20.309:Presentations

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20.309: Biological Instrumentation and Measurement

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Presentation grading guidelines

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

Uploading presentation file to wiki 6 hrs before presentation time (25%)
Presentation – clarity, interpretation of paper, organization, etc. (50%)
Attendance at the other two sessions (25%)

How to upload your file

  1. Go to:http://openwetware.org/wiki/Special:Upload
  2. In edit mode, add this double bracket phrase after your name in the Schedule section: [download] where filename.pptx is the full name of your presentation file
  3. Click on download to make sure it works!

Schedule

(please do not make edits to this page except to link your presentation)

Thursday, December 8
 Session A with Steve Wasserman in 16-336
Alicia and Zeina: [download] " The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae "
Raven and Omar: [download] "A microengraving method for rapid selection of single cells producing antigen-specific antibodies"
Megan and Xinqi: [download] “Tumor cells caught in the act of invading: their strategy for enhanced cell motility"

Session B with Peter So in 4-237
Max and Jonathan: [download] " Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing "
Arvind and Samuel [download]: " The effects of molecular noise and size control on variability in the budding yeast cell cycle"
Leanna and Brigitte: [download] “Isolation of rare circulating tumour cells in cancer patients by microchip technology”

Friday, December 9
Session A with Peter So in 16-336
Sachin and Yuan: [download] “DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets”
Nigel and Vivian: [download]“Towards single-molecule nanomechanical mass spectrometry”
Gabi and Susana: [download] [download] (Please pick the 2nd download file) Gupta and Massagué. "Cancer Metastasis: Building a Framework" Cell 2006
Anne and Jenny: "Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood"
[download] [download]

Session B with Steven Nagle in 4-231
Shikha and William: [download]“Electrical Spiking in Escherichia coli Probed with a Fluorescent Voltage-Indicating Protein”
Brian and Michael: [download] "Geometric control of cell life and death"
Nick and Colin: [download] “Detection of Mutations in EGFR in Circulating Lung-Cancer Cells"

Tuesday, December 13
Session A with Scott Manalis in 16-336
Ginger and Joseph: [download] “Multidimensional Drug Profiling by Automated Microscopy"
Tina: [download]“Visualizing the mechanical activation of Src"
Jacqueline and Manuel: [download] “NETRA: Interactive Display for Estimating Refractive Errors and Focal Range"
Jessica: [download]"Folding DNA to create nanoscale shapes and patterns"

Session B with Steve Wasserman in 4-237
Sahar and Pablo: [download] “Probing the kinesin reaction cycle with a 2D optical force clamp"
PJ Velez and Pei-Ann: [download] “Diffusion tensor spectroscopy and imaging”
Lisa and Dana [download]: “Field focusing nuclear magnetic resonance (FONAR): visualization of a tumor in a live animal”

Single cell analysis

  1. Mettetal et al., "The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae" Science 2008. supp info Alicia Kaestli and Zeina Ali Siam
  2. Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. "Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing."Nature. 2010 Max Wu and Jonathan Gootenberg
  3. Love, et al., "A microengraving method for rapid selection of single cells producing antigen-specific antibodies" Nature Biotechnology 2006. Raven Reddy and Omar Abudayyeh. Can't do Dec 6
  4. J. Kralj, D. R. Hochbaum, A. D. Douglass, A. E. Cohen, Electrical Spiking in Escherichia coli Probed with a Fluorescent Voltage-Indicating Protein, Science, 333, 345-348, 2011. Shikha Kaji and William Morejon
  5. Di Talia, et al., "The effects of molecular noise and size control on variability in the budding yeast cell cycle" Nature 2007. Arvind Thiagarajan
  6. Spencer, et al., "Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis" Nature 2009.

Metastasis and Circulating Tumor Cells

  1. Gupta and Massagué. "Cancer Metastasis: Building a Framework" Cell 2006 Gabriella de Paz and Susana S. Hak
  2. Nagrath, et al., "Tumor cells caught in the act of invading: their strategy for enhanced cell motility" TRENDS in Cell Biology 2005. Megan Roytman and Xinqi Li
  3. Nagrath, et al., "Isolation of rare circulating tumour cells in cancer patients by microchip technology" Nature 2007. -Leanna
  4. Maheswaran, et al., "Detection of Mutations in EGFR in Circulating Lung-Cancer Cells" NEJM 2008. Nick Swenson and Colin "Forizzle" Reisterer

