature:● James Keeler: Understanding NMR Spectroscopy - Wiley● Horst Friebolin: Ein- und zweidimensionale NMR-Spektroskopie. Eine Einführung - Wiley-VCH● M. H. Levitt: Spin Dynamics - Basics of Nuclear Magnetic Resonance - Wiley-VCH

37



Module Guide

● D. Neuhaus & M. P. Williamson: The Nuclear Overhauser Effect in Structural and Conformational Analysis - Wiley-VCH


Notes:


38


Module Guide

LS4020-IB C - Structural Biology of Infection C: Single Molecule Methods (StrukAnaSM)




Classes and lectures: Workload:● Protein Biophysics / Single molecule methods (Lecture, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Physical basics of fluorescence● Photo physics● Microscopical techniques for single molecule fluorescence● Protein labeling and immobilization● Fluorescence resonance energy transfer (FRET)● Enzymatic activity with single molecules● Protein folding with single molecules● Physical basics of optical tweezers● Protein folding with optical tweezers

Qualification-goals/Competencies:● Understanding of physical principles of fluorescence● Knowledge in photo physics and photo chemistry● Competence in deciding whether or not to use single molecule methods● Competence in choosing appropriate labeling techniques and equipment● Competence in data analysis● Competence in interpreting single molecule fluorescence data



Teacher:● Institute of Physics

● Prof. Dr. rer. nat. Christian Hübner● PD Dr. rer. nat. Hauke Paulsen

Literature:● Lakowicz, Joseph R :: Principles of Fluorescence Spectroscopy - ISBN 978-0-387-46312-4● Markus Sauer, Johan Hofkens, Jörg Enderlein: Handbook of Fluorescence Spectroscopy and Imaging: From Ensemble to Single

Molecules - ISBN: 978-3-527-31669-4


Notes:


39



Module Guide

LS4020-IB D - Structural Biology of Infection D: Microscopy, Methods and Applications (StrBioMikr)




Classes and lectures: Workload:● Microscopy, Methods and Applications (Lecture, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Light microscopy● Confocal microscopy● 2-photonen microscopy● Light sources and detectors● Fluorescent Dyes; GFP and genetically encoded fluorescence markers; Live Cell/tissue imaging: considerations/limitations● Labelling/identifying cell components using fluorescence techniques● Protein-protein Interactions in living cells: FRET, FLIM; Biosensors● Photo-activatable/-switchable Fluorescent Proteins; Fluorescent Timers● Advanced 3D-Fluoresence Microscopy, STED, PALM, STORM● In vivo imaging in tissues and living animals● Applications of Flow Cytometry & Fluorescence-activated Cell Sorting● Electron Microscopy: TEM, Immunogold label; Survey of cell ultrastructure; Correlative EM/light microscopy; Scanning Electron

Microscopy (SEM)● Bioluminescence; high-content screening; outlook: emerging technologies● Data storage/formats; Course discussion; and then: �Cinema of the Cell�

Qualification-goals/Competencies:● Basics of light and fluorescence microscopy and electron microscopy● Detailed knowledge of methods for labelling and visualization of proteins and subcellular compartments● Applications of live cell imaging, in vivo imaging and quantitative fluorescence techniques● Understanding how to employ imaging approaches for infection biology studies



Teacher:● Institute of Biomedical Optics● Institute for Biology

● Prof. Dr. rer nat. Rainer Duden● Prof. Dr. rer. nat. Alfred Vogel● PD Dr. rer. nat. Gereon Hüttmann

Literature:● : http://micro.magnet.fsu.edu/primer/index.html● : http://www.microscopyu.com/smallworld/● : http://www.olympusmicro.com/


Notes:


40


http://www.bmo.uni-luebeck.de


Module Guide

41


Module Guide

LS4020-IB E - Structural Biology of Infection E: Basic Membrane Biophysics (MemBiophy)




Classes and lectures: Workload:● Basics of Membrane Biophysics (Lecture, 2 SWS) ● 45 Hours Private studies


Contents of teaching:● Importance and function of cell membranes: structure, physical function and dynamic models● Basics of the membrane components● Thermodynamic self-assembling of lipids and reconstitution techniques● Transmembrane and intrinsic membrane potentials● Mechanical properties of lipid membranes● Physical basics of membrane transport mechanisms● Investigations using lipid monolayer● Electrical and optical experiments using planar lipid bilayers● Examples for interaction mechanisms between peptides/ proteins and planar membranes● Spectroscopic methods on membranes and membrane proteins● Light and force microscopy on membranes and membrane proteins

