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(Sept 28: Nucleic acid technologies)
m (Nov 9: O''Italic text''ptical Microscopy: Biomechanics)
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# Design of Fluorescence Wide Field Microscopy (2 person)
# Design of Fluorescence Wide Field Microscopy (2 person)
==Nov 9: O''Italic text''ptical Microscopy: Biomechanics==
==Nov 9: Optical Microscopy: Biomechanics==
#[http://www.media.mit.edu/nanoscale/courses/BE309/private/Presentations/Sessions345/block_PNAS2003.pdf S. M. Block ''et al.'', "Probing the kinesin reaction cycle with a 2D optical force clamp," ''PNAS'' '''100'''(5), pp. 2351-56 (2003).]
#[http://www.media.mit.edu/nanoscale/courses/BE309/private/Presentations/Sessions345/block_PNAS2003.pdf S. M. Block ''et al.'', "Probing the kinesin reaction cycle with a 2D optical force clamp," ''PNAS'' '''100'''(5), pp. 2351-56 (2003).]
#[http://www.media.mit.edu/nanoscale/courses/BE309/private/Presentations/Sessions345/verveer_science2000.pdf P. J. Verveer ''et al.'', "Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane," ''Science'' '''290''' pp. 1567-70 (2000).]
#[http://www.media.mit.edu/nanoscale/courses/BE309/private/Presentations/Sessions345/verveer_science2000.pdf P. J. Verveer ''et al.'', "Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane," ''Science'' '''290''' pp. 1567-70 (2000).]

Revision as of 00:44, 20 September 2007

20.309: Biological Instrumentation and Measurement

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Sept 28: Nucleic acid technologies

  1. J. W. Hong, et al. "A nanoliter-scale nucleic acid processor with parallel architecture," Nature Biotech. 22(4): pp. 435-439 (2004). Alice Macdonald
  2. L Warren, et al. "Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR" Proc. Nat. Acad. Sci. 2006. OR E.A. Ottesen et al. "Microfluidic Digital PCR Enables Multigene Analysis of Individual Environmental Bacteria" Science 2006. Kalvin Kao
  3. J. M. Nam, C. S. Thaxton, C. A. Mirkin "Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins," Science 301(5641): pp. 1884-1886 (2003). Angela Wu
  4. E. Winfree, et al. "Design and self-assembly of two-dimensional DNA crystals," Nature 394(6693): pp. 539-544 (1998). AND P. W. K. Rothemund "Folding DNA to create nanoscale shapes and patterns," Nature 440(7082): pp. 297-302(2006). Erika Erikson and Danielle Carpenter

Oct 12: Scanning probe microscopy I

  1. A. Engell and D. J. Muller "Observing single biomolecules at work with the atomic force microscope," Nature Stuct. Biol. 7(9): pp. 715-718 (2000). Sasha Brophy
  2. F. Schwesinger et al. "Unbinding forces of single antibody-antigen complexes correlate with their thermal dissociation rates" PNAS 97(18): pp. 9972-9977 (2000). Elizabeth Riley
  3. D. Rugar et al. "Single spin detection by magnetic resonance force microscopy," Nature 430(6997): pp. 329-332 (2004).
  4. 20.309 Lab Module 1 -- measuring DNA melting curves

Oct 16: Scanning probe microscopy II

  1. G. E. Fantner et al. "Sacrificial bonds and hidden length: Unraveling molecular mesostructures in tough materials" Biophys. J 90(4): pp. 1411-1418 (2006). Amanda Morris
  2. SY Lee et al. "Chemomechanical mapping of ligand-receptor binding kinetics on cells" PNAS 104: pp. 9609-9614 (2007). Naiyan Chen
  3. MJ Rosenbluth, WA. Lam, and DA Fletcher, “Force Microscopy of Nonadherent Cells: A Comparison of Leukemia Cell Deformability” Biophysical Journal 90: pp. 2994-3003 (2006). Sangjin Ryu
  4. I. Rousso et al., "Microsecond atomic force sensing of protein conformational dynamics: Implications for the primary light-induced events in bacteriorhodopsin," PNAS 94, pp. 7937-41 (1997).
  5. 20.309 Lab Module 2 – AFM Lab

