20.309:Presentations

Oct 10: Nucleic acid technologies

• Group A, Last name: A-L (Room 16-352) with Scott Manalis

1. Mettetal, et al., "The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae" Science 2008. supp info Emzo de los Santos [1]
2. J. W. Hong, et al. "A nanoliter-scale nucleic acid processor with parallel architecture," Nature Biotech. 22(4): pp. 435-439 (2004). Tiffany Guo File:Guo 20309.ppt
3. Winklelman, et al. "Density-Based Diamagnetic Separation: Devices for Detecting Binding Events and for Collecting Unlabeled Diamagnetic Particles in Paramagnetic Solutions" Analytical Chemistry 2007. Gina Fridley File:GFridley presentation.pdf
4. Kong, et al., "Parallel gene synthesis in a microfluidic device" Nucleic Acids Research 2007. Michael Lee File:MikeLeePresentation.pdf

• Group B, Last name: M-Z (Room 4-231) with Steve Wasserman

1. Mettetal, et al., "The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae" Science 2008. supp info Philip Samayoa
2. E. Winfree, et al. "Design and self-assembly of two-dimensional DNA crystals," Nature 394(6693): pp. 539-544 (1998). AND/OR P. W. K. Rothemund "Folding DNA to create nanoscale shapes and patterns," Nature 440(7082): pp. 297-302(2006).; Jerzy Szablowski

File:Jerzy szablowski folding dna.pdf File:Jerzy szablowski folding dna.pptx

1. Maerkl and Quake, "A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors" Science 2007. Augusto Tentori

File:AT309.ppt

1. DNA Melting Curve Module

• Not reviewed this year

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.

Oct 14: Nucleic acid technologies II and Scanning probes

• Group A, Last name: A-L (Room 16-352) with Steve Wasserman

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). Qing Han File:20.309 Qing Han.ppt
2. 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). Rob Warden File:RLWPresentation.ppt

• Group B, Last name: M-Z (Room 4-231) with Scott Manalis

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). Becky Kusko File:Rebecca Kusko presentation.pdf

• Not reviewed this session

1. D. Rugar et al. "Single spin detection by magnetic resonance force microscopy," Nature 430(6997): pp. 329-332 (2004).

Oct 24: Optical Microscopy: Imaging

1. Z. E. Perlman et al., "Multidimensional Drug Profiling by Automated Microscopy," Science 306 pp. 1194-98 (2004). Rebecca Adams (Oct. 14)
2. 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).
3. T. Ichimura et al., "Application of tip-enhanced microscopy for nonlinear Raman spectroscopy," Appl. Phys. Lett. 84(10), pp. 1768-70 (2004).
4. 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).
5. M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic reconstruction optical microscopy (STORM)," Nature Methods 3:793-795 (2006).
6. Design of Fluorescence Wide Field Microscopy (2 person)

Nov 20: Scanning probe microscopy

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). WuiSiew Tan
2. SY Lee et al. "Chemomechanical mapping of ligand-receptor binding kinetics on cells" PNAS 104: pp. 9609-9614 (2007).Aditya Kohli, Dawn Spelke
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). Sophie Wong, Aisha Bobb-Semple
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). Matt Gethers, Rosa María Álvarez
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). Jen Chao

Nov 25: 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). Neil Zimmerman, Vivek Thacker
2. P. J. Verveer et al., "Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane," Science 290 pp. 1567-70 (2000). Jessica Keenan
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).YW
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).Jen Logan, Vivian Hernandez
7. Y. Wang et al., "Visualizing the mechanical activation of Src," Nature 434, pp. 1040-45 (2005). Thomas Martinez, Matt Loper

Dec 9: Optical Trapping and 3D Imaging

1. Khalil, A.S., et al., "Single M13 bacteriophage tethering and stretching." Proceedings of the National Academy of Sciences 104, pp. 4892-4897 (2007). Jessie Wang
2. D. Axelrod, "Total Internal Reflection Fluorescence Microscopy in Cell Biology," Traffic 2 pp. 764-774 (2001). Roshini Zachariah
3. 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). Dylan Roden
4. Y. Nakayama, et al., "Tunable nanowire nonlinear optical probe." Nature 447, pp. 1098-1101 (2007). Arjun Naskar
5. JM. Walter, et al., "Light-powering Escherichia coli with proteorhodopsin" Proceedings of the National Academy of Sciences 104, pp. 2408–2412 (2007). Stephanie Nix, Kate B
6. M. J. Miller et al., "Two-Photon Imaging of Lymphocyte Motility and Antigen Response in Intact Lymph Node," Science 296 pp. 1869-73 (2002). Luis Somoza
7. 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).
8. 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).
9. 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). Juliana Rotter

PRESENTATION GUIDELINES

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.