Qualification-goals/Competencies:● Knowing the constituents and composition of biological membranes● Understanding the physical role and function of membrane lipids and proteins● Knowing the mechanical and electrical properties of membranes● Competence in various methods to investigate reconstituted and natural membranes




● Prof. Dr. rer. nat. Thomas Gutsmann● PD Dr. rer. nat. Andra Schromm

Literature:● Adam, P. Läuger, G. Stark: Physikalische Chemie und Biophysik - Springer-Verlag, 4. Auflage 2003● W. Hanke, R. Hanke: Methoden der Membranphysiologie - Spektrum Akademischer Verlag, Auflage 1997● O.G. Mouritzen: Life - As a Matter of Fat - Springer ISBN: 987-3-540-23248-3


Notes:


42



Module Guide

LS4020-IB F - Structural Biology of Infection F: Protein-Biophysics (ProBioPhy2)




Classes and lectures: Workload:● Part of the module B: Physics of Proteins (Lecture, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Protein structure● Energy landscapes● Thermodynamics of protein folding● Kinetics of protein folding● Thermodynamics of enzymatic reactions● Kinetics of enzymatic reactions

Qualification-goals/Competencies:● Understanding of physical principles of:● protein folding● protein dynamics● protein interactions




● Prof. Dr. rer. nat. Christian Hübner● PD Dr. rer. nat. Hauke Paulsen

Literature:● Hans Frauenfelder, Shirley Chan und Winnie Chan: Physics of Proteins: An Introduction to Molecular Biophysics (Biological and Medical

Physics, Biomedical Engineering) - von Springer, Berlin (Gebundene Ausgabe - 30. Dezember 2010)● Alan Fersht: Structure & Mechanism in Protein Science: Guide to Enzyme Catalysis and Protein Folding - W H Freeman & Co

(Gebundene Ausgabe - 15. Februar 1999)


Notes:


43



Module Guide

LS5200-IB1 - Consolidating in IB: Part of the module IB1 Tuberculosis (Tuberculos)

Duration: Turnus of offer: Credit points: Max. group size:

1 Semester Each winter semester 3 4

Course of study, specific field and term:● Master Infection Biology (Consolidating), Consolidation in IB, 3. Term

Classes and lectures: Workload:● Tuberculosis (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Disease aspects● Diagnosis● Genetics● Immunology and Zellbiology● Epidemiology

Qualification-goals/Competencies:● To understand in more detail the clinical and microbiological aspects of this important human infectious disease● to get an insight how to work practically with it in the lab using surrogate non-Safety Level 3 mycobacteria● to gain an up to date on TB research● to become aware of the important questions to be solved in TB research● to get the capacity to phrase strategies to tackle these questions experimentally

Grading through:● Presentation

Responsible for this module:● Prof. Dr. rer. nat. Norbert Tautz


● Prof. Dr. Ulrich Schaible● MitarbeiterInnen des Instituts ● Dr. rer. nat. Bianca Schneider


Notes:

Requirements: All modules of the 1st and 2nd semesters MSc Infection Biology must be passed.

44



Module Guide

LS5200-IB2 - Consolidating in IB: Part of the module IB2 Virus Host Interaction (VirHostIn)




Classes and lectures: Workload:● Virus Host Interaction (Seminar / practical course / exercise, 2

SWS)● 60 Hours Private studies● 30 Hours Presence studies

Contents of teaching:● Concepts of virus entry and differences in enveloped and non-enveloped viruses● The role of viral entry receptors on susceptibility, trafficking, and tropism.● Advanced molecular and virological methods● Critical reading and discussion of scientific primary literature● Presentation of scientific results

Qualification-goals/Competencies:● Virus-host interaction. How do viruses enter a susceptible host cell.● Introduction to viral entry, attachment versus entry receptors.● The role of glycans in viral host entry● Virus capsid, generation and analysis of virus-like particles and receptor-binding domains● Techniques: molecular techniques, protein expression, detection, and purification

Grading through:● Presentation● Regular and successful participation in practical course● Protocols



● Prof. Dr. rer. nat Stefan Taube● MitarbeiterInnen des Instituts


Notes:


45



Module Guide

LS5200-IB3 - Consolidating in IB: Part of the module IB3 Critical Appraisal of scientific papers (CritApp)




Classes and lectures: Workload:● Critical Appraisal of scientific papers (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● The course gives an introduction into evidence based medicine and critical appraisal. It will include two lectures (What is evidence

based medicine and why do we need it? What is critical appraisal and why do we need it?), three �refresher units� (diagnostic studies,prognostic studies, therapeutic studies), and seminars in which students will appraise scientific papers.

