Related Readings – Monday Lecture – Leor Weinberger, Ph.D.

Viral Genetic Circuits: How Noisy Transcriptional Feedback Controls Latency in HIV & Herpes

Monday, February 26, 2007
Welch Hall (2nd Floor)

3:45 p.m. Refreshments 4:00 p.m. Lecture


Recommended Review Article


Raser, J.M., and O’Shea, E.K. (2005). Noise in gene expression: Origins, consequences, and control. Science 309, 2010-2013.

Related Articles


Kaern, M., Elston, T.C., Blake, W.J., and Collins, J.J. (2005). Stochasticity in gene expression: From theories to phenotypes. Nature Reviews Genetics 6, 451-464.


Marcello, A. (2006). Latency: the hidden HIV-1 challenge. Retrovirology 3 7.


Weinberger, L.S., Burnett, J.C., Toettcher, J.E., Arkin, A.P., and Schaffer, D.V. (2005). Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122, 169-182.


Weinberger, L.S., Schaffer, D.V., and Arkin, A.P. (2003). Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection. Journal of Virology 77, 10028-10036.

Related Readings – Monday Lecture – Morgan Huse, Ph.D.

Imaging T cell signaling dynamics and effector responses

Tuesday, February 20, 2007
Welch Hall (2nd Floor)

3:45 p.m. Refreshments 4:00 p.m. Lecture



1.

Balada-Llasat, J. M., and Mecsas, J. (2006) Yersinia has a tropism for B and T cell zones of lymph nodes that is independent of the type III secretion system, Plos Pathogens 2, 816-828.


2.

Flavell, R. R., Huse, M., Goger, M., Trester-Zedlitz, M., Kuriyan, J., and Muir, T. W. (2002) Efficient semisynthesis of a tetraphosphorylated analogue of the type I TGF beta receptor, Organic Letters 4, 165-168.


3.

Haque, A., Chu, K., Easton, A., Stevens, M. P., Galyov, E. E., Atkins, T., Titball, R., and Bancroft, G. J. (2006) A live experimental vaccine against Burkholderia pseudomallei elicits CD4(+) T cell-mediated immunity, priming T cells specific for 2 type III secretion system proteins, Journal of Infectious Diseases 194, 1241-1248.


4.

Huse, M., Chen, Y. G., Massague, J., and Kuriyan, J. (1999) Crystal structure of the cytoplasmic domain of the type I TGF beta receptor in complex with FKBP12, Cell 96, 425-436.


5.

Huse, M., Eck, M. J., and Harrison, S. C. (1998) A Zn2+ ion links the cytoplasmic tail of CD4 and the N-terminal region of Lck, Journal of Biological Chemistry 273, 18729-18733.


6.

Huse, M., Holford, M. N., Kuriyan, J., and Muir, T. W. (2000) Semisynthesis of hyperphosphorylated type I TGF beta receptor: Addressing the mechanism of kinase activation, Journal of the American Chemical Society 122, 8337-8338.


7.

Huse, M., and Kuriyan, J. (2002) The conformational plasticity of protein kinases, Cell 109, 275-282.


8.

Huse, M., Lillemeier, B. F., Kuhns, M. S., Chen, D. S., and Davis, M. M. (2006) T cells use two directionally distinct pathways for cytokine secretion, Nature Immunology 7, 247-255.


9.

Huse, M., Muir, T. W., Xu, L., Chen, Y. G., Kuriyan, J., and Massague, J. (2001) The TGF beta receptor activation process: An inhibitor- to substrate-binding switch, Molecular Cell 8, 671-682.


10.

Kelly-Rogers, J., Madrigal-Estebas, L., O’Connor, T., and Doherty, D. G. (2006) Activation-induced expression of CD56 by T cells is associated with a reprogramming of cytolytic activity and cytokine secretion profile in vitro, Human Immunology 67, 863-873.


11.

Krogsgaard, M., Li, Q. J., Sumen, C., Huppa, J. B., Huse, M., and Davis, M. M. (2005) Agonist/endogenous peptide-MHC heterodimers drive T cell activation and sensitivity, Nature 434, 238-243.


12.

Li, J., Shen, W., Kong, K., and Liu, Z. (2006) Interleukin-21 induces T-cell activation and proinflammatory cytokine secretion in rheumatoid arthritis, Scandinavian Journal of Immunology 64, 515-522.


13.

Marcondes, M. C. G., Penedo, M. C. T., Lanigan, C., Hall, D., Watry, D. D., Zandonatti, M., and Fox, H. S. (2006) Simian immunodeficiency virus-induced CD4(+) T cell deficits in cytokine secretion profile are dependent on monkey origin, Viral Immunology 19, 679-689.


14.

