PhD & MS programs > Medical Biophysics: Biomolecular Imaging > Ph.D. Minor in Biomolecular Imaging > Introduction to Biomolecular Imaging

Advanced Molecular Imaging, G614

Course Description

The course goal is to introduce the imaging methods and concepts that are used in molecular structure and dynamics analysis. The course emphasizes general principles of macromolecular structure and dynamics applied to ensemble and single molecules. Methodologies use visible light, electrons, x-ray diffraction and atomic force mapping as modes of molecular imaging. Christoph Naumann is the Course Director.

Prerequisites

F592 (Introduction to Biomolecular Imaging)

Course Instructors

Instructor Department
Decca Physics
Gattone Anatomy & Cell Biology
Hurley Biochemistry & Molecular Biology
Naumann Chemistry
Yu Nephrology

Required and Recommended Texts

No textbook will be required for this course.

Evaluation and Grading

Three closed book exams will take ~2 hours each. The final is non-cumulative. Laboratory reports will be graded and contribute 10% of the final grade.

Syllabus

Lecture Topic Faculty
Fundamentals of biomolecular structure and dynamics
1

Introduction:
Proteins as enzymes, engines, partners in complexes DNA as encoder, gene regulator Chemicals as reporters of molecular events

 Naumann

2
3

Protein structure and dynamics

  • Energetics of folding, intramolecular bonding
  • Secondary and tertiary structure predictive algorithms
  • Conformational changes

Plasma membrane structure and dynamics

  • Phospholipid bilayer
  • Membrane protein
 Hurley

4
5

DNA structure and dynamics

  • Structure/function of transcription and replication
  • Histones and DNA accessibility
  • Specialized structures: centromeres/telomere

Cytoskeleton structure and dynamics

  • Cytoskeletal filaments (actin, tubulin, intermediate filaments)

Extracellular matrix structure and dynamics

  • Proteoglycans
  • Collagen
 Hurley
Structural Characterization of biomolecules: Ensemble-averaging techniques
6
7
8
9

X-ray Diffraction

  • Spatial Resolution, Physical limits
  • Technical and theoretical considerations of sample preparation
  • Data collection
  • Data analysis
  • Examples: Protein structure analysis, Lipid structure analysis, DNA structure analysis
 Hurley
10
11
12 		Crystallization and X-ray Diffraction
Laboratory Sessions I, II, III		 Hurley
13
14

NMR

  • Spatial resolution, Physical limits
  • Data collection/analysis
  • Examples: Protein structure analysis, Lipid structure analysis
 Hurley
15
16

Circular dichroism

  • Spatial resolution, Physical limits
  • Technical and theoretical considerations of crystal formation
  • Data collection/analysis
  • Examples: Protein structure analysis, DNA structure analysis
 Hurley
Dynamics and kinetics of biomolecules: Ensemble-averaging techniques
17

Fluorescence microscopy

  • Temporal resolution, Physical limits
  • Data collection/analysis
  • Examples: Lipid dynamics (FRAP), Actin filament dynamics
 Naumann
18

Light scattering

  • Resolution, Physical limits
  • Data collection/analysis
  • Examples: Receptor-ligand binding
 Naumann
19
20

Surface plasmon resonance spectroscopy

  • Temporal resolution, Physical limits
  • Data collection/analysis
  • Examples: Receptor-ligand binding kinetics
 Hurley
21
22

Fluorescence correlation spectroscopy

  • Temporal resolution, Physical limits
  • Data collection
  • Data analysis (Autocorrelation/Crosscorrelation)
  • Examples: Receptor-ligand binding kinetics
  • Single burst analysis
  • Examples: Lipid dynamics, Protein dynamics
 Yu
Single Molecule Imaging
23
24

Introduction: Ensemble averaging versus single molecule detection techniques

Optical single molecule imaging

  • Single molecule tracking
  • Spatial and temporal resolution, Physical limits
  • Data collection/analysis
  • Examples: Lipid dynamics, Protein dynamics
 Naumann
25

Fluorescence energy transfer (FRET)

  • Spatial and temporal resolution, Physical limits
  • Examples: Protein-protein interactions, Protein folding
 Naumann
26
27 		Single molecule dynamics
Laboratory Session IV-V 		Naumann/Decca

28
29
30

Laser tweezer

  • Spatial and temporal resolution, Physical limits
  • Signal analysis
  • Examples: Membrane receptor dynamics, Cytoskeleton morphology

Atomic force microscopy

  • Resolution, Physical limits
  • Data collection/analysis
  • Examples: Receptor-ligand binding strength, microtubule motor
 Decca
31
32
33

Electron microscopy (SEM/TEM)

  • Resolution, Physical limits
  • Data collection/analysis
  • Examples: Membrane, DNA structure
 Gattone
34 Molecular Electron Microscopy
Laboratory Session VI 		Gattone
Two Regular Exams and a Final Exam

 

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