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==Nov 30: Optical Trapping==
==Nov 30: Optical Trapping==
#[http://web.mit.edu/~langlab/Publications/ASKhalil-etal(2007).pdf Khalil, A.S., ''et al.'', "Single M13 bacteriophage tethering and stretching." ''Proceedings of the National Academy of Sciences'' '''104''', pp. 4892-4897 (2007).]
#[http://web.mit.edu/~langlab/Publications/ASKhalil-etal(2007).pdf Khalil, A.S., ''et al.'', "Single M13 bacteriophage tethering and stretching." ''Proceedings of the National Academy of Sciences'' '''104''', pp. 4892-4897 (2007).]''Kay Aull''
#[http://stacks.iop.org/JOptA/9/S103 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).]
#[http://stacks.iop.org/JOptA/9/S103 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).]
#[http://www.physics.berkeley.edu/research/liphardt/pdfs/probe.pdf Y. Nakayama, ''et al.'', "Tunable nanowire nonlinear optical probe."  ''Nature'' '''447''', pp. 1098-1101 (2007).]"Jaime Rivera"
#[http://www.physics.berkeley.edu/research/liphardt/pdfs/probe.pdf Y. Nakayama, ''et al.'', "Tunable nanowire nonlinear optical probe."  ''Nature'' '''447''', pp. 1098-1101 (2007).]"Jaime Rivera"

Revision as of 13:34, 7 November 2007

20.309: Biological Instrumentation and Measurement

Home        Course Information        Schedule        People        Student Presentations        LAB SIGNUP       


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 Image:Presentation alice.ppt
  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. 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: Nucleic acid technologies II

  1. 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 Image:Angi.ppt
  2. 20.309 Lab Module 1 - measuring DNA melting curves Stephen Payne Image:Photobleaching.ppt
  3. DNA Melting - an industry perspective Tami ShinkawaImage:Tamijeanindustry.ppt
  4. 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
  5. D. Rugar et al. "Single spin detection by magnetic resonance force microscopy," Nature 430(6997): pp. 329-332 (2004).

Nov 2: Optical Microscopy: Imaging

  1. Z. E. Perlman et al., "Multidimensional Drug Profiling by Automated Microscopy," Science 306 pp. 1194-98 (2004). Cokie Hu
  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). Sonal Sodha
  6. M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic reconstruction optical microscopy (STORM)," Nature Methods 3:793-795 (2006). Sisi Zhu
  7. Design of Fluorescence Wide Field Microscopy (2 person)

Nov 6: Scanning probe microscopy I

  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 Image:Morris 20309.ppt
  2. SY Lee et al. "Chemomechanical mapping of ligand-receptor binding kinetics on cells" PNAS 104: pp. 9609-9614 (2007).
  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 RyuImage:Sangjin Ryu.ppt
  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. 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
  6. Mike Yee

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). Sophia Kamran
  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). Meghana Limaye

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).Kay Aull
  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)."Jaime Rivera"
  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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