Molecular and Computational Biology

Profile: Molecular and Computational Biology

The programme introduces into molecular aspects in cell biology, developmental biology, microbiology, biophysics. Furthermore, topics and concepts in neuroscience, infection and immunity, integrative biology, and biomedicine are presented. Special attention is given to the eucaryotic cell and both the fundamental principles of molecular cell biology and the huge structural and functional diversity of molecules, organelles and cells. Molecular aspects are addressed using tools of bioinformatics and computational systems biology based approaches. These include functional genomics, dynamic analysis of the transcriptome, metabolic and regulatory networks. 

The two major topics are composed of two theory modules as well as a practical course unit each. Further research training is provided in a selected field of interest, and the students are actively involved in ongoing research projects and learn to independently plan and perform both theoretical and experimental work and finally, to summarize and discuss the results obtained in the thesis. 

Objectives and Learning Outcomes

The students become familiar with theoretical aspects and principles in cell biology, developmental biology, microbiology, biophysics, bioinformatics and understand recent results in systems biology. With several bioinformatics tools, they learn to use computer based approaches to address and resolve problems in various fields of molecular biology. They are also able to review and expand their knowledge of standard molecular techniques and are able to choose methods and techniques to design experiments in a specific research area. The students learn to perform biohazard risk assessments and to setup appropriate biosafety actions. They are aware of scenarios in research and environment that may be associated with biological hazards. 

Programme Schedule

• S1 TOPIC 1 (2 theory modules plus practical course) 
• S2 TOPIC 2 (2 theory modules plus practical course) 
• S3 Advanced experimental training (F2, 15CP) + additional special courses (15 CP) 
• S4 Thesis + final colloquium

Curriculum

For detailed informations on the following modules listed are available in the Online Course Book, Master Biosciences, Module Group 4  WueStudy

Year 1 (Winter-Semester)

• Methods in Life Sciences
• Topics and Concepts in Life Sciences - Model Organisms and Current Research
• Topics in Systems Biology
• Computational Biology F1 (Practical Course)
• Additional Courses

Year 1 (Summer-Semester)

• Molecular Biology
• Topics in Bioinformatics or Pathogenicity of Microorganisms
• Molecular Biology F1 (Practical Course)
• Additional Courses

Year 2

• Molecular Biology F2 or  Computational Biology F2 (Practical Course)
• Additional Courses

• Thesis
• Thesis Colloquium

•  

Modules - Theory

Topics in Systems Biology

C: Advances and current results of computational systems biology are explained and discussed. This includes results from functional genomics, dynamics of the transcriptome, of metabolism and metabolic networks as well as regulatory networks.
LO: Understand recent results in systems biology. Discuss their implications. Have an advanced (master) level knowledge of typical technologies and research questions of systems biology.

Topics in Bioinformatics

C: Advances and current results of bioinformatics are explained and discussed, this includes results from genome and sequence analysis, protein domains and protein families, large-scale data analysis (e.g. net generation sequences, proteomics data), analysis of different functional RNAs (e.g. miRNAs, lncRNAs).
LO: Understand recent results in bioinformatics. Discuss their implications. Have an advanced level knowledge of typical technologies and research questions in bioinformatics.

Molecular Biology (Lecture Series)

C: Molecular Biology of Prokaryotic and Eukaryotic Cells. The lecture series introduces into the fields of cell biology, developmental biology, microbiology, biophysics, bioinformatics. Based on current concepts in molecular biology, the lectures elucidate these with respect to the particular disciplines. 
Recommended literature: Alberts B, Bray D. et al. "Essential Cell Biology"; Garland Science, NY USA 
In the course sessions on “Cell Biology“ (comprising 25% of the total) focuses on  the eucaryotic cell and illustrates both the fundamental principles of molecular cell biology and the huge structural and functional diversity of molecules, organelles and cells.
The lectures on bioinformatics (25% of total) comprise many examples for application in order to demonstrate how to address problems in molecular biology with tools of bioinformatics. The lectures are in line with the textbook „Essential Cell Biology“, and include many examples covering the topics of all course sessions. Bioinformatics is presented as a computer based molecular biology tool allowing time saving experimental planning.   
The third part of the lecture series is dealing with fundamental aspects of prokaryotes and microbiology in general. Special topics are the organization of the bacterial genome, the machinery and regulation of transcription and translation, the transport of cellular components, cell division and   cellular differentiation processes, bacterial mobility and chemotaxis, signal transduction and bacterial communication.       
Recommended literature:
(a) Allgemeine Mikrobiologie (Fuchs) ???? (b) Madigan MT, Martinko JM, Stahl DA Clark DP Brock Biology of Microorganisms. Pearson educ., USA
LO: The students become familiar with theoretical aspects and principles in cell biology, developmental biology, microbiology, biophysics, bioinformatics. With several bioinformatics tools, they become familiar how to use computer based approaches to address and resolve problems in these bioscientific fields.

