Difference between revisions of "Fall 2012: Journal Presentations"
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− | *Shapiro et al. Measuring Binding of Protein to Gel-Bound Ligands Using Magnetic Levitation JACS 2012. [http://pubs.acs.org/doi/abs/10.1021/ja211788e link] | + | *Shapiro et al. Measuring Binding of Protein to Gel-Bound Ligands Using Magnetic Levitation JACS 2012. [http://pubs.acs.org/doi/abs/10.1021/ja211788e link] '''Alexa Schulte''' |
*Dong and Sahin. A nanomechanical interface to rapid single-molecule interactions. Nature Communications 2011. [http://www.nature.com/ncomms/journal/v2/n3/full/ncomms1246.html link] | *Dong and Sahin. A nanomechanical interface to rapid single-molecule interactions. Nature Communications 2011. [http://www.nature.com/ncomms/journal/v2/n3/full/ncomms1246.html link] | ||
*A. P. Fields, A. E. Cohen. Electrokinetic trapping at the one nanometer limit. PNAS 2011. [http://www.pnas.org/content/early/2011/05/09/1103554108.full.pdf+html?with-ds=yes link] | *A. P. Fields, A. E. Cohen. Electrokinetic trapping at the one nanometer limit. PNAS 2011. [http://www.pnas.org/content/early/2011/05/09/1103554108.full.pdf+html?with-ds=yes link] |
Revision as of 00:19, 19 November 2012
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 Aislyn Schalck & Krithi Sundaram (can do either Dec 6 or Dec 7, Dec 7 is preferred) ; John Chen, Yimin Chen & Daniel Glover (only 6 Dec. works)
- Love, et al. A microengraving method for rapid selection of single cells producing antigen-specific antibodies. Nature Biotechnology 2006. link Sabina Sood & Shireen Rudina
- 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 Divya Chhabra, Mariana Duran
- Zhang et al. Microfluidics separation reveals the stem-cell–like deformability of tumor-initiating cells. PNAS 2012. link Michael Hwang & Paul Muir
Biomolecular detection
- Shapiro et al. Measuring Binding of Protein to Gel-Bound Ligands Using Magnetic Levitation JACS 2012. link Alexa Schulte
- 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 Elizabeth Choe, Sneha Kannan (can only present on Dec. 4)
- 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) Laura Seaman & Shelley Ackerman
- 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). Nahum Seifeselassie & Gonzalo Guajardo
- 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). Philip Smith
- P. J. Verveer et al., "Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane," Science 290 pp. 1567-70 (2000). Jessica Li & Kevin Li (can only do Dec 7th)
- 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). Afrah Shafquat & Samira Daswani
- 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). Cara Brown (can do either 4th or 7th)
- 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). Anirudh Arun, Shirley Galbiati
- Y. Wang et al., "Visualizing the mechanical activation of Src," Nature 434, pp. 1040-45 (2005). Jamal Elkhader & Queenie Chan
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). Emily Brown, Meghan Nelson
- 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).Cuong Nguyen
- 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 Grant Robinson