PROTEIN CHEMISTRY: Structural Biology, Protein Chemistry and Biophysical Methods for High Resolution Analytics

Fundamentals in thermodynamics, reaction kinetics and theoretic aspects of molecular interactions are discussed. Examples include electromanipulation and dielectrical spectroscopy of cells, electrokinetic techniques, protein folding, single molecule fluorescence methodology, high resolution as well as dynamic microscopy.

Programme Profile: Protein Chemistry

The programme deals with fundamentals in structural biology and biochemistry with special focus on protein chemistry and biophysical methods for high resolution analytics. Fundamentals in thermodynamics, reaction kinetics and theoretic aspects of molecular interactions are discussed. The students get familiar with biophysical methods allowing to delineate both the structure of single cells “down” to single molecules. Examples include electromanipulation and dielectrical spectroscopy of cells, electrokinetic techniques, protein folding, single molecule fluorescence methodology, high resolution as well as dynamic microscopy. Further topics are current approaches in bioinformatics including the analysis of genomes and sequences, protein domains and protein families, further large-scale data analysis (e.g. next generation sequences, proteomics data), the analysis of different functional RNAs (e.g. miRNAs, lncRNAs). Aspects of  computational systems biology include functional genomics, dynamics of the transcriptome, of metabolism and metabolic networks as well as 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 understand the principles of biophysics and biochemistry including structural biology.  They also become familiar with fundamental methods in biophysics and get an idea to apply these in various experimental settings.  This enables the students to get deeper into the field by reading current scientific literature, by acquiring sufficient quantitative understanding of biophysical mechanisms.  They further understand recent results in systems biology and are able to work on related research projects. 

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

Contact

Dietmar Geiger
Plant Physiology & Biophysics
Phone: (+49) 931 31-86105

Eva Maria Fischer
Bioinformatics
Phone: (+49) 931 31 81812

Alois Palmetshofer
Coordinator BioCareers
Phone: (+49) 931 31 84239

Modules - Theory

Biophysics and Biochemistry

C: Theoretical and methodical aspects of membrane transport systems as well as structural biology and biochemistry are discussed, based on current research topics. 
The lecture series is comprised of four major methodical topics:
(a) Biophysical methods to investigate membrane transport processes;
(b) Biochemistry: protein crystallization for structure/function research;
(c) Overview on light microscopy from basic applications to high-resolution methods;
(d) Optogenetic tools, triggering physiological processes by light.

The lectures are enriched by demonstration experiments or excursions to state of the art laboratories (dependent on the number of students and the students’ interests).

LO: The students are able to apply basic methods in the fields of biophysics, biochemistry and structural biology in order to resolve and critically discuss questions with regard to soluble and membrane proteins.


Biophysics and Molecular Biotechnology

C: A broad overview is given on biophysical methods and corresponding applications.  Part 1 of the lecture deals with fundamental in thermodynamics, kinetics and molecular interactions. Then, biophysical methods are presented which allow to analyze single cells down to single molecules. Among special topics are the electromanipulation and dielectrical spectroscopy of cells,   further electrokinetic techniques, biomembranes, electrophysiology, ion channels, protein folding, single molecule fluorescence methodology, high resolution as well as dynamic microscopy.

LO: The students become familiar with fundamental methods in biophysics and get an idea to apply these in various settings.  This enables the students to get deeper into the field by reading current scientific literature, by acquiring sufficient quantitative understanding of biophysical mechanisms.


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.

Modules – Practical Courses

Biochemistry and Structural Biology F1

C: The module provides an in-depth insight into principle and modern strategies and methods of Protein Biochemistry and Structural Biology. The students will perform their studies integrated into research projects of current topics of “Biochemistry and Structural Biology”.

LO: The students have knowledge about general strategies and methods of Protein Biochemistry and Structural Biology with a focus on “Membrane Proteins”. They are qualified to perform and organize their scientific laboratory work independently and document the obtained results.

Biochemistry and Structural Biology F2

C: The students perform their research work within a current research project on the topic of “Biochemistry and Structural Biology” in a largely independent manner under supervision of a principle investigator.

LO: The students are qualified to address scientific issues within the research field of “Biochemistry and Structural Biology” by using appropriate biochemical and structural biological methods. They are capable to independently design the appropriate experiments and to analyze, document, present and discuss the results. 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 special courses (Elective Part 2, Common to all Study Programmes)

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.