Methods in Life Sciences (Lecture series)

C: Standard molecular techniques including PCR, lipid research methods, microscopic methods, immunohistochemistry, mouse models and gene-knockout approaches, protein and molecular biology techniques, advanced protein biochemistry, methods in bioinformatics and computational biology.

LO: Students are able to review and expand their knowledge of standard molecular techniques and are able to choose methods and techniques to design experiments in a specific research area.

Topics and Concepts in Life Sciences

C: A broad variety of topics and concepts from the areas of neuroscience, infection and immunity, integrative biology, and biomedicine include for example: Protein characterization, DNA repair, Drosophila, Computational Biology, and Neurocircuits, amongst others. Standard molecular technique including PCR, lipid research methods, microscopic methods, immunohistochemistry, mouse models and gene-knockout approaches, protein and molecular biology techniques, , advanced protein biochemistry, methods in bioinformatics and computational biology.
LO: Students have an overview of current research topics in the Research Groups in Life Sciences and possess knowledge about their scientific background.

 

Pathogenicity of Microorganisms

C: The major human pathogens will be presented and the mechanisms underlying diseases caused by them will be discussed. In addition, the current knowledge on the action of pathogenicity factors and how they are related to disease development will be introduced for both prokaryotic and eukaryotic pathogens. A further focus will be rapidly emerging new pathogens and the expected health and social-economic consequences. Current experimental approaches in infection biology will be explained in the general lectures. This includes aspects of biosafety and biosecurity.

LO: The students become familiar with the theoretic principles of infection biology and pathogenicity including principles and mechanistic details on the origin and spreading of infectious diseases. The students learn to perform biohazard risk assessments and to setup appropriate biosafety actions. They are aware of scenarios in research and environment that may be associated with biological hazards. 

Modules – Practical Courses

Computational Biology F1

C: Detailed insight into computational biology methods, depending on the topic selected, fields covered include: Genomics (sequence-, domain analysis and annotation), Omics data analysis (NGS, transcriptomics, metabolomics, proteomics), Topological and structural analysis of biological interactions including statistical methods, phylogenetic analysis, Protein structure analysis.LO: Master level knowledge on specific methods in computational biology, first insight into a scientific topic in computational biology including knowledge of current literature on the topic, first own independent analyses applying a sophisticated method from computational biology.

Computational Biology F2

C: Advanced insight into computational biology methods, depending on the topic selected, fields covered include: Genomics (sequence-, domain analysis and annotation), Omics data analysis (NGS, transcriptomics, metabolomics, proteomics), Topological and structural analysis of biological interactions including statistical methods, phylogenetic analysis, Protein structure analysis.LO: Master level knowledge on advanced methods in computational biology, advanced insight into a scientific topic in computational biology including knowledge of current literature on the topic, advanced own independent analyses applying a sophisticated method from computational biology. Students are trained to work independently according to the rules of best practice. They are qualified to conduct scientific work, perform statistical analysis and interpretation. The acquired knowledge qualifies the students to perform scientific activities in the content of F2 internship or a master thesis.

Molecular Biology F1

C: Practical course on a topic in molecular biology. Students work on a small, well-defined scientific lab project for 5 weeks and learn how to present their data. They learn to discuss their data in a seminar. The students learn to apply defined experimental procedures and methods, to address independently scientific questions and to appropriately document their experimental work.LO: Students reinforced previously acquired lab skills, acquired new molecular lab techniques, and learned how to transfer theoretical knowledge into experiments. Students have gained expertise in the analysis of raw data, their interpretation and their presentation.

Molecular Biology F2

C: Current research subjects in the field of molecular biology are addressed by critically reading and presenting means of original research papers. The participants will be involved in development of a research plan and learn to apply advanced techniques to answer a scientific question in molecular biology. This practical course lasts 12 weeks (three month) and is considered as preparation for the thesis.

LO: Students are qualified to scientifically work in a laboratory on their own. They are competent to answer and to discuss questions asked in the field of molecular biology. They are competent to work according to good practice and to document, interpret and to discuss their results. They acquire competence to apply specific molecular techniques required to answer scientific questions. They are qualified to conduct scientific work, perform statistical analysis and interpretation. The acquired knowledge qualifies the students to perform scientific activities in the content of F2 internship or a master thesis.

 

Additional Courses (5 ECTS unless indicated)

Biochemistry, Physiology and Genetics of Mammalian Cell Culture

C: Introduction to cell culture, cell culture lab equipment, cellular biochemistry and cell structures, cell proliferation, generation of in vitro cell models and their applications , cell culture formats, basic cell analytical technologies.