Qualification-goals/Competencies:● Understanding the rationale for evidence-based medicine● Understanding the rationale for and the principles of critical appraisal● Understanding the importance of assessing the reporting quality of a study and the quality of the study design● Practical experience in reading and critically appraising scientific papers



Teacher:● Institute for Social Medicine and Epidemiology

● Dr. rer. nat. Annika Waldmann● Dr. med. Maria Noftz


Notes:


46


http://www.sozmed.uni-luebeck.de/

Module Guide

LS5200-IB4 - Consolidating in IB: Part of the module IB4 Project Management (ProjectM)




Classes and lectures: Workload:● Project Management (Seminar / practical course / exercise, 2


Contents of teaching:● This introduction course gives an overall view on project management, which is the application of knowledge, skills and techniques to

execute projects effectively and efficiently. Project management is a strategic competency for individuals and organisations alike,enabling them to relate project results to business goals and thus improve their performance in their markets.

● 1.Introduction to Project Management2.Project Management as a Business Process3.Starting and Planning Projects4.Cross CulturalCollaboration5.Risk Management6.Quality Management7.Implementing and Controlling Projects8.Leading Projects9.CompletingProjects

● Different areas of knowledge and process groups will be covered over the course of the project life cycle. Various lectures andteam-oriented practices will lead to students familiarising themselves with the terminology, the tools and the techniques used inproject management.

Qualification-goals/Competencies:● Students can single-handedly apply knowledge, skills and techniques in order to execute projects (such as master and PhD theses,

among others) effectively and efficiently. They will also gain a thorough understanding of relevant differences between different levelsof project management, the importance of cultural dimensions and success factors to be considered in projects, methods of dealingand coping with certain peculiarities in projects as well as a guide to conduct projects. Students will further be able to do project andteam work, lead projects and argue with regards to their project solutions in a constructive manner.



Teacher:● University of Applied Sciences

● Prof. Dr. Leef Dierks


Notes:


47


http://www.fh-luebeck.de

Module Guide

LS5200-SB IB - Consolidating in IB: Part of the module SB Biochemistry of the bacterial envelope (BacEnv)




Classes and lectures: Workload:● Biochemistry of the bacterial envelope (Lecture with exercises

or seminar, 2 SWS)● 60 Hours Private studies● 30 Hours Presence studies

Contents of teaching:● Part 1: Glycolipids, lipoproteins, membrane components: Introduction● Structure, occurrence and properties● Synthesis, biosynthesis and decomposition● Structural analysis of lipids and lipoconjugates● Application and impact of lipoconjugates in bio-medicine: function● Lipoconjugates in Immunology● Pathobiochemistry of lipids (functional disorders)● Signal transduction in membranes● Part 2 Oligo- and polysaccharides and glycoproteins:Introduction● Structure, occurrence and properties● Synthesis, biosynthesis and decomposition● Structural analysis of polysaccharides and glycoproteins● Function: Impact and application of polysaccharides and glycoproteins● Pathobiochemistry

Qualification-goals/Competencies:● Understanding the structure-function ratio of biologically and biomedically important molecules● Understanding problems of modern bioinformatics● Knowledge of structures of molecules

Grading through:● Presentation● Test or Viva voce, made available by the lecturer● Test



● Prof. Dr. rer. nat. Ulrich Zähringer● Prof. Dr. rer. nat. Otto Holst

Literature:● F. Lottspeich und H. Zorbas (Hrsg.).: Bioanalytik - Spektrum, Akademischer Verlag, Heidelberg, Berlin, 1. Auflage 1998● Lehmann, Jochen: Kohlenhydrate: Chemie und Biologie - Wiley-VCH, 1996, ISBN 3-527-30859-8


Notes:


