Monthly Archives: November 2007

Related Readings – C. David Allis, Ph.D.

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Beyond the Double Helix: Writing and Reading the “Histone Code”

Monday, December 3, 2007
Welch Hall (2nd Floor)

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

Figure 3 from Ruthenburg et al. (2007) Nature Reviews Molecular Cell Biology 8:983-994

Figure 3. Modes of multivalent chromatin engagement. From Ruthenburg et al. (2007) Nature Reviews Molecular Cell Biology 8:983-994.

Recommended Review Article

Ruthenburg, AJ, Li, H, Patel, DJ and Allis, CD (2007). Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol 8:983-94.

Related Articles

Hake, S. B. and Allis, C. D. (2006). Histone H3 variants and their potential role in indexing mammalian genomes: The “H3 barcode hypothesis”. Proc Nat Acad Sci 103:6428-6435.

Jenuwein, T. and Allis, C. D. (2001). Translating the histone code. Science 293:1074-1080.

Taverna, SD, Li, H, Ruthenburg, AJ, Allis, CD and Patel, DJ (2007). How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14:1025-40.

Wang, G. G., Allis, C. D. and Chi, P. (2007). Chromatin remodeling and cancer, part I: covalent histone modifications. Trends Mol Med 13:363-372.

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Related Readings – Friday Lecture – Ronald Breaker, Ph.D.

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Riboswitches: Ancient Gene Control Elements Made of RNA

Friday, November 30, 2007

Caspary Auditorium 3:45 p.m. – 5:15 p.m. Tea at 3:15 p.m. in the Abby Lounge

Figure 3 from Mandal and Breaker (2004) Nature Reviews Molecular Cell Biology 5:451-463.

Figure 3. Consensus sequences and structures for known riboswitch classes. From Mandal and Breaker (2004) Nature Reviews Molecular Cell Biology 5:451-463.

Recommended Review Article

Mandal, M. and Breaker, R. R. (2004). Gene regulation by riboswitches. Nature Reviews Molecular Cell Biology 5:451-463.

Related Articles

Barrick, J. E., Corbino, K. A., Winkler, W. C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., Wickiser, J. K. and Breaker, R. R. (2004). New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proceedings of the National Academy of Sciences of the United States of America 101:6421-6426.
Cheah, M. T., Wachter, A., Sudarsan, N. and Breaker, R. R. (2007). Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497-500.
Sudarsan, N., Hammond, M. C., Block, K. F., Welz, R., Barrick, J. E., Roth, A. and Breaker, R. R. (2006). Tandem riboswitch architectures exhibit complex gene control functions. Science 314:300-304.
Weinberg, Z., Barrick, J. E., Yao, Z., Roth, A., Kim, J. N., Gore, J., Wang, J. X., Lee, E. R., Block, K. F., Sudarsan, N., Neph, S., Tompa, M., Ruzzo, W. L. and Breaker, R. R. (2007). Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research 35:4809-4819.
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Related Readings – Albert J. Libchaber, Ph.D.

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The Effect of Temperature Gradients from Geophysics to Biology

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

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

Figure 6 from Braun and Libchaber (2004) Physical Biology 1:P1-P8.

Figure 6. Hydrothermal scenario for molecular evolution of life. From Braun and Libchaber (2004) Physical Biology 1:P1-P8.

Recommended Review Article

Braun, D. and Libchaber, A. (2004). Thermal force approach to molecular evolution. Physical Biology 1 :P 1-P8.

Related Articles

Belmonte, A., Tilgner, A. and Libchaber, A. (1995). Turbulence and internal waves in side-heated convection. Physical Review E 51:5681-5687.
Braun, D., Goddard, N. L. and Libchaber, A. (2003). Exponential DNA replication by laminar convection. Physical Review Letters 91:Art. No. 158103.
Braun, D. and Libchaber, A. (2002). Trapping of DNA by thermophoretic depletion and convection. Physical Review Letters 89:Art. No. 188103.
Salman, H. and Libchaber, A. (2007). A concentration-dependent switch in the bacterial response to temperature. Nature Cell Biology 9:1098-U78.
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Related Readings – Monday Lecture – James G. Krueger, M.D., Ph.D.

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Psoriasis as a Model Inflammatory Disease in Molecular Medicine: The Interplay of Pathogenic Dissection and Targeted Therapeutics

Monday, November 19, 2007
Welch Hall (2nd Floor)

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

Figure 3 from Lowes et al. (2007) Nature 445:866-873.

Figure 2. A dynamic picture of the bidirectional flow of ‘information’ and cells in a mature psoriasis lesion: the yin and yang of psoriasis. From Lowes et al. (2007) Nature 445:866-873.