LO: Students are able to understand the biochemistry, physiology and genetics of mammalian cell culture, and possess the asset to use these techniques.

Molecular Techniques (3)

C: Introduction to new and cutting edge molecular techniques. As well as methods for scientific investigation.

LO: Students are able to recognize cutting edge methods, and techniques to improve experimental strategies and experimental set ups to answer scientific questions.

Molecular Tumour Biology

C: The lecture „Molecular Tumorbiology“discusses molecular characteristics of tumors and relevant biological processes (such as signal transduction, cell growth, cell proliferation, metabolism), tumor specific modifications and current molecular biological methods in tumor research.

LO: Understanding of the current topics and challenges in tumor research and understanding about the methods which could be used to deal with such challenges.

Clinical Tumor Biology

C: In the lecture series „Clinical Tumorbiology“current clinical aspects will be discussed. Several tumortypes will be considered (such as tumors of the skin, lung, intestine, breast, blood). Diagnostics & pathologiy, different treatments and therapies and clinical trials will be further topics.

LO: Knowledge about the similarities and differences of various tumor types. Understanding of requirements, possibilities and limitations in clinical medicine.

Animal Communication

C: The lectures deal with physiological and neurobiological principles of the different communication channels used by animals, but also highlight adaptive values and evolutionary aspects of animal signaling. In a follow-up seminar session students will deepen their knowledge by presenting and discussing actual papers related to the topic of the lecture.

LO: The students experience the benefit of an integrative approach when confronted with complex biological issues. They learn to connect the findings of different research areas like physiology, neurobiology, behavior and ecological conditions in order to gain a more complete picture of a topic. Participants learn to present and discuss actual papers within a broader scientific framework.

Experimental Sociobiology

C: The lectures highlight the diversity and the evolution of social behavior, but also focus on the physiological, neurobiological and behavioural mechanisms underlying the organization of social groups. In a follow-up seminar session students will deepen their knowledge by presenting and discussing actual papers related to the topic of the lecture.

LO: The students experience the benefit of an integrative approach when confronted with complex biological issues. They learn to connect the findings of different research areas like physiology, neurobiology, behavior and ecological conditions in order to gain a more complete picture of a topic. Participants learn to present and discuss actual papers within a broader scientific framework.

 Immunology 1 B

C: Basic concepts of modern cellular and molecular Immunology.

LO: Participants learn to read, critically discuss and present current concepts in immunology at (advanced) text book level. Reception of talks on current topics in immunology which are given by varying researchers covering a broad range of immunological topics.

 Immunology 2 B

C: Current topics in molecular and cellular immunology with emphasis on autoimmunity. allergy, immunomodulation, cancer and transplantation immunology, immunity of infection and evolution of the immune system.

LO: Capability to read, critically discuss and present current concepts in immunology on the basis of original literature and primary data.

Virology 1 B

C: This course offers an introduction to virology and current research in the field of virology.

LO: Students have gained the ability to understand and discuss in depth current issues in virology.

Virology 2 B

C: This course offers an introduction to virology and current research in the field of virology.

LO: Students will have gained the ability to understand and discuss in depth current issues in virology.

Nucleus Workshop

C: A combination of lecture and laboratory course
Topics include the nuclear envelope, nuclear pores, nuclear-cytoplasmic transport, nuclear lamina, chromatin, chromosomes and disease, structure and function of the nucleolus, communication between the cytoskeleton and the nucleus
Experiments include 
•    Electron microscopy of the nuclear envelope, pores and lamina; 
•    Growth of the nuclear envelope: Experiments using cultured cells and Drosophila
•    Preparation of a Xenopus-egg extract and in vitro-assembly of artificial nuclei
•    In-vitro assemly of lamina-filaments
•    Isolation of nuclear envelope  from cultured cells; Protein analyses using Western blotting.
•    Visualization of nucleosomal chromatin in EM (Miller-Speading).
•    Extraction of histones und analyses via one- and two-dimensional gelelectrophoresis.
•    Visualization of transcriptional active genes.
•    Structure and function of the nucleolus; influence of cellular toxins.
•    Isolation of ribosomes and ribosomal subunits using a sugar gradient centrifugation and protein analyses
•    Nucleolar behavior during mitosis (Immunofluorescence microscopy using a nucleolus specific antibody).
•    The nucleolar organizer region (NOR), Silver staining and immunolocalization
•    Localization of transcription sites in the cell nucleus (BrU incorporation).
•    Protein-Protein interaction in the cell nucleus (in situ proximity ligation assay).
•    Chromatin immunoprecipitation (Chip)

LO: The students understand structural and functional features of the cell nucleus. They know abput key cell biological methods and are able to perform experiments to anwer scientific questions using these trained methods.

