Contents

UE9.620 Transcriptomics, proteomics, bioinformatics

High- and low-throughput transcriptomics; DNA and RNA chips; sequencing techniques (libraries, long-SAGE, nano-CAGE, RNASeq); new tools for high-throughput sequencing

Proteomics: separation systems coupled to mass-spectrometry; qualitative and quantitative mass-spectrometry; clinical applications of proteomics

Bioinformatics: sequence alignment algorithms; prediction of RNA and protein secondary and tertiary structures; approaches for analysis of high-throughput sequencing data

UE 9.621 Advanced genetic engineering

Strategies for recombinant DNA cloning; PCR and optimization of amplification conditions; coning of cDNA; methods for 5′- and 3′-RACE; recombinant protein expression in bacteria; fusion protein tags and purification of the recombinant proteins by affinity chromatography

UE 9.622 Research & development project

Practical course on the conception and development of a university- or industry-based research project; writing a bibliography, data analysis and interpretation; bibliographic database mining; informatics tools for database mining

Personal training: student will prepare an oral presentation on the research project which will be developed in the lab during the second semester

UE 9.623 Scientific communication and management

Structure and preparation of scientific presentations in oral or in poster form; technical tools for data treatment and presentation; ethical issues concerning data manipulation

Organizational aspects of scientific and industrial research in different European countries; Universities, international, European and national agencies for scientific research; foundations, funding of scientific projects and individual fellowships for PhD and post-doctoral studies

UE 10.000 Lab training period (preparing of Master’s Thesis)

Each student will have an opportunity to join a leading European lab for 6 months, during which he/she will carry out a scientific project. At the end of this period, the student will write a report and present orally his(her) data.

UE 9.630 Fundamental RNA Science: Unit A – Diversity, structure, genomics, biosynthesis, processing, cell trafficking (60 h)

Brief introduction to genome architecture and gene expression; synthesis, maturation and functions of various cellular RNAs; differential gene expression during development and cell differentiation; biogenesis and cellular trafficking of RNA-protein complexes

UE 9.630 Fundamental RNA Science: Unit B – Function of RNAs in normal biological process and pathologies (30 h)

Multiple roles of non-coding RNAs (long ncRNA, microRNA and piRNA) in development and differentiation; implication of ncRNAs in pathologies; RNA modification and defects of RNA modification in various human pathologies; biogenesis and cellular trafficking of RNA-protein complexes; links between human pathologies and defects in RNA-protein assembly; splicing regulation in human diseases

UE 9.632 Methods for studying RNAs and RNA-protein complexes

Analysis of synthetic RNA transcripts and native cellular RNAs; techniques and approaches for RNA purification, and quantification and characterization of RNAs; in vitro chemical and enzymatic RNA synthesis; techniques for 2D and 3D analysis of RNA structure

Techniques for in vivo localization of cellular RNAs and studies of their intracellular traffic

Assembly and purification of RNA-protein complexes, and their characterization by different physico-chemical approaches; reconstitution of such complexes in vitro or in cell-free extracts

UE 9.634 RNA-engineering. RNA as target and therapeutic tool

RNA as a biomarker; approaches using antisense RNAs; development and application of siRNA, shRNA, miRNA, ribozymes and other RNA interference tools; correction of defects of RNA splicing in human pathologies

Practical training on RNA manipulation: in vitro synthesis and purification of RNA transcripts; characterization of obtained RNA; application of RT and RT-PCR approaches; RNA modification and analysis of the resulting modified residues

UE 9.631 Molecular enzymology: Unit A – Fundamental enzymes (30 h)

Principles of enzymatic catalysis; cofactors; structure-function relationships; regulation of the enzymatic activity; oligomeric enzymes and their properties (allosteric regulation and cooperativity)

UE 9.631 Molecular Enzymology: Unit B – Enzymes engineering and impact on health sciences (30 h)

Catalytic mechanisms and structural specificity: concepts and experimental tools; enzymes of medical of biotechnological interest; Action mechanisms of chemical or biological inhibitors; Molecular mechanisms of antibiotic resistance and synthesis of a new antibiotics; Drug metabolism; Catalytic antibodies and their therapeutic applications.

UE 9.635 Methods: Unit A – Methods for studying enzymes (30 h)

Kinetic methods for enzyme studies (steady-state, pre-steady-state, and coupled systems); characterization of reaction intermediates − techniques and strategies; methods to study protein-protein and protein-ligand interactions (ITC, SPR, FRET, and mass-spectrometry); approaches for large scale screening and ligand design

UE 9.635 Methods: Unit B – Structural biology (30 h)

X-ray crystallography of biological macromolecules; crystallization conditions and their optimization (soluble and insoluble proteins, membrane proteins, protein-nucleic acid complexes); diffraction of biological crystals; theoretical aspects and applications for macromolecular complexes

Nuclear Magnetic Resonance (NMR) of biological macromolecules; resolution of the 3D structure of biomolecules and the study of their dynamics; studies of macromolecule-ligand interactions; structural proteomics and screening of ligands by NMR

UE 9.633 Molecular Bioengineering: Unit A – Therapeutic applications and biotechnology (30 h)

Links between enzymes and metabolic disorders; directed evolution as a tool for the improvement and creation of new enzymatic activities, including applications, advantages and limitations compared to traditional rational design; new enzymatic technologies; metabolic engineering and its applications

UE 9.633 Molecular Bioengineering: Unit B – Bioengineering and metabolism-associated pathologies (30 h)

Bioengineering of metabolism; metabolomics; principal techniques for biomarkers analysis by LS-MS/MS, GC-MS and NMR; bioinformatics; cell biology tools; phenotyping of mitochondrial metabolism; animal models

Cellular and molecular basis of rare metabolic disorders; dysfunction of mitochondrial b-oxidation; monocarbon metabolism; vitamin B12, isoprenoid, iron, copper and iodine deficiencies

Cellular and molecular basis of complex nutritional disorders; mitochondrial energy metabolism and overnutrition; dysregulation of epigenetic and fetal programming