Systems Biology and Metabolomics

Profile: Systems Biology and Metabolomics

C: The programme focuses on the reprogramming mechanisms of the metabolism in association with phenotypic, physiological or behavioural changes including disease development. Current techniques of Metabolomics and Bioanalytics including quantitative metabolite analysis methods (chromatography, mass spectrometry) are applied for comprehensive gene function- or stress response analyses. Both bioinformatics and complex computational approaches give insights into the field of computational biology. 

In particular, advances and current results of bioinformatics including genome and sequence analysis, protein domains or protein families, large-scale data analysis (e.g. next generation sequences, proteomics data), analysis of different functional RNAs (e.g. miRNAs, lncRNAs) are explained and discussed. Furthermore, aspects of functional genomics, the dynamics of either the transcriptome or of metabolism and metabolic networks up to regulatory networks are illustrated.

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 state of the art approaches to comprehensively analyze physiological changes using current techniques of Metabolomics and Bioanalytics. They are trained to understand recent results in systems biology and to discuss corresponding implications. The students become familiar with theoretical aspects and principles in comprehensive bioanalytical approaches in cell biology, developmental biology, microbiology.  They experience the complex interactions of living organisms including the importance of time and place to result in successful reproduction or synergy.  With several bioinformatics tools, they are able to use computational biology based approaches to address and resolve problems in selected bioscientific fields. 

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)

• Neurobiology, Behavioural Physiology and Animal Ecology
• Topics in Systems Biology
• Systems Biology F1 (Practical Course)
• Additional Courses

Year 1 (Summer-Semester)

• Molecular Biology
• Topics in Bioinformatics
• or Signals and Differentiation
• Pharmaceutical Biology & Metabolomics F1  (Practical Course)
• Additional Courses

Year 2

• Pharmaceutical Biology & Metabolomics F2 or
  Systems Biology F2 (Practical Course)
• Additional Courses
   
• Thesis
• Thesis Colloquium

Modules - Theory

Topics in Systems Biology

C: Advances and current results of computational systems in 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.

Neurobiology, Behavioural Physiology and Animal Ecology

C: "Timing matters":  Temporal organization in the animal kingdom
Timing plays an important role in all living systems. Animals make use of endogenous clocks to predict and adapt to daily or seasonal changes in environmental parameters. To be at the right time at the right place is of great fitness relevance if -for example- a mating partner or enough food has to be found. Many mutualistic, antagonistic or social interactions can only take place if animals are at the same time at the same place and in the appropriate developmental stage.
The lecture series give an introduction into the mechanisms underlying the temporal organization in the animal kingdom. Adopting an integrative approach, the lecture goes from timing mechanisms on the neuronal level to individual behaviour and then to interactions in social groups, populations or partners in complex and variable ecosystems.

LO: The students get an overview in organismic biology including neurobiology, behavioral biology and ecology. They experience the complex interactions of living organisms including the importance of time and place to result in successful reproduction or synergy.

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.

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.

Cell and Developmental Biology Master

C: The module consists of the lecture "Signals and Differentiation" and the seminar "Milestones and Perspectives of Developmental Biology".
The lecture "Signals and Differentiation" does not attempt to impart pure textbook knowledge. Instead, historically important as well as particularly interesting and important trend-setting topics in developmental biology are presented. The topics range from classical developmental subjects such as tissue regeneration and morphogenetic cell migration to molecular stem cell biology, epigenetic plasticity, origins of multicellularity and development within changing environments. 
In the seminar "Milestones and Perspectives of Developmental Biology" classic ground-breaking publications in the field of developmental biology are discussed in an unorthodox way.

LO: Participants gain the expertise to acquire scientific background knowledge of developmental biology to include it into a broader frame of cell biology research.

Modules – Practical Courses

Pharmaceutical Biology & Metabolomics F1

C: All organisms are able to reprogram their metabolism in response to various endogenous or exogenous perturbations. Reprogramming of metabolism is often correlated to phenotypic changes e.g. in disease development, physiology or behaviour. In the Department of Pharmaceutical Biology, we apply metabolomics for gene function- or stress response analysis. Students can choose a topic from the diverse running projects. Depending on the scientific question of the research team at the department, the methodological approach involves techniques in the field of “Metabolomics/Bioanalytics” and/or “Molecular Biology”. In this module, students are trained to use quantitative metabolite analysis methods (chromatography, mass spectrometry) and apply advanced molecular biology techniques. Depending on the project, different model organisms are studied. Prior knowledge in metabolite analysis or mass spectrometry are not required.Current scientific questions in the life sciences form the basis to impart scientific concepts and to train students in the laboratory. The module involves the experimental design, realisation and critical evaluation of scientific experiments as well as documentation and presentation of the progress. More information is available on request or can be found at https://www.biozentrum.uni-wuerzburg.de/pbio/

LO: Students are trained in using specific molecular biology methods and/or metabolomics approaches to address scientific questions, in the documentation of experimental procedures and results, and in the interpretation of data.

Pharmaceutical Biology & Metabolomics F2

C: Students will be involved in current research projects in Pharmaceutical Biology or in collaborative research projects that focus on the regulation of metabolism and analysis of metabolic pathways (e.g. in the context of reactions towards biotic or abiotic stress, functional and phenotypic analysis of mutants, or drug metabolism). Aspects of the scientific question will be independently addressed by the student. Molecular biology methods and/or metabolomic approaches will be optimized for and adapted to the specific problem. Experimental results and progress in the understanding of biological problems will be documented in protocol form and presented in a seminar. 

LO: Students are qualified to independently perform scientific experiments and to use specific molecular biology and bioanalytical methods to address current scientific questions in the field of metabolic regulation and metabolomics. 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.

Systems Biology F1

C: Detailed insight into systems biology computational methods, depending on the topic selected, fields covered include: modelling of metabolic networks, modelling of regulatory networks, systems biological analyses including mathematical methods for these, dynamical analysis of biological interactions including statistical methods, dynamics of evolution, modelling adaptation and signaling responses.

LO: Master level knowledge on specific methods in systems biology, first insight into a scientific topic in systems biology including knowledge of current literature on the topic, first own independent analyses applying a sophisticated method from systems biology.

Systems Biology F2

C: Advanced insight into systems biology computational methods, depending on the topic selected, fields covered include: modelling of metabolic networks, modelling of regulatory networks, systems biological analyses including mathematical methods for these, dynamical analysis of biological interactions including statistical methods, dynamics of evolution, modelling adaptation and signaling responses.
LO: Master level knowledge on advanced methods in systems biology, advanced insight into a scientific topic in systems biology including knowledge of current literature on the topic, advanced own independent analyses applying a sophisticated method from systems biology. 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.