Shi, M. Q., Hao, S. G., Chan, T., and Xiang, J. (2006) CD4(+) T cells stimulate memory CD8(+) T cell expansion via acquired pMHC I complexes and costimulatory molecules, and IL-2 secretion, Journal of Leukocyte Biology 80, 1354-1363.


15.

Thiel, A., Wu, P. H., Lanowska, M., Dong, J., Radbruch, A., and Sieper, J. (2006) Identification of immunodominant CD4+T cell epitopes in patients with Yersinia-induced reactive arthritis by cytometric cytokine secretion assay, Arthritis and Rheumatism 54, 3583-3590.


16.

Wang, W. G., Graeler, M. H., and Goetzl, E. J. (2005) Type 4 sphingosine 1-phosphate G protein-coupled receptor (S1P(4)) transduces S1P effects on T cell proliferation and cytokine secretion without signaling migration, Faseb Journal 19, 1731-1733.


17.

Wu, J. W., Hu, M., Chai, J. J., Seoane, J., Huse, M., Li, C., Rigotti, D. J., Kyin, S., Muir, T. W., Fairman, R., Massague, J., and Shi, Y. G. (2001) Crystal structure of a phosphorylated Smad2: Recognition of phosphoserine by the MH2 domain and insights on Smad function in TGF-beta signaling, Molecular Cell 8, 1277-1289.

Related Readings – Monday Lecture – Adam Cohen, Ph.D.

Trapping and Manipulating Individual Molecules in Solution.

Adam Cohen, Ph.D., Stanford University.

Related readings



1.

Berglund, A. J., and Mabuchi, H. (2005) Tracking-FCS: Fluorescence correlation spectroscopy of individual particles, Optics Express 13, 8069-8082.


2.

Cang, H., Wong, C. M., Xu, C. S., Rizvi, A. H., and Yang, H. (2006) Confocal three dimensional tracking of a single nanoparticle with concurrent spectroscopic readouts, Applied Physics Letters 88.


3.

Chiu, D. T., Wilson, C. F., Karlsson, A., Danielsson, A., Lundqvist, A., Stromberg, A., Ryttsen, F., Davidson, M., Nordholm, S., Orwar, O., and Zare, R. N. (1999) Manipulating the biochemical nanoenvironment around single molecules contained within vesicles, Chemical Physics 247, 133-139.


4.

Chiu, D. T., and Zare, R. N. (1997) Optical detection and manipulation of single molecules in room-temperature solutions, Chemistry-a European Journal 3, 335-339.


5.

Cohen, A. E. (2005) Control of nanoparticles with arbitrary two-dimensional force fields, Physical Review Letters 94.


6.

Cohen, A. E., and Moerner, W. E. (2006) Suppressing Brownian motion of individual biomolecules in solution, Proceedings of the National Academy of Sciences of the United States of America 103, 4362-4365.


7.

Cole, K. D., Gaigalas, A., and Akerman, B. (2006) Single-molecule measurements of trapped and migrating circular DNA during electrophoresis in agarose gels, Electrophoresis 27, 4396-4407.


8.

Fleury, L., Sick, B., Zumofen, G., Hecht, B., and Wild, U. P. (1998) High photo-stability of single molecules in an organic crystal at room temperature observed by scanning confocal optical microscopy, Molecular Physics 95, 1333-1338.


9.

Gurrieri, S., Smith, S. B., and Bustamante, C. (1999) Trapping of megabase-sized DNA molecules during agarose gel electrophoresis, Proceedings of the National Academy of Sciences of the United States of America 96, 453-458.


10.

Li, H. T., Zhou, D. J., Browne, H., and Klenerman, D. (2006) Evidence for resonance optical trapping of individual fluorophore-labeled antibodies using single molecule fluorescence spectroscopy, Journal of the American Chemical Society 128, 5711-5717.


11.

Machara, N. P., Goodwin, P. M., Enderlein, J., Semin, D. J., and Keller, R. A. (1998) Efficient detection of single molecules eluting off an optically trapped microsphere, Bioimaging 6, 33-42.


12.

Osborne, M. A., Balasubramanian, S., Furey, W. S., and Klenerman, D. (1998) Optically biased diffusion of single molecules studied by confocal fluorescence microscopy, Journal of Physical Chemistry B 102, 3160-3167.


13.

Pandey, K. K., and Hirayama, S. (1996) Enhanced excitation energy transfer in microdroplets – A study by time-resolved fluorescence microscopy, Journal of Photochemistry and Photobiology a-Chemistry 99, 165-175.


14.

Xu, X. H. N., and Yeung, E. S. (1998) Long-range electrostatic trapping of single-protein molecules at a liquid-solid interface, Science 281, 1650-1653.