48



Module Guide

LS5200-SC IB - Consolidating in IB: Part of the module SC Structure-based design and synthesis of an antiviral

compound (antiviralc)




Classes and lectures: Workload:● Structure-based design and synthesis of an antiviral compound

(Seminar, 2 SWS)● 60 Hours Private studies● 30 Hours Presence studies

Contents of teaching:● Experiment 1: Recombinant production of 3C-protease (3Cpro) of Coxsackievirus B3 in E. coli, purification of protein, activity assays● Experiment 2: Crystallization of 3Cpro. Conditions are chosen allowing for crystal growth in only few hours● Experiment 3: Collection of diffraction data of these crystals or, in case of not sufficient quality, of primed crystals● Experiment 4: Interpretation of electron densitiy and modelling of an inhibitor● Experiment 5: Practical performance of two steps of the synthesis of an inhibitor, determination of the identity of the product via ESI

mass spectrometry and NMR spectroscopy● Experiment 6: Determination of kinetic parameters using FRET: IC50 and kkat/KM● Experiment 7: Working with replicons, transfection, determination of EC50 - values

Qualification-goals/Competencies:● This practical course offers an interdisciplinary insight in design and chemical synthesis of antiviral compounds. All practical work is

performed by the students themselves. The course is based on the knowledge of the following courses: virology, biochemistry,structure analysis/crystallography, rational drug design, organic chemistry, biological chemistry

Grading through:● Protocols



● Prof. Dr. rer. nat. Rolf Hilgenfeld● MitarbeiterInnen des Instituts


Notes:


49



Module Guide

LS5200-SE IB - Consolidating in IB: Part of the Module SE Molecule Dynamics (MolDynam)




Classes and lectures: Workload:● Molecule Dynamics (Lecture, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Energy minimization and discrete Newtonian dynamics (Verlet algorithm)● Force fields: stretching, bending, torsion, fields of application (proteins, DNA, universal)● Coulomb and van der Waals interactions (cutoffs, Ewald summation)● Influence of temperature and pressure: thermostats and barostats● Hybrid methods: classical force fields combined with quantum mechanical treatment● Examples using gromacs (www.gromacs.org)

Qualification-goals/Competencies:● Fundamentals of molecule dynamics● Applications of molecule dynamics to biomolecules

Grading through:● Test● Recitation



● PD Dr. rer. nat. Hauke Paulsen

Literature:● A. Leach: Molecular modelling


Notes:

Requirements: All modules of the 1st and 2nd semester must be passed

50



Module Guide

LS5200-SG IB - Consolidating in IB: Part of the module SG Structural Aspects of Protein biosynthesis

(ProtBSynth)




Classes and lectures: Workload:● Structural Aspects of Protein biosynthesis (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Seminar series● Analysis of the most recent and relevant scientific publications and presentation thereof followed by a discussion

Qualification-goals/Competencies:● Expanding basic knowledge of the protein-biosynthesis process● Expanding basic knowledge in structural biology● Handling of scientific literature● Presentation of scientific results● To rank and discuss scientific results● Apply acquired knowledge from other fields to structural biology

Grading through:● Presentation in English● Participation on discussions



● Dr. math. et dis. nat. Jeroen Mesters

Literature:● Anders Liljas: Structural Aspects of Protein Synthesis - World Scientific Publishing, London Singapore, ISBN 981-238-867-2● : Aktuelle Forschungs- und Übersichtsartikel


Notes:


51



Module Guide

LS5200-SI IB - Consolidating in IB: Part of the module SI Characterization of Protein Complexes in Structural

Biology (ProtCompl)




Classes and lectures: Workload:● Characterization of Protein Complexes in Structural Biology

(Seminar and practical course, 2 SWS)● 60 Hours Private studies● 30 Hours Presence studies

Contents of teaching:● Protein complex formation as the basis of all biochemical cascade● Basic techniques to study protein complexes. Theories to be covered: Fluorescence Resonance Transfer (FRET)/ Isothermal Calorimetry

(ITC)/ Surface Plasmon Resonance (SPR)/ Circular Dichroism (CD)● Experimental techniques to be covered: Protein Complex Preparation/ FRET and SPR

Qualification-goals/Competencies:● This module aims to address at expanding the knowledge of biophysical and biochemical characterization methods of protein

complexes, which is the basis of all working enzymatic cascades. The module will include lectures and hands-on practical sessions. Wewill also visit CSSB/DESY

