PHYS 498 EBP :: Physics Illinois :: University of Illinois at Urbana-Champaign
Library: required and optional readings
0-1. How to use micropipettes?
- Lab manual: How to use micropipettes?
0-2. MATLAB
0-3. Forensic PCR
- Lab manual
- Information about the genes we used (PER1, ACTN3, TAS2R38)
- Information about F13A1: https://strbase.nist.gov/str_f13a.htm
- Gel images
- For those who did not have clear bands in the gel image: use this.
- Sequencing Results, Instruction for analyzing sequencing results
1. Luria-Delbruck experiment
- Luria-Delbruck Module Overview
- Protocol for Luria-Delbruck Fluctuation Test
- Additional resources for Luria-Delbruck
- Previous Plate Data
- Lenski_Evolution of Mutators
- online Luria-Delbruck and Phylogenetic experiment guidelines
2. Phylogenetics
- Bacterial Phylogenetics Module Description
- PCR + Electrophoresis Protocol
- Additional resources for Bacterial Phylogenetics module
- Sanger Sequences, Additional 16S sequences, and Carbon Sourcing/Antibiotic Resistance Data
- Carbon Sourcing and Antibiotic Resistance Protocol
- Wose and Fox_Phylogenetic structure
- online Luria-Delbruck and Phylogenetic experiment guidelines
3. Super-resolution fluorescence miccroscopy
- Lab manual social distancing version (Last update: 3/24/2020)
- Paper reading assignment (Last update: 3/24/2020)
- Lab manual (Last update: 03/09/2020)
Main reading
- Introduction to Fluorescence Microscopy: https://www.microscopyu.com/techniques/fluorescence/introduction-to-fluorescence-microscopy
- The Diffraction Barrier in Optical Microscopy: https://www.microscopyu.com/techniques/super-resolution/the-diffraction-barrier-in-optical-microscopy
- Single Molecule Super-Resolution Microscopy: https://www.microscopyu.com/techniques/super-resolution/single-molecule-super-resolution-imaging
- Simple SMLM setup: H. Ma, R. Fu, J. Xu, Y. Liu, A simple and cost-effective setup for super-resolution localization microscopy, Scientific Reports 7, 1542 (2017)
- What is resolution? (Nikon)
- Accuracy vs. Resolution
Further reading
Optical microsopy
- Airy pattern formation: https://micro.magnet.fsu.edu/primer/java/imageformation/airydiskformation/index.html
Fluorescence
- Jablonski Energy Diagram: https://www.olympus-lifescience.com/en/microscope-resource/primer/java/jablonski/jabintro/
4. Optical trap
- Lab manual, Supplementary information
- Reading assignment
- https://phet.colorado.edu/en/simulation/optical-tweezers : This is a cool Java applet that lets you visualize the motion of a bead in the optical trap. Try playing with the fluid properties (changing fluid speed, viscosity and temperature) to see what effect it has on the stability of the trap.
- J. Shaevitz, A Practical Guide to Optical Trapping (http://genomics.princeton.edu/shaevitzlab/OT_Practicle_Guide.pdf)
- K. C. Neuman and S. M. Block, “Optical Trapping,” Rev. Sci. Instrum. 75, 2787 (2004). Pay particular attention to the overview and theory of optical trapping and the sections on calibration techniques.