Fall 2012: Journal Presentations

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20.309: Biological Instrumentation and Measurement

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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.


Presentation grade is worth 8% 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.
  • 25%: Uploading presentation file to Stellar 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.
  • 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 Katie Vogel & Hannah Johnsen
  • 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 ; Robin Yeo & Colin Beckwitt

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 Maxwell T Pruner
  • 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); Edgar Matias and Steven Carreno
  • J. C. Crocker et al., "Two-Point Microrheology of Inhomogeneous Soft Materials," Phys. Rev. Lett. 85(4), pp. 888-91 (2000). Elizabeth Rowland and Stephanie Fung
  • C. S. Chen et al., "Geometric control of cell life and death," Science 276 pp. 1425-28 (1997). Anirudh Arun, Shirley Galbiati; Divya Chhabra, Mariana Duran
  • Y. Wang et al., "Visualizing the mechanical activation of Src," Nature 434, pp. 1040-45 (2005). Jamal Elkhader and Queenie Chan; Lauren Berry

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

Optical manipulation (laser tweezers)

Magnetic Resonance Imaging and Contrast

Molecular Imaging with MRI

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