Grading through:● Presentation● Regular and successful participation in practical course



● Dr. Young-Hwa Song


Notes:


52



Module Guide

LS5200-SK IB - Consolidating in IB: Part of the module SK Light up the Dark: modern fluorescence techniques in

structural biology (ModernF)




Classes and lectures: Workload:● Light up the Dark: modern fluorescence techniques in

structural biology (Lecture, 2 SWS)● 60 Hours Private studies● 30 Hours Presence studies

Contents of teaching:● Basics in fluorescence● Photo physics● Energy transfer● Single molecule fluorescence● Fluorescence correlation spectroscopy

Qualification-goals/Competencies:● Knowledge of modern methods of fluorescence● Confidence in literature management● Presentation of scientific results● Assessment of scientific results

Grading through:● Recitation● Regular and successfull participation in the course



● Prof. Dr. rer. nat. Christian Hübner

Literature:● : Current publications


Notes:


53



Module Guide

LS5200-ZB - Consolidating in IB: Part of the module ZB Cell Biology of the Senses (ZellBioSen)




Classes and lectures: Workload:● Cell Biology of the Senses (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Cellular and molecular mechanisms that enable our perception of the outside world● Impaired cell and tissue function and genetic diseases as causes of sensory failures● Introduction to cell physiology and neurobiology of the senses (signal processing)● Diseases and sensory failures: human genetic disorders and animal models● Techniques: in vivo imaging, electrophysiology, knockout mice, molecular techniques

Qualification-goals/Competencies:● Survey of cellular & molecular mechanisms of human sensory perception● Survey of specialized cell types involved in signal perception and processing● Impaired cell and tissue function and genetic diseases as causes of sensory failures● Critical reading and discussion of scientific primary literature● Presentation of scientific results

Grading through:● Regular and successfull participation in the course● Oral presentation of original research papers


Teacher:● Institute for Biology

● Prof. Dr. rer nat. Rainer Duden

Literature:● : The Cell Biology of the Senses - Sonderheft des �Journal of Cell Biology� 2011● : - http://jcb.rupress.org/cgi/collection/rss?coll_alias=cell_biol_of_senses● : Primary literature for student presentations will be announced at the start of the module


Notes:


54



Module Guide

LS5200-ZD - Consolidating in IB: Part of the module ZD Experimental Immunology (ExpImmu)




Classes and lectures: Workload:● Experimental Immunology (Lecture with exercises or seminar, 2


Contents of teaching:● Animal models● Organisation and function of the immune system● Pathogens● The unspecific immune system● B lymphocytes and antibodies● T cells● Effector mechanims against infectious agents● Inflammation● Allergy● Tumour immunology● Tolerance and autoimmunity● Immun defects● Vaccination● Ethics in animal experiments● Biometric design and statistical evaluation of immunological experiments

Qualification-goals/Competencies:● Immunological topics should be discussed on the basis of ex-perimental examples● Relevant scientific publications should be comprehended in an accompanying seminar

Grading through:● Attendance, min. 90%● Presentation



● Dr. rer. nat. Christoph Hölscher● Dr. rer.nat. Hanna Erdmann● Dr. rer. nat. Jochen Behrends

Literature:● Charles A. Janeway, Paul Travers, Mark Walport: Immunobiology: The Immune System in Health and Disease; - Garland Science

Publishing, 6th edition, 2005, ISBN 0815341016


Notes:


55



Module Guide

LS5200-ZE - Consolidating in IB: Part of the module ZE Advanched course in Immunology (AdvancedIm)




Classes and lectures: Workload:● Advanched course in Immunology (Seminar, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● To understand the structure and function of lymphatic organs● Overview on the analysis and role of the T- and B-cell receptors● Overview on next- generation- sequencing● Critical appraisal on research literature● Overview on mechanisms and pathogenesis of human pathogens

Qualification-goals/Competencies:● To understand the structure and function of lymphatic organs● Antigen presentation● T- and B-cell subsets● T- and B-cell receptors● The function of T- and B-cell repertoires in diseases● Methods of analyzing T- and B-cell repertoires (next- generation- sequencing)