Recommended Review Article

Lowes, M. A., Bowcock, A. M. and Krueger, J. G. (2007). Pathogenesis and therapy of psoriasis. Nature 445:866-873.

Related Articles

Gottlieb, A. B., Chamian, F., Masud, S., Cardinale, I., Abello, M. V., Lowes, M. A., Chen, F., Magliocco, M. and Krueger, J. G. (2005). TNF inhibition rapidly down-regulates multiple proinflammatory pathways in psoriasis plaques. Journal of Immunology 175:2721-2729.
Haider, A. S., Cardinale, I. R., Whynot, J. A. and Krueger, J. G. (2007). Effects of etanercept are distinct from infliximab in modulating proinflammatory genes in activated human leukocytes. Journal of Investigative Dermatology Symposium Proceedings 12:9-15.
Haider, A. S., Lowes, M. A., Gardner, H., Bandaru, R., Darabi, K., Chamian, F., Kikuchi, T., Gilleaudeau, P., Whalen, M. S., Cardinale, I., Novitskaya, I. and Krueger, J. G. (2007). Novel insight into the agonistic mechanism of alefacept in vivo: Differentially expressed genes may serve as biomarkers of response in psoriasis patients. Journal of Immunology 178:7442-7449.
Liu, Y., Krueger, J. G. and Bowcock, A. M. (2007). Psoriasis: genetic associations and immune system changes. Genes and Immunity 8:1-12.
Wang, F., Lee, E., Lowes, M. A., Haider, A. S., Fuentes-Duculan, J., Abello, M. V., Chamian, F., Cardinale, I. and Krueger, J. G. (2006). Prominent production of IL-20 by CD68(+)/CD11c(+) myeloid-derived cells in psoriasis: Gene regulation and cellular effects. Journal of Investigative Dermatology 126:1590-1599.
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Related Readings – Friday Lecture – Nathaniel Heintz, Ph.D.

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Addressing Brain Complexity

Friday, November 16, 2007

Caspary Auditorium 3:45 p.m. – 5:15 p.m. Tea at 3:15 p.m. in the Abby Lounge

Figure 3 from Gong et al. (2003) Nature 425:917-925.

Figure 3. Predicting developmental functions for specific genes on the basis of expression data in BAC transgenic mice. From Gong et al. (2003) Nature 425:917-925.

Recommended Review Article

Hatten, M. E. and Heintz, N. (2005). Large-scale genomic approaches to brain development and circuitry. Annual Review of Neuroscience 28:89-108.

Related Articles

Anthony, T. E., Mason, H. A., Gridley, T., Fishell, G. and Heintz, N. (2005). Brain lipid-binding protein is a direct target of Notch signaling in radial glial cells. Genes & Development 19:1028-1033.
Gong, S. C., Doughty, M., Harbaugh, C. R., Cummins, A., Hatten, M. E., Heintz, N. and Gerfen, C. R. (2007). Targeting Cre recombinase to specific neuron populations with bacterial artificial chromosome constructs. Journal of Neuroscience 27:9817-9823.
Gong, S. C., Zheng, C., Doughty, M. L., Losos, K., Didkovsky, N., Schambra, U. B., Nowak, N. J., Joyner, A., Leblanc, G., Hatten, M. E. and Heintz, N. (2003). A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425:917-925.
Heintz, N. (2001). Bac to the future: The use of bac transgenic mice for neuroscience research. Nature Reviews Neuroscience 2:861-870.
Miwa, J. M., Stevens, T. R., King, S. L., Caldarone, B. J., Ibanez-Tallon, I., Cheng, X., Fitzsimonds, R. M., Pavildes, C., Lester, H. A., Picciotto, M. R. and Heintz, N. (2006). The prototoxin lynx1 acts on nicotinic acetylcholine receptors to balance neuronal activity and survival in vivo. Neuron 51:587-600.
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Related Readings – Monday Lecture – Tarun Kapoor, Ph.D.

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Chemical Biology of Cell Division

Monday, November 12, 2007
Welch Hall (2nd Floor)

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

Recommended Review Article

Lampson, MA and Kapoor, TM (2006). Unraveling cell division mechanisms with small-molecule inhibitors. Nature Chemical Biology 2:19-27.