Additional Courses & Final Thesis

Ecology of Honey Bees and Wild Bees

C: Introduction to the life of honey bees and wild bees; principles and techniques of beekeeping (colony management, breeding, diseases); resource use of honey bees and wild bees (bee dances, flower visiting, pollen analysis, foraging behavior, nesting aid); Taxonomy of wild bees, opponent of bees, wild bees in different habitats (excursion), honey bee excursion, e.g. visiting of the bee center in Veitshöchheim.

LO: The students expand their knowledge on Biology and Ecology of wild- and honey bees, on interactions between bees and plants, and on aspects of nature conservation. They become qualified to handle experimental methods of Pollination Ecology, management of trial colonies, pollen analysis, and determination of wild bees.

Ecology and Taxonomy of Insects

C: Identification and classification of the characteristics of different groups of arthropods, especially insects. Knowledge of special form is provided. Observation and recording of arthropods in habitats. Experimental laboratory and field work on ecological or behavior biological characteristics of the respective groups of arthropods. In addition, also compilation of species richness and niche differentiation. The aim is to link the phylogenetic and morphological characteristics of arthropods with their ecological functions.

LO: The students gain knowledge of defining typical families and representatives of major insect orders. They are qualified to apply special identification keys, record and evaluate special behaviors. They are able to design and evaluate experimental approaches in ecological laboratory and field studies.

Modelling in Ecology

C: On the basis of exemplary tasks in Ecology, the students will learn about different simulation techniques and modelling methods. In the same time, they will also develop their own simulation program to address demographical or evolutionary questions.

LO: The students expand their knowledge in theory and practice of ecological modelling and they are qualified to develop, apply, and interpret adequate modelling techniques.

Tropical Ecology

C: In a tropical ecosystem, small project with ecological or nature conservation related issues will be performed. Here the students should learn about the steps of experiment design, implementation, data analysis, up to data presentation. In the evening seminar, recent publications are presented in the field of tropical Ecology and will be discussed.

LO: The students learn about various tropical Ecosystems and acquire further knowledge of ecological and nature conservation related research in the tropics. They learn field ecological methods for quantitative detection of insects and their biotic interactions, as well as acquire statistical knowledge in the field of data analysis.

Linux and Perl 

C: Introduction into the operation system Linux, writing computer programs using the programming language Perl to answer bioinformatical questions.

LO: Students are able to handle the Linux as user and they are able to write simple Perl scripts to answer bioinformatical questions.

Presentation of Scientific Data

C: The students write a scientific mini review including correct citation and learn various options to present scientific data including manuscript writing followed by an oral presentation (15 min).The manuscript is based on original papers as well as on reviews and follows the instructions of a scientific journal of choice, which may be found at the home page under e.g. “Instructions to Authors”. Both length of chapters and structure of the article should be based on the style of the selected journal.Attendance at 20 or more scientific talks (e.g. defense of doctoral thesis, presentation of research projects, retreats ) including presentation by guest speakers.

LO: The students are familiar with the deatails of publishing scientific data in written and oral form. They have become familiar with the methodology of scientific publishing in oral or written fashion. Furthermore, they have trained English skills in both reading, talking and writing.

Quality Assurance, Good Practice, Biosafety and Biosecurity

C: Good Practice in the Biosciences, quality assurance approaches and quality culture. Structure, idea and basic principles of quality management approaches, DIN EN ISO 9001, regulatory documents and framework in the biosciences  including biotechnology, biosafety, biosecurity, risk assessment.

LO: The students are familiar with basics of “Good Practices” in Research and Development, and have understood the basic principles of quality management circles. They have a distinct sensibility in biosafety and biosecurity issues and know the proper handling of biological agents and organisms. In addition, they have developed a sense to the complex interdependences in nature and can critically discuss socio-ethical issues in the bioscience area.

FINAL THESIS

Thesis (25)

C: A defined scientific question is addressed by adequate techniques. Students plan and perform experiments to solve problems or summarize and interpret existing data. The students have to develop a research plan and apply advanced and novel techniques in the context of a given research project according to good scientific practice. The results are summarized in a written thesis. The project lasts for six month.

LO: Students are qualified to scientifically work on a topic on their own. They are competent to discuss the current research in the field. They are competent to work according to good practice and to document, interpret and to discuss their results. They are competent to discuss and to defend their data in the scientific community.

Thesis Defense / Oral examination Biology (3)

C: Verification of thesis content through oral examination. Total length should not exceed 45 min. (30 min. plus 15 min. of questions pertaining to the thesis, as well as related subjects) 

LO: The students are able to present the results of their thesis work to a public audience in a limited time and they are able to critically discuss questions and concerns.