Course Coordinators: I. Zarkadis (Professor), V. Stamatopoulou (Assistant Professor)

The course is divided into two modules (I and II), taught in the first and second semester, respectively. The aim of this course is to familiarize graduate students with the fundamental principles and concepts governing the methods for approaching research and analytical problems in Biomedical Sciences. The course includes 4 hours of lectures and 1 hour of laboratory demonstration per week.

Educational Objectives

The course “Research Methodology I and II” introduces the basic methodological approaches applied in research or diagnostics in Biomedical Sciences, as well as advanced emerging biomedical research technologies.

The course aims to:

• Provide students with essential knowledge on methodological approaches currently applied in modern biomedical sciences for research and diagnostics, along with the necessary skills to select the appropriate methodologies and stay updated with future developments.
• Attract graduate students’ interest in research and its methodologies through solving specific problems.
• Familiarize students with research thinking and in particular:
  • Understanding how to formulate and address research problems.
  • Selecting a study strategy.
  • Identifying the prerequisites for applying a methodology (materials, equipment, resources).
  • Evaluating research findings.

Course Content

The syllabus is divided into modules. Each module includes research or clinical examples of applications in Biomedical Sciences, in order to highlight the importance of experimental approaches to biological problems. The presentation of a research or a clinical problem often precedes the discussion of methodological approaches. In addition to theoretical presentations, laboratory demonstrations are included.

Introduction to Research Methodology

Module 1: Structural-Functional Analysis of Biological Macromolecules
Coordinator: V. Stamatopoulou (Assistant Professor)

• Topics Covered:

Principles of solution preparation, biomolecule separation methods (fractional precipitation, centrifugation, electrophoretic and chromatographic methods), structural determination methods (NMR spectroscopy, macromolecular crystallography principles), footprinting analysis, cross-linking techniques, and affinity photolabeling techniques, determination of macromolecule activity through enzymatic kinetics, quantification of biomolecules spectroscopically, either directly or indirectly using enzymology.

• Laboratory Demonstration:

Centrifugation, ultracentrifugation, protein, RNA, and DNA electrophoresis, DNA microarrays, Bioanalyzer, qRT-PCR, Phosphoimager, NGS platform.

Module 2: Qualitative and Quantitative Analysis of Biological Macromolecules
Coordinator: A. Mouzaki (Professor)

• Topics Covered:

Antibodies and their production in vivo and in vitro, ELISA principles and its applications, FACS principles and its applications for cell and soluble molecule characterization (Cytometric bead arrays, CBA), principles of creating protein and gene-based vaccines for prevention and therapy, immunohistochemistry, automated clinical chemistry analysis methods.

• Laboratory Demonstration:

FACS and CBA

• Laboratory Exercises:

Techniques for identifying red blood cell antigens and antibodies. Direct and indirect Coombs tests for detecting anti-red blood cell autoantibodies in blood.

Module 3: Functional Analysis of Genes and Genomes – Large-Scale Methods
Coordinator: V. Roukos (Assistant Professor)

• Topics Covered:

In silico Analysis – Bioinformatics, PCR, sequencing, Next-generation sequencing, mutation/Polymorphism detection (SNPs, Copy Number Variations), chromosomal analysis, karyotyping, FISH, gene expression analysis, methods for studying protein interactions and functions, gene silencing/overexpression (reverse/forward genetics, knock-out, RNAi, transgenic animals), principles of large-scale methodologies, functional genomics, microarrays, proteomics, systems biology, and modeling.

• Laboratory Demonstration:

Confocal, PCR, Real-Time PCR, Microarray hybridizater-scanner.