Programme

Topics

Fundamentals of light propagation in biological tissues
Interactions between light and molecules; electronic states of a molecule and the transitions between them: difference between bioluminescence, phosphorescence, fluorescence and other non-radiative phenomena; interactions between light, cell and tissues; effects of light propagation in biological tissues; fundamentals of the most employed light sources used in biomedical diagnostic devices.

Basics of biology
Cellular structure and types; chemical building blocks; cellular processes (central dogma of Biology): replication, transcription, translation, biosynthesis and energy production; protein classification and function; organization of cells in tissues; morphological and physiological description of the main tissue in human body.

Basic principles of genetic engineering and DNA manipulation
Polymerase chain reaction (PCR); restriction enzymes; cloning process. Genetic manipulation of microorganisms and superior organisms.

Biosensors
Principles; biorecognition; optical transduction; molecular basis of biosensors generation; bioluminescence, colorimetric, fluorescence and FRET-based sensors. Applications of biosensors in human oncology, bioremediation, food safety and drug production. Main devices and imaging techniques employed for biosensor detection.

Super-resolution imaging: techniques and biological applications
Physical principles and biomedical applications of different optical-super-resolution techniques (i.e., two and multi-photon microscopy, STORM, PALM, STED, expansion microscopy, rescan confocal microscopy, LLS, SIM). Physical principles and biomedical applications of different non-optical super-resolution techniques: electron microscopy (TEM, SEM, STEM); AFM.

Microarray Technology
Definitions and applications of Omic Sciences; typology of microarrays (DNA, protein, cell and tissue microarrays).

Photosynthesis
Plastids in plants; light and dark reactions; Calvin cycle and carbon fixation; ecological aspects on photosynthesis; natural and artificial photosynthesis for green energy generation.

Spectral tuning in Biology
Major pigments in biological systems; chemistry behind pigment photoefficiency (resonance theory, chemical environment and modifications in light absorption properties); chromatic acclimation and chromatic adaptation; molecular aspects of chromatic acclimation.

Visual tuning in humans
Human eye anatomy; human eye aberration: wave and chromatic aberrations, intraocular scattering; OCT; retina tissue organization; cytology of rod and cone cells; rhodopsin and retinal: structure and functions; retinal photocycle: molecular isomerization at the basis of vision; phototransduction cascade in vertebrate photoreceptors.
Optogenetics
General description of optogenetic molecular tools; opsins in animals; mechanisms of genetic construct delivery into mammalians; optrodes: applications and limitations.
Photophysiology and Phototoxicity
Vitamin D: photosynthesis and metabolism in human body; evolutionary aspects of vitamin D-mediated regulation of calcium homeostasis; human skin organization and differentiation of skin cell types; melanin production and functions; effects of ultraviolet radiation; effects of photodamaging on cells; mechanisms of DNA repair after photodamaging: homologous recombination, mismatch repair, Nucleotide Excision Repair, photolyase and UVR-mediated repair; photosensitivity diseases; light-dependent circadian cycle.

Fundamentals of the photothermal therapeutic effects of light sources
Interaction of light and physical sensing; phototherapy; photodynamic therapy; photosensitizing drugs.

Guided tour in the RomaTre Department of Sciences on the facilities and equipment studied in the course (luminometer, fluorimeter, flow-cytometer, devices for genetic manipulation).
Guided tour in the RomaTre Department of Sciences on confocal microscopes.
Guided tour in the LIME laboratories on the TEM, SEM and AFM microscopes.

Core Documentation

Prasad PN. Introduction to Biophotonics 2nd edition. Wiley-Interscience, Hoboken, NJ. 2003;
Björn LO. Photobiology: The Science of Life and Light, 2nd edition. Springer-Verlag, New York. 2008.
Alberts B, Bray D, Hopkin K, Johnson AD, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Essential Cell Biology. 3rd edition. Garland Science. 2010.

