Related Readings – David M. Kingsley, Ph.D.

Fishing for the Secrets of Vertebrate Evolution

Friday, February 1, 2008

Caspary Auditorium 3:45 p.m. – 5:00 p.m. Tea at 3:15 p.m. in the Abby Lounge

Figure 5 from Miller et al. (2007) Cell 131:1179-1189.

Figure 5. Reduced Kit ligand expression in gills of Fishtrap Creek fish. From Miller et al. (2007) Cell 131:1179-1189.

Recommended Review Article

Peichel, C. L. (2005). Fishing for the secrets of vertebrate evolution in threespine sticklebacks. Developmental Dynamics 234:815-823.

Further Reading

Kingsley, D. M. and Peichel, C. L. (2007). The molecular genetics of evolutionary change in sticklebacks. In: Ostlund-Nilsson, S., Mayer, I. and Huntingford, F. A., eds. Biology of the Three-Spined Stickleback. Boca Raton: CRC Press, pp. 41–81.

Related Articles

Albert, A. Y. K., Sawaya, S., Vines, T. H., Knecht, A. K., Miller, C. T., Summers, B. R., Balabhadra, S., Kingsley, D. M. and Schluter, D. (2008). The genetics of adaptive shape shift in stickleback: Pleiotropy and effect size. Evolution 62:76-85.
Knecht, A. K., Hosemann, K. E. and Kingsley, D. M. (2007). Constraints on utilization of the EDA-signaling pathway in threespine stickleback evolution. Evolution & Development 9:141-154.
Miller, C. T., Beleza, S., Pollen, A. A., Schluter, D., Kittles, R. A., Shriver, M. D. and Kingsley, D. M. (2007). cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell 131:1179-1189.
Shapiro, M. D., Bell, M. A. and Kingsley, D. M. (2006). Parallel genetic origins of pelvic reduction in vertebrates. Proceedings of the National Academy of Sciences 103:13753-13758.

Related Readings – Tali Kimchi, Ph.D.

Special Seminar Series: Evolution, Ecology and Ethology

Neural Circuits Underlying Sexual Dimorphic Social and Reproductive Behaviors

Welch Hall Level 2 Wednesday January 30 4 p.m.

Recommended Review Article:

Dulac, C. and S. Wagner. (2006) Genetic analysis of brain circuits underlying pheromone signalling. Annual Review of Genetics 40:449-467

Related Articles:

Kimchi, T., J. Xu and C. Dulac. (2007) A functional circuit underlying male sexual behaviour in the female mouse brain. NATURE 448(7157):1009-1015

Zufall, F. and T. Leinders-Zufall. (2007) Mammalian pheromone sensing. Current Opinion in Neurobiology 17(4):483-489

Brennan, P.A. and Frank Zufall. (2006) Pheromonal communication in vertebrates. NATURE 444(7117):308-315

Spehr, M., J. Spehr, K. Ukhanov, K.R. Kelliher, T. Leinders-Zufall, and F. Zufall. (2006) Parallel processing of social signals by the mammalian main and accessory olfactory systems. Cellular and Molecular Life Sciences 63(13):1476-1484

Related Readings – Winrich Freiwald, Ph.D.

Taking Apart the Neural Machinery of Face Processing

Monday, January 28, 2008
Welch Hall (2nd Floor)

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

 Figure 3 from Tsao et al. (2006) Science 311:670-674.

Figure 3. Face identity and category information are carried by the population of face-selective cells. From Tsao et al. (2006) Science 311:670-674.

Recommended Review Article

Peissig, J. J. and Tarr, M. J. (2007). Visual object recognition: Do we know more now than we did 20 years ago? Annual Review of Psychology 58:75-96.

Related Articles

Pinsk, M. A., DeSimone, K., Moore, T., Gross, C. G. and Kastner, S. (2005). Representations of faces and body parts in macaque temporal cortex: A functional MRI study. Proceedings of the National Academy of Sciences 102:6996-7001.
Tsao, D. (2006). A dedicated system for processing faces. Science 314:72-73.
Tsao, D. Y. and Freiwald, W. A. (2006). What’s so special about the average face? Trends in Cognitive Sciences 10:391-393.
Tsao, D. Y., Freiwald, W. A., Knutsen, T. A., Mandeville, J. B. and Tootell, R. B. H. (2003). Faces and objects in macaque cerebral cortex. Nature Neuroscience 6:989-995.
Tsao, D. Y., Freiwald, W. A., Tootell, R. B. H. and Livingstone, M. S. (2006). A cortical region consisting entirely of face-selective cells. Science 311:670-674.

Related Readings – Elliot M. Meyerowitz, Ph.D.

Computational Morphodynamics: Live Imaging and Computational Modeling of Plant Stem Cells in the Shoot Apical Meristem

Friday, January 25, 2008

Caspary Auditorium 3:45 p.m. – 5:00 p.m. Tea at 3:15 p.m. in the Abby Lounge

Figure 4 from Reddy et al. (2007) Nature Reviews Molecular Cell Biology 8:491-501.

