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Biophysical Techniques

SIGNUP SHEET on googledocs

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This section is a collection of presentations of students made as a part of their assignments. Topics are picked by you from a list. The presentation time is 15 minutes and scoring is based on

. The talk itself must have the following components (i) introduction to the technique, (ii) physical principle/algorithm/maths, and (iii) biological application. Please enter topic of choice here. The dates will be updated on a weekly basis.

S. No. Date Presenter Technique Reference
1 14-Sep-2012 A. Pathak Atomic force microscopy for imaging Kuznetsova (2007) Atomic force microsopy probing of cell elasticity. Micron. 38: 824
2 14-Sep-2012 Ketakee Ghate Fluorescence activated cell sorting (FACS) Freed NE et al. (2008) A simple screen to identify promoters conferring high levels of phenotypic noise. PLoS Genet. 4(12):e1000307.
3 21-Sep-2012 V. Krithika Microfluidics for bacterial chemotaxis Mao et al. (2003) A sensitive, versatile microfluidic assay for bacterial chemotaxis. PNAS USA 100: 5449-5454.
4 21-Sep-2012 Roopali Pradhan Fluorecence recovery after photobleaching (FRAP) to estimate diffusion coefficients of molecules Mika JT et al. (2011) Evaluation of pulsed-FRAP and conventional-FRAP for determination of protein mobility in prokaryotic cells.PLoS One. 6(9):e25664.
5 12-Oct-2012 2D gel electrophoresis for quantification of protein abundance Fey & Larsen (2001) 2D or not 2D. Curr. Op. Chem. Biol. 5:p26
6 12-Oct-2012 DNA sequencinging by Sanger dye termination and denaturation. Chen et al. (2010) DNA sequencing by denaturation: experimental proof of concept with an integrated fluidic device. Lab on a Chip. 10:p1153.
7 12-Oct-2012 DNA nanopore sequencing (a) Cherf et al. (2012) Automated forward and reverse ratcheting of DNA in a nanopore at 5-Angstrom precision. Nat. Biotech. 30, p344-348.
8 12-Oct-2012 DNA nanopore sequencing (b) Manrao et al. (2012) Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotech.30, 349–353
9 Atomic force microscopy for DNA flexibility measurement Wiggins et al. (2006) High flexibility of DNA on short length scales probed by atomic force microscopy. Nat. Nanotech. 1: 137 - 141
10 DNA devices Modi et al. (2009) A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nature Nanotech. 4: 325
11 DNA origami and motors Wickham et al. (2012) A DNA-based molecular motor that can navigate a network of tracks. 7: 169.
12 Dynamic light scattering Y. Georgalisa et al. (2012) Light scattering studies on Ficoll PM70 solutions reveal two distinct diffusive modes. J. Colloid & Interface Science. Volume 386, Issue 1, Pages 141–147
13 Surface plasmon resonance in biology Kim D. et al. (2012) Heptameric Targeting Ligands against EGFR and HER2 with High Stability and Avidity.PLoS One. 7(8):e43077.
14 Two-photon microscopy for tissue imaging Johannssen HC, Helmchen F. (2012) Two-photon imaging of spinal cord cellular networks. Exp Neurol.
15 Confocal laser scanning microscopy Cheng et al. (1999) Amplitude distribution of calcium sparks in confocal images: theory and studies with an automatic detection method. Biophys J. 76(2): 606–617.
16 4pi Microscopy Hüve et al. (2008) 4Pi Microscopy of the Nuclear Pore Complex. Biophys J. 95(2): 877-885.
17 Fluorescence loss in photobleaching (FLIP) to estimate molecular mobility Judd et al. (2003) Fluorescence bleaching reveals asymmetric compartment formation prior to cell division in Caulobacter. PNAS 100(14):8235-40.
18 Single plane illumination microscopy (SPIM)
19 Dynamic light scattering for in vitro protein measurements
20 Photoactivation in diffusion measurements Bakshi S et al. (2011) Subdiffraction-limit study of Kaede diffusion and spatial distribution in live Escherichia coli.Biophys J.101(10):2535-44.
21 STORM nanoscopy
22 STED nanoscopy
23 Second harmonic generation and CARS
24 Magnetic tweezers to study molecular motors Kim & Saleh (2009) A high-resolution magnetic tweezer for single-molecule measurements Saleh1,2,Nucleic Acids Res. 37(20): e136.
25 Optical tweezers Moffit et al. (2008) Recent advances in optical tweezers. Ann. Rev. Biochem. 77: 205-228.
26 Optical tweezers to study forces in constant force mode Chen et al. (2009) Stretching Submicron Biomolecules with Constant-Force Axial Optical Tweezers. Biophys J. 96: 4710-4708
27 Cell traction force microscopy
28 Laser nanosurgery
29 Femtosecond resolved absorption spectroscopy
30 Isothermal calorimetry (ITC)
31 ITC to measure enzyme kinetics
32 Patch clamp
33 Patch clamp for measuring single ion-channel potentials
34 Scanning electron microscopy (SEM)
35 Scanning tunneling microscope (STM)
36 Fluorescence resonance energy transfer (FRET) Violin et al. (2003) A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C. J Cell Biol. 161(5):899-909.