EXPERIMENTAL BIOPHYSICS

The course is one of the compulsory educational activities of the Master's Degree in Engineering Physics, curriculum physics of the Brain, and will allow the student to acquire the knowledge and the understanding of the fundamental and applied concepts of experimental biophysics.

1. Knowledge and Understanding
At the end of the course, the student must demonstrate having acquired the fundamental principles of biophysics, with particular reference to molecular biophysics, membrane biophysics, and cellular biomechanics. The student must also understand both qualitative and quantitative aspects of the experimental techniques used in these fields, such as Atomic Force Microscopy, Optical Tweezers, Magnetic and Acoustic Tweezers, Electron Microscopy, Vibrational Microscopy, Super-Resolution Optical Microscopy, and X-ray Diffraction and Scattering.

2. Ability to Apply Knowledge and Understanding
At the end of the course, the student must be able to apply the knowledge acquired in point D1 to hypothesize biophysics experiments with the introduced techniques, discuss and analyze in detail the experimental data provided in order to independently interpret the experiment results. The student must know the statistical rules for interpreting biological results and be able to apply significance tests to the data.

3. Autonomy of Judgment
At the end of the course, the student will be able to evaluate the experimental methods discussed in various contexts, judge which is most appropriate for studying the mechanical properties of biological systems with different rigidity, size, and corrugation, and critically evaluate the literature articles on these topics that will be proposed.

4. Communication Skills
At the end of the course, the student must demonstrate having acquired the basic concepts referred to in point D1, as well as appropriate language to precisely discuss various biophysics topics. The student must be able to critically and constructively judge the topics covered in the course.

5. Learning Skills
At the end of the course, the student must be able to show an adequate level of understanding of the topics covered, be able to critically read published works in specialized journals in the field, and evaluate the proposed techniques on specific systems in a comparative manner, highlighting the quantitative aspects of the experiments.

The students are not required to have followed any specific course. Knowledge of basic solid mechanics and statistical mechanics could be an advantage.

From inter-molecular forces to mechano-biology: an introduction to experimental biophysics. The course will introduce the students to physicals concepts, formalisms, methodologies and instrumentation which can be/have been usefully applied to biology and medicine.

The course is composed by two parts. In the first part, after an introduction to the fundamental concepts of molecular biology, we will describe the structure and function of proteins and nucleic acids, together with fundaments of the physics of biopolymers, inter molecular forces and self-assembling. Protein structure-function relationship will be discussed, folding/unfolding and formation of amyloid fibrils. Finally, we will discuss the structural organization of the cell membrane, protein-ligand interactions and molecular bio-recognition.
In the second part of the course, after a rapid overview of the main concepts of solid mechanics, fluid dynamics and statistical mechanics, we will concentrate on the main aspects of molecular mechanics, cell membrane and whole cell mechanics, describing phenomena as cell adhesion, migration and mechano-transduction which most of the vital functions at the cell level as well as at the superior organism level.

For all the topics examples taken from the recent literature and from the research activity of the teachers will be given. Also, the main modern experimental techniques applied to biophysics will be described in detail. At the end of the course there will be a visit of the life science laboratories in Area Campus in Basovizza, where the students might take part to an experiment, concurred with the course teachers.

First part – Fundaments of molecular biophysics

1. Introduction to cellular biophysics and biomolecules. Self-assembling and inter-molecular forces (2h)
2. Proteins: structure, shape and function. The folding-structure problem. Protein folding/unfolding and protein fibers. Membrane proteins (4h)
3. Nucleic Acids: structure, transmission of genetic information, basic genetic engineering; other biopolymers (4h)
4. Structure and transport in cell membrane. Ions in water, ion and molecular transport through the membrane. Formation of extracellular vesicles. Cell signalling (2h)
5. Techniques to study macromolecules structure/function (4h):
Optical spectroscopies (fluorescence, IR, Raman)
X-ray Crystallography
ElectronMicroscopy
NMR
6. Protein-ligand equilibrium interactions; biochemical kinetics; techniques used (Surface plasmon resonance, calorimetry) (2h)
7. Biosensors (2h)
8. Single molecule interactions and relative techniques (FRET, Foster Resonant Energy Transfer, Atomic Force Microscopy, Coherent X-ray diffraction (2h)


Secon part – Cellular mechanics and mechano-biology

1. Introduction to mechano-biology (2h)
2. Physical principles (8h)
2.1. Mechanical forces, viscoelasticity at molecular and cell level
2.2. Thermal forces and diffusion
2.3. Chemical forces
2.4. Motor proteins (types, working principles)
3. Mechanics of the Cytoskeleton (4h)
3.1. Cytoskeleton structure
3.2. Force generation by the cytoskeleton and cell motility
4. Cellular Mechanotransduction (2h)
5. Experimental techniques – for cell mechanics (6h)
5.1. Overview on force application and force sensing techniques
5.2. Optical Tweezers – force spectroscopy and manipulation
5.3. Magnetic and Acoustic Tweezers
5.4. Advanced Optical Microscopy techniques (Super-Resolution, FRET, DHM)


Third part – Experimental activity

1. Individual or small groups experimental activities, to be defined during part one and two of the course (4-8h)

1. J. Howard, Mechanics of Motor Proteins and the Cytoskeleton, Sinauer Associates Inc., 2001
2. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell, 4th edition, New York: Garland Science; 2002.
3. D. Boal, Mechanics of the Cell, Cambridge Univ. Press, 2012
4. C.R. Jacobs, H. Huang, R. Y. Kwon, Introduction to Cell Mechanics and Mechanobiology, Garland Science Taylor & Francis, 2013.
5. J.N. Israelachvili, Intermolecular and Surface Forces, Elsevier, Third edition 2011.
6. Scientific articles – pdf collection; cited with the slides associated to the lectures.
7. Slides presentation for the lectures, pdf.

Oral exam

-Excellent (30 -30 cum laude): excellent knowledge of topics, remarkable language property, excellent analytical ability; the student/ess is able to brilliantly apply theoretical knowledge to concrete cases.
-Very good (27 -29): good knowledge of topics, remarkable language property, good analytical ability; the student/ess is able to correctly apply theoretical knowledge to concrete cases.
-Good (24-26): good knowledge of main topics, fair language property; the student/ess shows adequate ability to apply theoretical knowledge to concrete cases.
-Satisfactory (21-23): the student/ess does not show full mastery of the topics
main topics of the teaching, although he/she possesses the fundamental knowledge; however, he/she shows satisfactory ownership of language and sufficient ability to apply theoretical knowledge to concrete cases.
-Sufficient (18-20): minimal knowledge of the main topics of the teaching and of the
technical language, limited ability to adequately apply theoretical knowledge to concrete cases.
-Insufficient (<18): the student(s) does not possess acceptable content knowledge of the various program topics.

Lectures and lab experiences under the teachers’ guide.

English

oral