Nov 2: Optical Microscopy: Imaging

  1. Z. E. Perlman et al., "Multidimensional Drug Profiling by Automated Microscopy," Science 306 pp. 1194-98 (2004).
  2. D. Axelrod, "Total Internal Reflection Fluorescence Microscopy in Cell Biology," Traffic 2 pp. 764-774 (2001).
  3. E. Chung, D. Kim, and P. T. C. So, "Extended resolution wide-field optical imaging: objective-launched standing-wave total internal reflection fluorescence microscopy," Opt. Lett. 31(7) pp. 945-7 (2006).
  4. T. Ichimura et al., "Application of tip-enhanced microscopy for nonlinear Raman spectroscopy," Appl. Phys. Lett. 84(10), pp. 1768-70 (2004).
  5. T-W. Koo, S. Chan, and A. A. Berlin, "Single-molecule detection of biomolecules by surface-enhanced coherent anti-Stokes Raman scattering," Opt. Lett. 30(9), pp. 1024-6 (2005).
  6. M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic reconstruction optical microscopy (STORM)," Nature Methods 3:793-795 (2006).
  7. Design of Fluorescence Wide Field Microscopy (2 person)

Nov 9: Optical Microscopy: Biomechanics

  1. S. M. Block et al., "Probing the kinesin reaction cycle with a 2D optical force clamp," PNAS 100(5), pp. 2351-56 (2003).
  2. P. J. Verveer et al., "Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane," Science 290 pp. 1567-70 (2000).
  3. S. Yamada, D. Wirtz, and S. C. Kuo, "Mechanics of Living Cells Measured by Laser Tracking Microrheology," Biophys. J 78(4), pp. 1736-47 (2000).
  4. B. Yap and R. D. Kamm, "Cytoskeletal remodeling and cellular activation during deformation of neutrophils into narrow channels," J Appl. Physiol. 99, pp. 2323-30 (2005).
  5. J. C. Crocker et al., "Two-Point Microrheology of Inhomogeneous Soft Materials," Phys. Rev. Lett. 85(4), pp. 888-91 (2000).
  6. C. S. Chen et al., "Geometric control of cell life and death," Science 276 pp. 1425-28 (1997). Jessica Lee
  7. Y. Wang et al., "Visualizing the mechanical activation of Src," Nature 434, pp. 1040-45 (2005).

Nov 16: Imaging and biomechanics (continuation of Nov 2 and 9)

Nov 30: Optical Trapping

  1. Khalil, A.S., et al., "Single M13 bacteriophage tethering and stretching." Proceedings of the National Academy of Sciences 104, pp. 4892-4897 (2007).
  2. Brau, R.R., et al., "Passive and active microrheology with optical tweezers." Journal of Optics A: Pure and Applied Optics 9, pp. S103-S112 (2007).
  3. Y. Nakayama, et al., "Tunable nanowire nonlinear optical probe." Nature 447, pp. 1098-1101 (2007).
  4. JM. Walter, et al., "Light-powering Escherichia coli with proteorhodopsin" Proceedings of the National Academy of Sciences 104, pp. 2408–2412 (2007). Emilienne Repak

Dec 7: Optical Microscopy: 3D Imaging

  1. M. J. Miller et al., "Two-Photon Imaging of Lymphocyte Motility and Antigen Response in Intact Lymph Node," Science 296 pp. 1869-73 (2002).
  2. H. Wang et al., "Coherent Anti-Stokes Raman Scattering Imaging of Axonal Myelin in Live Spinal Tissues," Biophys. J 89(1), pp. 581-91 (2005).
  3. K. M. Hanson et al., "Two-Photon Fluorescence Lifetime Imaging of the Skin Stratum Corneum pH Gradient" Biophys. J 83(3) pp. 1682-90 (2002).
  4. P. J. Campagnola et al., "Three-Dimensional High-Resolution Second-Harmonic Generation Imaging of Endogenous Structural Proteins in Biological Tissues," Biophys. J 81(1) pp. 493-508 (2002).


Presentation time should be 10 minutes (it's very important that you do not go over this time). We will have 5 minutes for questions and discussion. It's also important that all non-presenters read the papers carefully before the session as this will make the discussion much more interesting.

Your presentation should provide background to motivate why the research was conducted, describe the key results of the paper (not necessarily all of the results) and the essence of the measurement method, and explain the significance of the results to the general field. Remember that 10 minutes will not be nearly enough time to discuss every aspect of the paper so you will need to identify the most important aspects to include in your presentation.

Make sure to upload a Powerpoint or PDF file of your presentation the day before the meeting so that we can use only one computer to avoid connection problems.

Feel free to see 20.309 staff outside of class to discuss any questions or ideas that you might have about the paper.

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