Difference between revisions of "Fall 2012: Journal Presentations"

Presentation guidelines

• The allotted time is 10 minutes plus 2-3 minutes Q&A
• Provide background to motivate why the research was conducted
• Describe the key results of the paper (not necessarily all of the results) and explain the measurement method in an appropriate level of detail
• Explain the significance of the results to the general field.
• 10 minutes will not be nearly enough time to discuss every aspect of the paper so. Identify the most important aspects to include in your presentation.
• Discuss the paper you select with 20.309 staff outside of class to address questions or thoughts you have about the paper.
• Upload a Powerpoint or PDF file of your slides to Stellar the day before you present so the session organizer can use only one computer to avoid connection problems.

Non-presenters should read the papers carefully before the session to facilitate whorthwhile discussion.

Grading

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

• 10%: sign up for your paper by the deadline: 'Monday, Nov 19. To sign up, add both presenter's names after the link to the paper on this page.
  • There are three presentation days (Dec 4, 6 and 7). If you or your partner will be away on one of these days, indicate this by your name on the wiki page.
• 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%)
• 40%: Presentation – clarity, interpretation of paper, organization, adhering to the 10min time limit, ability to answer questions.
• 25%: Attendance at the other two sessions

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)
• 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).

Superresolution microscopy

• M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic reconstruction optical microscopy (STORM)," Nature Methods 3:793-795 (2006).
• Molecular Architecture and Assembly Principles of Vibrio cholerae Biofilms Berk, et. al. cience 13 July 2012: Vol. 337 no. 6091 pp. 236-239 DOI: 10.1126/science.1222981
• Aptamers as potential tools for super-resolution microscopy. Opazo, et. al. Nature Methods 9, 938–939 (2012) doi:10.1038/nmeth.2179
• Scanning angle interference microscopy reveals cell dynamics at the nanoscale Paszek, et. al. Nature Methods 9, 825–827 (2012) doi:10.1038/nmeth.2077

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.

Electron microscopy

Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy Martell, et. al. Nature Biotechnology (2012) doi:10.1038/nbt.2375