Reference Bibliography

Alberts B, Bray D, Hopkin K, Johnson AD, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Essential Cell Biology. 3rd edition. Garland Science. 2010. Artal P. Image Formation in the Living Human Eye. Annu Rev Vis Sci. 2015;1:1-17. doi:10.1146/annurev-vision-082114-035905. Björn LO. Photobiology: The Science of Life and Light, 2nd edition. Springer-Verlag, New York. 2008. Dai C, Choi S. Technology and Applications of Microbial Biosensor. Open Journal of Applied Biosensor 2013;2(3):83–93. doi:10.4236/ojab.2013.23011. Deubner J, Coulon P, Diester I. Optogenetic approaches to study the mammalian brain. Curr Opin Struct Biol. 2019;57:157-163. doi:10.1016/j.sbi.2019.04.003. Dolmans DE, Fukumura D, Jain RK. Photodynamic therapy for cancer. Nat Rev Cancer. 2003 May;3(5):380-7. doi: 10.1038/nrc1071. Dufour S, De Koninck Y. Optrodes for combined optogenetics and electrophysiology in live animals. Neurophotonics. 2015;2(3):031205. doi:10.1117/1.NPh.2.3.031205. Gutu A, Kehoe DM. Emerging perspectives on the mechanisms, regulation, and distribution of light color acclimation in cyanobacteria. Mol Plant. 2012;5(1):1-13. doi:10.1093/mp/ssr054. Lim JW, Ha D, Lee J, Lee SK, Kim T. Review of micro/nanotechnologies for microbial biosensors. Front Bioeng Biotechnol. 2015 May 11;3:61. doi: 10.3389/fbioe.2015.00061. Lodish H, Berk A, Zipursky SL, et al. Molecular Cell Biology. 4th edition. New York: W. H. Freeman; 2000. Lucidi M, Runci F, Rampioni G, Frangipani E, Leoni L, Visca P. New Shuttle Vectors for Gene Cloning and Expression in Multidrug-Resistant Acinetobacter Species. Antimicrob Agents Chemother. 2018 Mar 27;62(4):e02480-17. doi: 10.1128/AAC.02480-17. Lucidi, M, Hristu, R, Nichele, L, et al. STED nanoscopy of KK114‐stained pathogenic bacteria. J. Biophotonics. 2020; e202000097. doi: 10.1002/jbio.202000097. Palczewski K. G protein-coupled receptor rhodopsin. Annu Rev Biochem. 2006;75:743-767. doi:10.1146/annurev.biochem.75.103004.142743. Pastrana E. Optogenetics: controlling cell function with light. Nature Methods. 2011; 8:24-25. Prasad PN. Introduction to Biophotonics, 2nd edition. Wiley-Interscience, Hoboken, NJ. 2003. Schermelleh L, Ferrand A, Huser T, et al. Super-resolution microscopy demystified. Nat Cell Biol. 2019;21(1):72-84. doi:10.1038/s41556-018-0251-8. Sezgin E. Super-resolution optical microscopy for studying membrane structure and dynamics. J Phys Condens Matter. 2017;29(27):273001. doi:10.1088/1361-648X/aa7185. Stracy M, Jaciuk M, Uphoff S, et al. Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli. Nat Commun. 2016;7:12568. Published 2016 Aug 26. doi:10.1038/ncomms12568. Wang W, Nossoni Z, Berbasova T, et al. Tuning the electronic absorption of protein-embedded all-trans-retinal. Science. 2012;338(6112):1340-1343. doi:10.1126/science.1226135. Zheng DW, Chen Y, Li ZH, et al. Optically-controlled bacterial metabolite for cancer therapy. Nat Commun. 2018;9(1):1680. Published 2018 Apr 26. doi:10.1038/s41467-018-03233-9.

Type of delivery of the course

Lectures Laboratory experiences Seminars

Type of evaluation

The exam consists of an oral evaluation on the topics presented during the course