Basic Courses

The four Basic Courses form the core structure of the educational program of BioToP. These courses allow doctoral candidates with different educational backgrounds to comprehend the basic principles of all research fields of BioToP.

Basic Course I: Analysis, Design and Engineering of Proteins

Lecturers: HALTRICH, HOFBAUER, LUDWIG, OBINGER, PETERBAUER, SCHÄFFER, TRAXLMAYR

A. Protein structure, kinetics and thermodynamics of protein folding

• Chemistry of non-covalent interactions and structural building blocks in proteins
  
• Protein diversity − evolution of structure and function
  
• Protein structure I: X-ray crystallography
  
• Protein structure II: NMR-spectroscopy of proteins
  
• Protein structure III: Electronic circular dichroism, fluorescence and FTIR-spectroscopy of proteins
  
• Protein structure IV: Self-assembling proteins - Light scattering and electron microscopy
  
• Folding pathways, conformational and thermal stability of proteins
  
• Measurement of changes in stability − differential scanning calorimetry and isothermal titration calorimetry

Outcomes: Profound understanding of kinetics and thermodynamics of protein unfolding, aggregation and (re)folding. Increased knowledge of methods in analysis of protein structure, purity and quality.

B. Functionality, design and engineering of proteins

• Measurement of protein − ligand (protein) interaction: surface plasmon resonance and atomic force microscopy
• Enzyme kinetics: steady−state versus presteady−state kinetics
• Protein libraries: design and construction
  
• Mutagenesis I: Site−directed mutagenesis, saturation mutagenesis, casette mutagenesis
  
• Mutagenesis II: Directed evolution by non−recombinative and recombinative methods
  
• Surface display technologies
  
• Screening criteria and methods
  
• Case study: Engineered therapeutic antibodies
  

Outcomes: Improved knowledge of kinetics of protein-ligand interaction and enzyme kinetics. Profound understanding of rational design and directed evolution, design of protein libraries, surface display techniques and screening strategies

Basic Course II: Biosynthesis, post-translational modifications and trafficking of recombinant proteins

Lecturers: ALTMANN, GASSER, MACH, MATTANOVICH, STÖGER, STRASSER, WILSON

A. Biosynthesis and post-translational modifications of recombinant proteins

• Biosynthesis of cytosolic and secretory proteins
  
• Protein folding, quality control and co-factor incorporation (heme, flavin) within the cytosol and the secretory pathway
  
• Post-translational modification I: N- and O-glycosylation in biotechnologically relevant organisms
  
• Post-translational modification II: Role of glycosylation in targeting, turnover and immunology of recombinant proteins
  
• Post-translational modification III: phosphorylation, hydroxylation, carboxylation, acetylation, methylation etc. and their functional relevance
  
• Analysis of post-translational modifications I : Chromatographic and electrophoretic techniques
  
• Analysis of post-translational modifications II: Mass spectrometry
  
• Proteomics: Concepts and recent developments
  

Outcomes: Improved knowledge of protein biosynthesis and post-translational protein modifications and their functionalities. Profound understanding of the relevance of post-translational protein modifications for the production and application of recombinant proteins. Knowledge of state-of-the-art proteomics techniques.

B. Intracellular protein trafficking and its biotechnological relevance

• General concepts of intracellular transport processes
  
• The secretory pathway: Events within the endoplasmic reticulum
  
• The secretory pathway: Roles of the Golgi apparatus
  
• Regulated and non-canonical secretion
  
• Endocytosis, endosomes and lysosomes
  
• Protein secretion in yeasts and filamentous fungi
  
• Protein storage organelles
  
• Intracellular protein degradation pathways

Outcomes: Profound understanding of intracellular protein trafficking and protein modification and degradation in eukaryotic cells. Comprehensive knowledge of the properties of eukaryotic expression systems with respect to protein secretion and protein sorting.

Basic Course III: Expression systems and cell factories

Lecturers: BORTH, BUYEL, GASSER, GRABHERR, GRILLARI, KUNERT, MATTANOVICH, PETERBAUER

A. Protein expression systems

• Regulation of gene expression
  
• Protein production and stress caused by high-expression levels
  
• Vector design and transfection methods
  
• Establishment of recombinant cell cultures
  
• Strain development and strain optimization
  
• Metabolic engineering, metabolomics and metabolite quantification
  

Outcomes: Students will be made familiar with the principles of recombinant protein production in an integrative, multi-dimensional approach. Increased understanding of the impact of various cellular parameters on recombinant protein quality and yield.

B. Cell factories

• Bacterial cell factories
  
• Yeast and fungal cell factories
  
• Plant cell factories
  
• Insect cell factories
  
• Mammalian cell factories
  
• Viruses as vectors for recombinant protein production
  
• Bioprocess requirements for different cell factories
  
• Cell-free protein expression systems
  

Outcomes: Improved knowledge of specific properties of different protein factories, their advantages and disadvantages, specific requirements for cultivation and large scale production.

Basic Course IV: Bioinformatics and molecular modelling

Lectures: LUDWIG,OOSTENBRINK, ZANGHELLINI

A. Bioinformatics

• What is a gene
  
• How do we measure its activity
  
• Genome Scale Assays I
  
• Genome Scale Assays II
  
• Microarray analysis
  
• New trends in comp. genomics
  
• Multivariate data analysis
  
• Phylogenetics
  
• Multivariate data analysis
  
• Biostatistics

Outcomes: Knowledge on how to use relevant tools of bioinformatics in all steps of production of recombinant proteins, ranging from genome and gene analysis, expression profiling, genomic and postgenomic technology platforms, data acquisition, analysis and interpretation.

B. Molecular modelling

• Structure determination/design
  
• Virtual screening / drug design
• Modeling and mol. interactions
• Sampling and ensembles
• Boundary conditions and analysis
• Calculation of free energies
• Mass transfer properties of biomolecules
  
• Modelling of protein chromatography

Outcomes: Understanding of basic concepts of modelling strategies for proteins. Ability to link the biophysical properties of proteins with design strategies for protein purification.