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OSE4721 - Biophotonics

This course is an introduction to photobiology (interaction of light with biological matter), tissue optics, light-induced cellular processes, optical biosensors, and cellular and molecular imaging.

Credits: 3 hours

Prerequisite: Not specifically required but OSE 3052 (Introduction to Photonics) would be a helpful course.

Detailed Description:
Biophotonics is an emerging multidisciplinary field where light-based methods are utilized to reveal biological mechanisms, and diagnose or treat several diseases. This course introduces the basics of biology and photonics, and provides the most relevant and important application examples selected from chemistry, biology, pharmacology and medicine. For examples, it includes how to detect and identify new viruses and how to manipulate the brain of mouse with light, etc. More than ten Nobel prizes will be mentioned during the lecture. No prior knowledge is required to take the course; however, basic knowledge of optics will be helpful.

List of Topics:

  1. Overview of Biophotonics
    • Biology and Biophotonics
    • Medicine/Clinics and Biophotonics
  2. Fundamentals of Biology
    • The facts of life (Building blocks, central dogma, components of cells…)
    • Biology by the numbers
  3. Basics of light-matter interactions in molecules, cells and tissues
    • Nature of light
    • Refraction, reflection, interference, diffraction
    • Intensity, phase, polarization, scattering, Raman, fluorescence
    • Optical properties of bio-materials
  4. Central dogma #1: DNA
    • How to use light to find out information of our genomes: DNA sequencing
    • DNA replication/repair
    • Illumina and PacBio sequencing
    • Virus detection and identification using PCR
  5. Central dogma #2: RNA
    • Why is each tissue different from others?
    • DNA to RNA transcription
    • Count RNA numbers in cells/tissues: qPCR and RNA-FISH
  6. Central dogma #3: Proteins
    • Enzyme, antibody
    • Every cell has different gene expression level: Flow cytometry
    • Dissect folding dynamics of proteins: Single molecule FRET
    • Drug screening: SPR sensor
  7. Bioimaging #1: Non-fluorescence-based microscopy
    • Bright-field/Phase contrast/Dark-field/DIC microscopy
    • Raman imaging (SRS microscopy)
  8. Bioimaging #2: Fluorescence-based microscopy
    • Fluorophores (Green fluorescent proteins…)
    • Epi/Confocal/TIRF microscopy
    • Super-resolution fluorescence imaging
  9. BRAIN initiative
    • Interrogate brain with light: Optogenetics
    • Deep tissue imaging with multi-photon microscopy & light-sheet microscopy
  10. Diagnosing diseases with light
    • Endoscopy
    • Optical coherence tomography (OCT): Application to ophthalmology
    • Photoacoustic tomography: Application to early cancer detection
  11. Treatment of diseases with light
    • Killing cancer cells with light: Photodynamic therapy
    • Tissue engineering with light

Learning Outcomes:
A main goal of the lecture is to help the students become familiar with the field and thus they will be able to understand language of biology and photonics, and digest contemporary biophotonics techniques.