Figure 4. Multi-channel confocal imaging of Arabidopsis thaliana SAM, labelled with three spectrally variant fluorescent proteins. From Reddy et al. (2007) Nature Reviews Molecular Cell Biology 8:491-501.

Recommended Review Article

Reddy, G. V., Gordon, S. P. and Meyerowitz, E. M. (2007). Unravelling developmental dynamics: transient intervention and live imaging in plants. Nature Reviews Molecular Cell Biology 8:491-501.

Related Articles

Gordon, S. P., Heisler, M. G., Reddy, G. V., Ohno, C., Das, P. and Meyerowitz, E. M. (2007). Pattern formation during de novo assembly of the Arabidopsis shoot meristem. Development 134:3539-3548.
Heisler, M. G., Ohno, C., Das, P., Sieber, P., Reddy, G. V., Long, J. A. and Meyerowitz, E. M. (2005). Patterns of auxin transport and gene expression during primordium development revealed by live imaging of the Arabidopsis inflorescence meristem. Current Biology 15:1899-1911.
Jonsson, H., Heisler, M. G., Shapiro, B. E., Meyerowitz, E. M. and Mjolsness, E. (2006). An auxin-driven polarized transport model for phyllotaxis. Proceedings of the National Academy of Sciences 103:1633-1638.
Jonsson, H., Heisler, M., Reddy, G. V., Agrawal, V., Gor, V., Shapiro, B. E., Mjolsness, E. and Meyerowitz, E. M. (2005). Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem. Bioinformatics 21:i232-i240.

Related Readings – Laurent Keller, Ph.D.

Special Seminar Series: Evolution, Ecology and Ethology

Ant Behavior is Modulated by Complex Interactions
Between Genes and Social Environment

Welch Hall Level 2   Wednesday   January 23   4 p.m.

Recommended Review Article:

Lehmann, L. and Laurent Keller. (2006). The evolution of cooperation and altruism – a general framework and a classification of models. Journal of Evolutionary Biology 19(5):1365-1376

Recommended Book:

Keller, Laurent. (1999). Levels of selection in evolution. Princeton University Press. 272 p.

Related Articles:

Schwander, Tanja, Laurent Keller and Sara Helms Cahan. (2007). Two alternate mechanisms contribute to the persistence of interdependent lineages in Pogonomyrmex harvester ants. Molecular Ecology 16(17):3533-3543

Lehmann, Laurent, Francois Rousset, Denis Roze and Laurent Keller. (2007) Strong reciprocity or strong ferocity? A population genetic view of the evolution of altruistic punishment. American Naturalist 170(1):21-37

Sachs, J.L., U.G. Mueller, T.P. Wilcon and J.J. Bull. (2004) The evolution of cooperation. Quarterly Review of Biology 79(2):135-160

Bowles, S., J.K. Choi and A. Hopfensitz. (2003) The co-evolution of individual behaviors and social institutions. Journal of Theoretical Biology 223(2):135-137

LeGailliard, J.F., R. Ferriere, and U. Dieckmann. (2003) Adaptive dynamics of altruism in spatially heterogeneous populations. Evolution 57(1):1-17

Related Readings – Kevan M. Shokat, Ph.D.

Chemical Genetic Analysis of Kinase Signaling

Friday, January 18, 2008

Caspary Auditorium 3:45 p.m. – 5:00 p.m. Tea at 3:15 p.m. in the Abby Lounge

 Graphical abstract from Zhang and Shokat (2007) Tetrahedron 63: 5832-5838.


Graphical abstract from Zhang and Shokat (2007). Enhanced selectivity for inhibition of analog-sensitive protein kinases through scaffold optimization.Tetrahedron 63: 5832-5838.

Recommended Review Article

Elphick, L. M., Lee, S. E., Gouverneur, V. and Mann, D. J. (2007). Using chemical genetics and ATP analogues to dissect protein kinase function. ACS Chemical Biology 2:299-314.

Related Articles

Allen, J. J., Li, M. Q., Brinkworth, C. S., Paulson, J. L., Wang, D., Hubner, A., Chou, W. H., Davis, R. J., Burlingame, A. L., Messing, R. O., Katayama, C. D., Hedrick, S. M. and Shokat, K. M. (2007). A semisynthetic epitope for kinase substrates. Nature Methods 4:511-516.
Blair, J. A., Rauh, D., Kung, C., Yun, C. H., Fan, Q. W., Rode, H., Zhang, C., Eck, M. J., Weiss, W. A. and Shokat, K. M. (2007). Structure-guided development of affinity probes for tyrosine kinases using chemical genetics. Nature Chemical Biology 3:229-238.
Dephoure, N., Howson, R. W., Blethrow, J. D., Shokat, K. M. and O’Shea, E. K. (2005). Combining chemical genetics and proteomics to identify protein kinase substrates. Proceedings of the National Academy of Sciences 102:17940-17945.
Snead, J. L., Sullivan, M., Lowery, D. M., Cohen, M. S., Zhang, C., Randle, D. H., Taunton, J., Yaffe, M. B., Morgan, D. O. and Shokat, K. M. (2007). A coupled chemical-genetic and bioinformatic approach to polo-like kinase pathway exploration. Chemistry & Biology 14:1261-1272.