Grading through:● Oral presentation and written report


Teacher:● Institute of Anatomy

● Dr. rer. nat. Kathrin Kalies● Prof. Dr. med. Jürgen Westermann

Literature:● Fred Rosen, Raif Geha: Case studies in Immunology: a clinical companion - Garland Science Publishing, 3rd edition● : Reviews, scientific articles


Notes:


56



Module Guide

LS5200-ZF - Consolidating in IB: Part of the module ZF Gene Expression (GenExpr)




Classes and lectures: Workload:● Gene Expression (Seminar / Exercises, 2 SWS) ● 60 Hours Private studies


Contents of teaching:● Theoretical part (Seminar on topics A - E)● Hands on course (transcriptional analyses)

Qualification-goals/Competencies:● Knowledge of the different levels of gene regulation and the DNA-elements required for basal and regulated transcription: (i) core

promoter, (ii) enhancer, silencer, bi-functional elements, (iii) transcription by RNA polymerases I, II and III (processes and proteincomplexes)

● Knowledge of the role of the chromatin structure in gene regulation: (i) Chromatin, (ii) histones, (iii) regulatory relevanthistonemodifications, (iv) �histone-code�, (v) chromatin condensation and de-condensation (processes and protein complexes),(vi)related ontogenetic aspects

● Knowledge of processes resulting in permanent repression of chromatin and overview about the proteins involved: (i)SWI/SNF, (ii) HAT,(iii) HDAC, (iv) NURD, (v) CoR, (vi) related ontogenetic aspects

● Knowledge of the role of RNA-species for the regulation of gene expression (processes and types of RNA-species)● Overview of regulation principles used by different cell types and transcription factors: (i) e.g. agonists or antagonists, phosphorylation,

limited and specific proteolyses; (ii) gene regulation in the context of development, homeostasis and tumors; (iii) mechanisms thatregulate the activity of transcription factors such as AP1, p53, NFΚ, nuclear receptors, bHLH-family, Hox-family, Notch

Grading through:● Recitation● Evaluated protocol


Teacher:● Department of Neurosurgery

● PD Dr. rer. nat. Christina Zechel

Literature:● Lodish et al.: Textbook Molecular Cell Biology● Alberts et al.: Textbook Molecular Biology of the Cell● : Originalliteratur zu den einzelnen Themenabschnitten


Notes:


57


http://www.neurochirurgie.uni-luebeck.de/

Module Guide

LS5200-ZK - Consolidating in IB: Part of the module ZK Cellular Microbiology & Inflammatory Diseases

(MicroInfDi)




Classes and lectures: Workload:● Cellular Microbiology & Inflammatory Diseases (Seminar, 2


Contents of teaching:● Lecture: Cell Biology of inflammatory and infectious diseases: how pathogens maipulate the host cell�s membranes, organelles,

cytoskeleton, signalling and cell-cycle● Host-Pathogen Interactions● Bacterial toxins and mechanisms of intoxication● ER stress associated with infectious and inflammatory diseases● "Classic� studies in infectious disease: Robert Koch, Ilya Metchnikoff, Louis Pasteur● Practical part:● Live cell fluorescence microscopy to study the action of AB5 toxins on mammalian cells

Qualification-goals/Competencies:● Understanding of mechanisms leading to infectious and inflammatory diseases● Critical reading and discussion of primary scientific literature● Presentation of scientific results

Grading through:● Regular and successfull participation in the course● Oral presentation of original research papers


Teacher:● Institute for Biology

● PD Dr. Nauk Irina Majoul

Literature:● Cossart, Boquet, Normark, and Rappuoli: Cellular Microbiology, - ASM Press, 2nd Edition 2005, ISBN: 1-55581-302-X● : - Primary literature for student presentations will be handed out at the beginning of the course


Notes:


58



Module Guide

LS5200-ZM - Consolidating in IB: Part of the module ZM Molecular biology of virus infections of cytopathogenic

and non-cytopathogenic viruses (MolbioViru)




Classes and lectures: Workload:● Molekularbiologie von Virusinfektionen zytopathogener und

nicht-zytopathogener Viren (Seminar / Exercises, 2 SWS)● 60 Hours Private studies● 30 Hours Presence studies

Contents of teaching:● characteristics of viral infections● host cell influence on viral infections● characterization of host factors of viral infections● RNA technologies● different analysing methods ( plaque assay, Immune fluorescence, RT-PCR, growth curve)● Usage of stable cell lines for analysis and characterization of virus- host- interaction● cell culture techniques