Biomolecular detection

  1. Fan HC, Wang J, Potanina A, Quake SR. "Whole Genome Molecular Haplotyping of Single Cells" Nature Biotechnology. 2010
  2. Fordyce PM, Gerber D, Tran D, Zheng J, Li H5, DeRisi JL, Quake SR. "De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis"Nature Biotechnology. 2010 -Brigitte
  3. Dong and Sahin, "A nanomechanical interface to rapid single-molecule interactions" Nature Communications 2011.
  4. A. P. Fields, A. E. Cohen, Electrokinetic trapping at the one nanometer limit, PNAS 2011.
  5. E. Winfree, et al. "Design and self-assembly of two-dimensional DNA crystals," Nature 394(6693): pp. 539-544 (1998). OR P. W. K. Rothemund "Folding DNA to create nanoscale shapes and patterns," Nature 440(7082): pp. 297-302(2006).
  6. Fan et al. "Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood," Nature Biotechnology 2008. Jenny Zhou and Anne Ye (Date preference: December 6, 9, 8)
  7. S. Husale, H. HJ. Persson, and O. Sahin, “DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets” Nature 2009.Sachin Shinde and Yuan Zhao
  8. Appleyard et al. "Multiplexed Protein Quantification with Barcoded Hydrogel Microparticles" Analytical Chemistry 2011.
  9. Naik et al. "Towards single-molecule nanomechanical mass spectrometry," Nature Nanotechnology 2009.Nigel Chou and Vivian Hecht

Optical Microscopy: Imaging

  1. 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
  2. Z. E. Perlman et al., "Multidimensional Drug Profiling by Automated Microscopy," Science 306 pp. 1194-98 (2004). Joseph Martinez and Jingkun (Ginger) Yang (Can't do 12/6)
  3. 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).
  4. T. Ichimura et al., "Application of tip-enhanced microscopy for nonlinear Raman spectroscopy," Appl. Phys. Lett. 84(10), pp. 1768-70 (2004).
  5. 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).
  6. M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic reconstruction optical microscopy (STORM)," Nature Methods 3:793-795 (2006).
  7. Design of Fluorescence Wide Field Microscopy
  8. 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. Jacqueline Söegaard and Manuel Legrand [download]

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).Sahar Alkhairy, Pablo
  1. P. J. Verveer et al., "Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane," Science 290 pp. 1567-70 (2000).
  2. 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).
  3. 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). Samuel Acquah
  4. J. C. Crocker et al., "Two-Point Microrheology of Inhomogeneous Soft Materials," Phys. Rev. Lett. 85(4), pp. 888-91 (2000).
  5. C. S. Chen et al., "Geometric control of cell life and death," Science 276 pp. 1425-28 (1997). Brian Carvalho + Michael Batista
  6. Y. Wang et al., "Visualizing the mechanical activation of Src," Nature 434, pp. 1040-45 (2005). Tina Stutzman, Can't do Dec. 8th

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). - Pablo
  2. D. Axelrod, "Total Internal Reflection Fluorescence Microscopy in Cell Biology," Traffic 2 pp. 764-774 (2001).
  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).
  4. Y. Nakayama, et al., "Tunable nanowire nonlinear optical probe." Nature 447, pp. 1098-1101 (2007).
  5. JM. Walter, et al., "Light-powering Escherichia coli with proteorhodopsin" Proceedings of the National Academy of Sciences 104, pp. 2408–2412 (2007).
  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).
  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).
  10. Muller cells are living optical fibers in the vertebrate retina, Franze, et. al
  11. The Optical Stretcher: A Novel Laser Tool to Micromanipulate Cells, Guck, et. al

Magnetic Resonance Imaging and Contrast

  1. Basser PJ, Mattiello J, LeBihan D, “Diffusion tensor spectroscopy and imaging,” Biophys J 1994.
  2. Brunner et al, “Travelling-wave nuclear magnetic resonance,” Nature 2009. PJ Velez and Pei-Ann Lin
  3. Damadian R et al, “Field focusing nuclear magnetic resonance (FONAR): visualization of a tumor in a live animal,” Science 1976. Lisa Foo and Dana Braff
  4. Gleich B & Weizenecker J, “Tomographic imaging using the nonlinear response of magnetic particles,” Nature 2005.
  5. Ogawa S et al, “Brain magnetic resonance imaging with contrast dependent on blood oxygenation,” Proc Natl Acad Sci USA 1990.
  6. Rugar D et al, “Single spin detection by magnetic resonance force microscopy,” Nature 2004.
  7. 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

  1. Ahrens ET et al, “In vivo imaging platform for tracking immunotherapeutic cells,” Nat Biotechnol 2005.
  2. 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.
  3. Cohen B et al, “MRI detection of transcriptional regulation of gene expression in transgenic mice,” Nat Med 2007. Derek Ju and John Kucharczyk
  4. 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.
  5. Louie AY et al, “In vivo visualization of gene expression using magnetic resonance imaging,” Nat Biotechnol 2000.
  6. Higuchi M et al, “19F and 1H MRI detection of amyloid beta plaques in vivo,” Nat Neurosci 2005.

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.

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