Related Readings – Xiaoyong Yang, Ph.D.

Nutrient and Circadian Control of Metabolism

Monday, January 14, 2008
Welch Hall (2nd Floor)

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

Figure 3 from Yang et al. (2006) Cell 126:801-810.

Figure 3. Tissue-Specific Diurnal Rhythm of PPARs and Target Gene Expression. From Yang et al. (2006) Cell 126:801-810.

Related Articles

Hart, G. W., Housley, M. P. and Slawson, C. (2007). Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins. Nature 446:1017-1022.
Kohsaka, A. and Bass, J. (2007). A sense of time: how molecular clocks organize metabolism. Trends in Endocrinology and Metabolism 18:4-11.
Whisenhunt, T. R., Yang, X. Y., Bowe, D. B., Paterson, A. J., Van Tine, B. A. and Kudlow, J. E. (2006). Disrupting the enzyme complex regulating O-GlcNAcylation blocks signaling and development. Glycobiology 16:551-563.
Yang, X. Y., Downes, M., Yu, R. T., Bookout, A. L., He, W. M., Straume, M., Mangelsdorf, D. J. and Evans, R. M. (2006). Nuclear receptor expression links the circadian clock to metabolism. Cell 126:801-810.
Zhang, F. X., Su, K. H., Yang, X. Y., Bowe, D. B., Paterson, A. J. and Kudlow, J. E. (2003). O-GlcNAc modification is an endogenous inhibitor of the proteasome. Cell 115:715-725.

Related Readings – Andrew W. Murray, Ph.D.

Friday Night at the Singles Bar: How Budding Yeast Cells Find a Mate

Friday, January 11, 2008

Caspary Auditorium 3:45 p.m. – 5:00 p.m. Tea at 3:15 p.m. in the Abby Lounge


Figure 1(A). Pheromone response pathway - The wild-type pheromone signaling pathway. From Ingolia and Murray (2007) Current Biology 17:668-677.


Figure 1(A). Pheromone response pathway – The wild-type pheromone signaling pathway. From Ingolia and Murray (2007) Current Biology 17:668-677.

Recommended Review Article

Elion, E. A. (2000). Pheromone response, mating and cell biology. Current Opinion in Microbiology 3:573-581.

Related Articles

Ingolia, N. T. and Murray, A. W. (2007). Positive-feed back loops as a flexible biological module. Current Biology 17:668-677.
Leu J. Y, Murray A. W. (2006). Experimental evolution of mating discrimination in budding yeast. Current Biology 16:280-286.
Paliwal, S., Iglesias, P. A., Campbell, K., Hilioti, Z., Groisman, A. and Levchenko, A. (2007). MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast. Nature 446:46-51.
Yi, T. M., Chen, S. Q., Chou, C. S. and Nie, Q. (2007). Modeling yeast cell polarization induced by pheromone gradients. Journal of Statistical Physics 128:193-207.

Related Readings – James E. Ferrell Jr., M.D., Ph.D.

Dissecting the Mitotic Oscillator

Friday, January 4, 2008

Caspary Auditorium 3:45 p.m. – 5:00 p.m. Tea at 3:15 p.m. in the Abby Lounge


Figure 3-29 from Morgan, D. O. (2007) The Cell Cycle: Principles of Control.


Figure 3-29. A biochemical oscillator. From Morgan, D. O. (2007) The Cell Cycle: Principles of Control.

Recommended Overview

Morgan, D. O. The Cell Cycle: Principles of Control. London: New Science Press Ltd; 1999-2007. Chapter 3: The Cell-Cycle Control System.

Related Articles

Gong, D. Q., Pomerening, J. R., Myers, J. W., Gustavsson, C., Jones, J. T., Hahn, A. T., Meyer, T. and Ferrell, J. E. (2007). Cyclin A2 regulates nuclear-envelope breakdown and the nuclear accumulation of cyclin B1. Current Biology 17:85-91.
Kim, S. Y. and Ferrell, J. E. (2007). Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell 128:1133-1145.
Pomerening, J. R., Kim, S. Y. and Ferrell, J. E. (2005). Systems-level dissection of the cell-cycle oscillator: Bypassing positive feedback produces damped oscillations. Cell 122:565-578.
Pomerening, J. R., Sontag, E. D. and Ferrell, J. E. (2003). Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nature Cell Biology 5:346-351.

AAAS Names New Editor-in-chief for Science

Bruce Alberts

The Board of Directors for the American Association for the Advancement of Science has named president emeritus of the U.S. National Academy of Sciences, Bruce Alberts, as the next editor-in-chief of their prestigious journal Science.   Dr. Alberts’ tenure in his new post begins March 1, 2008.   Alberts, also a former Chair of the National Research Council, is professor of biochemistry and biophysics at the University of California, San Francisco.  Donald Kennedy, president emeritus of Stanford University and the current editor-in-chief, announced his retirement plans in 2007, and will remain in his post through Feburary 2008.    Dr. Alberts (Harvard 1965) is well known for his research on protein complexes that facilitate chromosome replication.   He is also well known as one of the original authors of the leading textbook, The Molecular Biology of the Cell, now in its 5th edition.