20.109(S07): Student presentations, module 2

The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You will notice that the papers fall roughly into three categories- calcium imaging sensors and methods, protein reporters for imaging, and smart molecules in cell and systems biology.

You are not limited to the following list of primary research articles. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search pubmed yourself to find articles of interest to you. Once you have decided on a paper for your presentation, please email it to nkuldell AT mit DOT edu, and also "reserve" it by putting your (initials/lab section/team color) next to the listing here. As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

Calcium imaging sensors and methods

 * 1) Gilland, E., Miller, A. L., Karplus, E., Baker, R. & Webb, S. E. Imaging of multicellular large-scale rhythmic calcium waves during zebrafish gastrulation. Proc Natl Acad Sci U S A 96, 157-61 (1999).
 * 2) Kerr, R. et al. Optical imaging of calcium transients in neurons and pharyngeal muscle of C. elegans. Neuron 26, 583-94. (2000).
 * Li, W., Fraser, S. E. & Meade, T. J. A Calcium-Sensitive Magnetic Resonance Imaging Contrast Agent. J. Am. Chem. Soc. 121, 1413-1414 (1999).
 * Lin, Y. J. & Koretsky, A. P. Manganese ion enhances T1-weighted MRI during brain activation: an approach to direct imaging of brain function. Magn Reson Med 38, 378-88. (1997). [SN/TR/Green]
 * 1) Nakai, J., Ohkura, M. & Imoto, K. A high signal-to-noise Ca(2+) probe composed of a single green fluorescent protein. Nat Biotechnol 19, 137-41. (2001). [EDLS/TR/RED]
 * 2) Niell, C. M. & Smith, S. J. Functional imaging reveals rapid development of visual response properties in the zebrafish tectum. Neuron 45, 941-51 (2005). [DS/TR/Green]
 * 3) Ohki, K., Chung, S., Ch'ng, Y. H., Kara, P. & Reid, R. C. Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex. Nature (2005). [MG/WF/Purple]
 * 4) Palmer, A. E., Jin, C., Reed, J. C. & Tsien, R. Y. Bcl-2-mediated alterations in endoplasmic reticulum Ca2+ analyzed with an improved genetically encoded fluorescent sensor. Proc Natl Acad Sci U S A 101, 17404-9 (2004).
 * 5) Stosiek, C., Garaschuk, O., Holthoff, K. & Konnerth, A. In vivo two-photon calcium imaging of neuronal networks. Proc Natl Acad Sci U S A 100, 7319-24 (2003). [IJ/WF/pink]
 * 6) Wang, J. W., Wong, A. M., Flores, J., Vosshall, L. B. & Axel, R. Two-photon calcium imaging reveals an odor-evoked map of activity in the fly brain. Cell 112, 271-82 (2003). [JAC/WF/Green]

Protein reporters for imaging

 * 1) Genove, G., DeMarco, U., Xu, H., Goins, W. F. & Ahrens, E. T. A new transgene reporter for in vivo magnetic resonance imaging. Nat Med 11, 450-4 (2005). [ANK/TR BLUE]
 * 2) Griffin, B. A., Adams, S. R. & Tsien, R. Y. Specific covalent labeling of recombinant protein molecules inside live cells. Science 281, 269-72. (1998). [ALJ/WF/BLUE]
 * 3) Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. The structure of the chromophore within DsRed, a red fluorescent protein from coral. Proc Natl Acad Sci U S A 97, 11990-5 (2000).
 * 4) Luker, K. E. et al. Kinetics of regulated protein-protein interactions revealed with firefly luciferase complementation imaging in cells and living animals. Proc Natl Acad Sci U S A 101, 12288-93 (2004). [RLW/WF Yellow]
 * 5) Nagai, Y. et al. A fluorescent indicator for visualizing cAMP-induced phosphorylation in vivo. Nat Biotechnol 18, 313-6 (2000).  [NSZ/TR/Green] 
 * 6) Paulmurugan, R. & Gambhir, S. S. An intramolecular folding sensor for imaging estrogen receptor-ligand interactions. Proc Natl Acad Sci U S A 103, 15883-8 (2006). [KB/WF/Blue]
 * 7) Plautz, J. D., Kaneko, M., Hall, J. C. & Kay, S. A. Independent photoreceptive circadian clocks throughout Drosophila. Science 278, 1632-5 (1997). [AGK/WF/RED]
 * 8) Shaner, N. C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22, 1567-72 (2004). ML/TR/YELLOW
 * 9) Spotts, J. M., Dolmetsch, R. E. & Greenberg, M. E. Time-lapse imaging of a dynamic phosphorylation-dependent protein-protein interaction in mammalian cells. Proc Natl Acad Sci U S A 99, 15142-7 (2002).
 * 10) Weissleder, R. et al. In vivo magnetic resonance imaging of transgene expression. Nat Med 6, 351-5 (2000). RA/WF/Pink

Smart molecules in cell and systems biology

 * 1) Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G. & Deisseroth, K. Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8, 1263-8 (2005). [SW/TR/PINK]
 * 2) Fawell, S. et al. Tat-mediated delivery of heterologous proteins into cells. Proc Natl Acad Sci U S A 91, 664-8 (1994).  [DY/TR/Red] 
 * 3) Glieder, A., Farinas, E. T. & Arnold, F. H. Laboratory evolution of a soluble, self-sufficient, highly active alkane hydroxylase. Nat Biotechnol 20, 1135-9 (2002). [HZ/TR/purple]
 * 4) Jhaveri, S., Rajendran, M. & Ellington, A. D. In vitro selection of signaling aptamers. Nat Biotechnol 18, 1293-7 (2000). [BCH/WF/red]
 * 5) Karpova, A. Y., Tervo, D. G., Gray, N. W. & Svoboda, K. Rapid and reversible chemical inactivation of synaptic transmission in genetically targeted neurons. Neuron 48, 727-35 (2005).  [MSO/TR/Yellow] 
 * Liu, H. et al. Control of a biomolecular motor-powered nanodevice with an engineered chemical switch. Nat Mater 1, 173-7 (2002). [JS/WF/purple] [KTLV/TR/blue]
 * 1) Looger, L. L., Dwyer, M. A., Smith, J. J. & Hellinga, H. W. Computational design of receptor and sensor proteins with novel functions. Nature 423, 185-90 (2003). [MR/TH/purple]
 * 2) Miller, J. C., Silverman, S. K., England, P. M., Dougherty, D. A. & Lester, H. A. Flash decaging of tyrosine sidechains in an ion channel. Neuron 20, 619-24 (1998).
 * 3) Scott, Benjamin and Lois, Carlos. Generation of tissue-specific transgenic birds with lentiviral vectors. PNAS vol. 102, no. 45, 16443-16447 (2005). [ER/WF/yellow]
 * 4) Spencer, D. M., Wandless, T. J., Schreiber, S. L. & Crabtree, G. R. Controlling signal transduction with synthetic ligands. Science 262, 1019-24 (1993).(TG/WF/Green)
 * 5) Tanabe, T. et al. Multiphoton excitation-evoked chromophore-assisted laser inactivation using green fluorescent protein. Nat Methods 2, 503-5 (2005). [JL/TH/pink]