Difference between revisions of "Fall 2012: Journal Presentations"

Presentation guidelines

Presentation time should be 10 minutes (it's very important that you do not go over this time). We will have 2-3 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.

Grading

Presentation grade is worth 10% of your total grade and is divided into the following categories:

• Signing up for your paper by Monday, Nov 19. You must do this by placing both names (you and your partner) after the paper link on this wiki page. There are three presentation days (Dec 4, 6 and 7). If you or your partner will be away on one of these days, you must indicate this by your name on the wiki page. (10%)
• Uploading presentation file to Dropbox 6 hours before presentation session begins and ensuring that the file works. This is important since there will not be time to do this during the session. (25%)
• Presentation – clarity, interpretation of paper, organization, adhering to the 10min time limit, ability to answer questions, etc. (40%)
• Attendance at the other two sessions (25%)

Presentation sessions

Suggested publications

Single cell analysis

• Mettetal et al. The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae. Science 2008. link see also supplemental section
• Love, et al. A microengraving method for rapid selection of single cells producing antigen-specific antibodies. Nature Biotechnology 2006. link
• J. Kralj, D. R. Hochbaum, A. D. Douglass, A. E. Cohen. Electrical Spiking in Escherichia coli Probed with a Fluorescent Voltage-Indicating Protein. Science 2011. link
• Gossett et al Hydrodynamic stretching of single cells for large population mechanical phenotyping. PNAS 2012. link
• Tyson et al Fractional proliferation: a method to deconvolve cell population dynamics from single-cell data. Nature Methods 2012. link
• Zhang et al. Microfluidics separation reveals the stem-cell–like deformability of tumor-initiating cells. PNAS 2012. link

Biomolecular detection

• Shapiro et al. Measuring Binding of Protein to Gel-Bound Ligands Using Magnetic Levitation JACS 2012. link
• Dong and Sahin. A nanomechanical interface to rapid single-molecule interactions. Nature Communications 2011. link
• A. P. Fields, A. E. Cohen. Electrokinetic trapping at the one nanometer limit. PNAS 2011. link
• S. Husale, H. HJ. Persson, and O. Sahin. DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets. Nature 2009. link
• Hanay et al. Single-protein nanomechanical mass spectrometry in real time. Nature Nanotechnology 2012. link

Optical Microscopy: Imaging

• AR. Lowe, JJ. Siegel, P. Kalab, M. Sui, K. Weis and J. Liphardt, "Selectivity Mechanism of the Nuclear Pore Complex Characterized by Single Cargo Tracking" Nature 2010
• Z. E. Perlman et al., "Multidimensional Drug Profiling by Automated Microscopy," Science 306 pp. 1194-98 (2004).
• 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).
• T. Ichimura et al., "Application of tip-enhanced microscopy for nonlinear Raman spectroscopy," Appl. Phys. Lett. 84(10), pp. 1768-70 (2004).
• 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).
• M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic reconstruction optical microscopy (STORM)," Nature Methods 3:793-795 (2006).
• Design of Fluorescence Wide Field Microscopy
• VF Pamplona, A Mohan, MM Oliveira, R Raskar "NETRA: Interactive Display for Estimating Refractive Errors and Focal Range," Proc. of SIGGRAPH 2010 (ACM Transactions on Graphics 29, 4), 2010.

Optical Microscopy: Biomechanics

• S. M. Block et al., "Probing the kinesin reaction cycle with a 2D optical force clamp," PNAS 100(5), pp. 2351-56 (2003).
• P. J. Verveer et al., "Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane," Science 290 pp. 1567-70 (2000).
• 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).
• 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).
• J. C. Crocker et al., "Two-Point Microrheology of Inhomogeneous Soft Materials," Phys. Rev. Lett. 85(4), pp. 888-91 (2000).
• C. S. Chen et al., "Geometric control of cell life and death," Science 276 pp. 1425-28 (1997).
• Y. Wang et al., "Visualizing the mechanical activation of Src," Nature 434, pp. 1040-45 (2005).

3D Imaging

• D. Axelrod, "Total Internal Reflection Fluorescence Microscopy in Cell Biology," Traffic 2 pp. 764-774 (2001).
• JM. Walter, et al., "Light-powering Escherichia coli with proteorhodopsin" Proceedings of the National Academy of Sciences 104, pp. 2408–2412 (2007).
• M. J. Miller et al., "Two-Photon Imaging of Lymphocyte Motility and Antigen Response in Intact Lymph Node," Science 296 pp. 1869-73 (2002).
• 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).
• 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).
• 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).

Optical manipulation (laser tweezers)

• Ultrafast force-clamp spectroscopy of single molecules reveals load dependence of myosin working stroke Capitanio, et. al. Nature Methods 9, 1013–1019 (2012) doi:10.1038/nmeth.2152
• The Optical Stretcher: A Novel Laser Tool to Micromanipulate Cells, Guck, et. al
• 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).
• Muller cells are living optical fibers in the vertebrate retina, Franze, et. al
• Khalil, A.S., et al., "Single M13 bacteriophage tethering and stretching." Proceedings of the National Academy of Sciences 104, pp. 4892-4897 (2007).
• Y. Nakayama, et al., "Tunable nanowire nonlinear optical probe." Nature 447, pp. 1098-1101 (2007).

Magnetic Resonance Imaging and Contrast

• Basser PJ, Mattiello J, LeBihan D, “Diffusion tensor spectroscopy and imaging,” Biophys J 1994.
• Brunner et al, “Travelling-wave nuclear magnetic resonance,” Nature 2009.
• Damadian R et al, “Field focusing nuclear magnetic resonance (FONAR): visualization of a tumor in a live animal,” Science 1976.
• Gleich B & Weizenecker J, “Tomographic imaging using the nonlinear response of magnetic particles,” Nature 2005.
• Ogawa S et al, “Brain magnetic resonance imaging with contrast dependent on blood oxygenation,” Proc Natl Acad Sci USA 1990.
• Rugar D et al, “Single spin detection by magnetic resonance force microscopy,” Nature 2004.
• Zhou J et al, “Using the amide proton signals of intracellular proteins and peptides to detect pH effects in MRI,” Nat Med.

Molecular Imaging with MRI

• Ahrens ET et al, “In vivo imaging platform for tracking immunotherapeutic cells,” Nat Biotechnol 2005.
• Ardenkjaer-Larsen JH et al, “Increase in signal-to-noise ratio of > 10,000 times in liquid-state NMR,” Proc Natl Acad Sci USA 2003.
• Cohen B et al, “MRI detection of transcriptional regulation of gene expression in transgenic mice,” Nat Med 2007.
• Lin YJ & Koretsky AP, “Manganese ion enhances T1-weighted MRI during brain activation: an approach to direct imaging of brain function,” Magn Reson Med 1997.
• Louie AY et al, “In vivo visualization of gene expression using magnetic resonance imaging,” Nat Biotechnol 2000.
• Higuchi M et al, “19F and 1H MRI detection of amyloid beta plaques in vivo,” Nat Neurosci 2005.