Related Articles

Kwok, BH and Kapoor, TM (2007). Microtubule flux: drivers wanted. Current Opinion in Cell Biology 19:36-42.
Lampson, M. A., Renduchitala, K., Khodjakov, A. and Kapoor, T. M. (2004). Correcting improper chromosome-spindle attachments during cell division. Nature Cell Biology 6:232-237.
Peters, U, Cherian, J, Kim, JH, Kwok, BH and Kapoor, TM (2006). Probing cell-division phenotype space and Polo-like kinase function using small molecules. Nature Chemical Biology 2:618-626.
Yang, G, Houghtaling, BR, Gaetz, J, Liu, JZ, Danuser, G and Kapoor, TM (2007). Architectural dynamics of the meiotic spindle revealed by single-fluorophore imaging. Nature Cell Biology 9:1233-42.
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Related Readings – Friday Lecture – Consuelo de Moraes, Ph.D.

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Chemical Communication among Plants and Insects

Friday, November 9, 2007

Caspary Auditorium 3:45 p.m. – 5:15 p.m. Tea at 3:15 p.m. in the Abby Lounge

Recommended Overview Article

Schardl, C.L. (Article Online Posting Date: May 30, 2001). Plant defences against herbivore and insect attack. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd.

Related Articles

Baldwin, I. T., Halitschke, R., Paschold, A., von Dahl, C. C. and Preston, C. A. (2006). Volatile signaling in plant-plant interactions: “Talking trees” in the genomics era. Science 311:812-815.
Engelberth, J., Alborn, H. T., Schmelz, E. A. and Tumlinson, J. H. (2004). Airborne signals prime plants against insect herbivore attack. Proceedings of the National Academy of Sciences of the United States of America 101:1781-1785.
Frost, C. J., Appel, M., Carlson, J. E., de Moraes, C. M., Mescher, M. C and Schultz, J. C. (2007). Within-plant signalling via volatiles overcomes vascular constraints on systemic signalling and primes responses against herbivores. Ecology Letters 10:490-498.
Heil, M. and Silva Bueno, J. C. (2007). Within-plant signaling by volatiles leads to induction and priming of an indirect plant defense in nature. Proceedings of the National Academy of Sciences of the United States of America 104:5467-5472.
Runyon, J. B., Mescher, M. C. and de Moraes, C. M. (2006). Volatile chemical cues guide host location and host selection by parasitic plants. Science 313:1964-1967.
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Related Readings – Monday Lecture – Thomas P. Sakmar, M.D.

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Heptahelical Receptors: Ligand Recognition and Conformational Dynamics in Bilayers

Monday, November 5, 2007
Welch Hall (2nd Floor)

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

Recommended Review Article

Botelho, A. V., Huber, T., Sakmar, T. P. and Brown, M. F. (2006). Curvature and hydrophobic forces drive oligomerization and modulate activity of rhodopsin in membranes. Biophysical Journal 91:4464-4477

Related Articles

Huber, T., Botelho, A. V., Beyer, K. and Brown, M. F. (2004). Membrane model for the G-protein-coupled receptor rhodopsin: Hydrophobic interface and dynamical structure. Biophysical Journal 86:2078-2100.
Janz, J. M., Sakmar, T. P. and Min, K. C. (2007). A novel interaction between atrophin-interacting protein 4 and beta-p21-activated kinase-interactive exchange factor is mediated by an SH3 domain. Journal of Biological Chemistry 282:28893-28903.
Kobilka, B. K. (2007). G protein coupled receptor structure and activation. Biochimica Et Biophysica Acta-Biomembranes 1768:794-807.
Periole, X., Huber, T., Marrink, S. J. and Sakmar, T. P. (2007). G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. Journal of the American Chemical Society 129:10126-10132.
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Related Readings – Friday Lecture – Jennifer Lippincott-Schwartz, Ph.D.

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Emerging Fluorescence Technologies for the Analysis of Protein Localization and Organelle Dynamics

Friday, November 2, 2007

Caspary Auditorium 3:45 p.m. – 5:15 p.m. Tea at 3:15 p.m. in the Abby Lounge

Recommended Review Article

Lippincott-Schwartz, J., Snapp, E. and Kenworthy, A. (2001). Studying protein dynamics in living cells. Nature Reviews Molecular Cell Biology 2:444-456.

Related Articles

Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S., Bonifacino, J. S., Davidson, M. W., Lippincott-Schwartz, J. and Hess, H. F. (2006). Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642-1645.
Kim, P. K., Mullen, R. T., Schumann, U. and Lippincott-Schwartz, J. (2006). The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER. Journal of Cell Biology 173:521-532.
Snapp, E. L., Sharma, A., Lippincott-Schwartz, J. and Hegde, R. S. (2006). Monitoring chaperone engagement of substrates in the endoplasmic reticulum of live cells. Proceedings of the National Academy of Sciences of the United States of America 103:6536-6541.
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