Qualification-goals/Competencies:● Knowledge about infections of cytopathogenic and non-cytopathogenic viruses● Overview about current methods for characterization of virus- host- interaction● Application of different RNA techniques for analysing viral infections● Overview about current techniques of virus detection in cell culture● Work under BSL2- conditions with viral pathogens● Work with stable cell lines and their characterization

Grading through:● Oral presentation and written report



● Prof. Dr. rer. nat. Norbert Tautz● Dr. rer. nat. Olaf Isken

Literature:● Lackner T, Müller A, Pankraz A, Becher P, Thiel HJ, Gorbalenya AE, Tautz N. J. Virol.: Temporal modulation of an autoprotease is crucial

for replication and pathogenicity of an RNA virus. - 2004 Oct; 78 (19):10765-75.● Rinck G, Birghan C, Harada T, Meyers G, Thiel HJ, Tautz N. J Virol.: A cellular J-domain protein modulates polyprotein processing and

cytopathogenicity of a pestivirus. - 2001 Oct;75(19):9470-82.● Lackner T, Müller A, König M, Thiel HJ, Tautz N. J Virol.: Persistence of bovine viral diarrhea virus is determined by a cellular cofactor of a

viral autoprotease. - 2005 Aug;79(15):9746-55● Gallei A, Blome S, Gilgenbach S, Tautz N, Moennig V, Becher P. J Virol.: Cytopathogenicity of classical Swine Fever virus correlates with

attenuation in the natural host. - 2008 Oct;82(19):9717-29.


Notes:


59



Module Guide

LS5200-ZP - Consolidating in IB: Part of the module ZP Inflammatory skin diseases from bench to bedside

(SkinDeas)




Classes and lectures: Workload:● Inflammatory skin diseases: From bench to bedside (and back)

(, 2 SWS)● 60 Hours Private studies● 30 Hours Presence studies

Contents of teaching:● Clinical presentation, diagnosis and current treatment options of autoimmune skin blistering diseases● In vitro and ex vivo models of AIBD● Animal models of AIBD● Isolation of immunoglobulin● Practical work: Isolation and characterization of immune IgG, and coating of 96-wells with immune complexes● Practical work: Activation of human neutrophils with immune complexes and other activators● Preparation of student presentations on in vitro models of inflammatory skin diseases such as psoriasis, allergic contact dermatis,

atopic dermatitis

Qualification-goals/Competencies:● To obtain an overview of the clinical presentation, diagnosis, pathogenesis and treatment of inflammatory skin diseases● Hands on training on methods in immunological research; e.g. isolation of IgG and cells from blood

Grading through:● Recitation● Protocols


Teacher:● Department of Dermatology, Allergology and Venerology

● Prof. Dr. med. Ralf Ludwig● Prof. Dr. med. Saleh Ibrahim

Literature:● : Original papers and reviews to the above topics


Notes:


60



Module Guide

LS5200-ZR - Consolidating in IB: Part of the module ZR Animal experimentation: A comprehensive introduction

into laboratory mice (AnimalExp)




Classes and lectures: Workload:● Animal experimentation: A comprehensive introduction into

laboratory mice (, 2 SWS)● 60 Hours Private studies● 30 Hours Presence studies

Contents of teaching:● Commonly used mouse stains● Generation of knock-out mice● Selected mouse models of AIBD● Isolation of immunoglobulin● Practical work: Isolation and characterization of immune IgA● Practical work: Mouse handling, including injection techniques● Preparation of student presentations on mouse models of inflammatory skin diseases (Ibrahim, Ludwig)

Qualification-goals/Competencies:● An introduciton (theoretical and practical) to conduce experimental research with mice● Basic understanding of mouse lines, knock-out and transgenic mice

Grading through:● Recitation● Protocols


Teacher:● Department of Dermatology, Allergology and Venerology

● Prof. Dr. med. Ralf Ludwig● Prof. Dr. med. Saleh Ibrahim

Literature:● : Original papers and reviews to the above topics


Notes:


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Documents

Module Guide for the Study Path - uni-luebeck.de · 2014-09-30 · Module Guide Interdisciplinary competence Ethics in Sciences / Scientific Writing (PS4610-IB, EthScWrIB) 1 Scientific