Related Readings – Andrea Ventura, M.D., Ph.D.

Investigating Tumor Maintenance and miRNA Biology in Mice

Monday, February 25, 2008
Welch Hall (2nd Floor)

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

Figure 2 from Ventura et al. (2007) Nature 445:661-665.

Figure 2. p53 restoration leads to tumour regression in vivo. From Ventura et al. (2007) Nature 445:661-665.

Related Articles

Fuster, J. J., Sanz-Gonzalez, S. M., Moll, U. M. and Andres, V. (2007). Classic and novel roles of p53: prospects for anticancer therapy. Trends in Molecular Medicine 13:192-199.
He, L., He, X. Y., Lowe, S. W. and Hannon, G. J. (2007). microRNAs join the p53 network – another piece in the tumour-suppression puzzle. Nature Reviews Cancer 7:819-822.
Ventura, A., Kirsch, D. G., McLaughlin, M. E., Tuveson, D. A., Grimm, J., Lintault, L., Newman, J., Reczek, E. E., Weissleder, R. and Jacks, T. (2007). Restoration of p53 function leads to tumour regression in vivo. Nature 445:661-665.
Xue, W., Zender, L., Miething, C., Dickins, R. A., Hernando, E., Krizhanovsky, V., Cordon-Cardo, C. and Lowe, S. W. (2007). Senescence and tumour clearance is triggered by p53 restoration in murine liver carcinomas. Nature 445:656-660.
Zhang, B. H., Pan, X. P., Cobb, G. P. and Anderson, T. A. (2007). microRNAs as oncogenes and tumor suppressors. Developmental Biology 302:1-12.

Related Readings – Roger D. Kornberg, Ph.D.

Structural Basis of Eukaryotic Transcription

Friday, February 22, 2008

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

Figure 12 from Kornberg - Nobel Lecture

Figure 12. Release of RNA transcript from DNA–RNA hybrid revealed in the structure of an RNA polymerase II transcribing complex. From Dr. Kornberg’s Nobel Lecture (8 December 2006). Reprinted in: Cell Death and Differentiation 14:1989-1997, 2007.

Recommended Review Article

Kornberg, R. D. (2006). Nobel Lecture: The molecular basis of eukaryotic transcription. [Aula Magna, Stockholm University: The Nobel Foundation; 8 December 2006]

Related Articles

Kornberg, R. D. and Lorch, Y. (2007). Chromatin rules. Nature Structural & Molecular Biology 14:986-988.
Lorch, Y., Maier-Davis, B. and Kornberg, R. D. (2006). Chromatin remodeling by nucleosome disassembly in vitro. Proceedings of the National Academy of Sciences 103:3090-3093.
Takagi, Y., Calero, G., Komori, H., Brown, J. A., Ehrensberger, A. H., Hudmon, A., Asturias, F. and Kornberg, R. D. (2006). Head module control of mediator interactions. Molecular Cell 23:355-364.
Takagi, Y. and Kornberg, R. D. (2006). Mediator as a general transcription factor. Journal of Biological Chemistry 281:80-89.
Wang, D., Bushnell, D. A., Westover, K. D., Kaplan, C. D. and Kornberg, R. D. (2006). Structural basis of transcription: Role of the trigger loop in substrate specificity and catalysis. Cell 127:941-954.

Related Readings – Yang Shi, PH.D.

Special Seminar Series: Biology of Single Cells

Histone Demethylases and Dynamic Regulation of Histone Methylation

Welch Hall Level 2 Wednesday February 27  4 p.m.



Recommended Review Article:

Shi, Yang, and J. R. Whetstine.  (2007) Dynamic regulation of histone lysine methylation by demethylases. Molecular Cell 25 :1-14

Related Articles:

Shi, Yang.  (2007)   Histone lysine demethylases: emerging roles in development, physiology and disease.  Nature Reviews Genetics  8 (11):829-833

Garcia-Bassets, Ivan et al.  (2007)  Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptorsCell  128 :505-518

Huang, Yi et al.   (2007)  Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silent genes.  PNAS 104: 8023-8028

Kloze, Robert J. , Eric Kallin, and Yi Zhang.  (2006)  JmjC-domain-containing proteins and histone demethylation.  Nature Review Genetics  7 :715-727

Margueron, Raphael, Patrick Trojer and Danny Reinberg.  (2005) The key to development: interpreting the histone code?  Current Opinion in Genetics and Development 15 :163-176

Related Readings – Satinder Kaur Singh, Ph.D.

Antidepressant Binding Site in a Bacterial Homologue of Neurotransmitter Transporters

Tuesday, February 19, 2008
Welch Hall (2nd Floor)

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

Figure 3 from Singh et al. (2007) Nature 448:952-956.

Figure 3. Clomipramine-binding site. From Singh at al. (2007) Nature 448:952-956.

Recommended Review Article

Gether, U., Andersen, P. H., Larsson, O. M. and Schousboe, A. (2006). Neurotransmitter transporters: molecular function of important drug targets. Trends in Pharmacological Sciences 27:375-383.

Related Articles

Rudnick, G. (2007). What is an antidepressant binding site doing in a bacterial transporter? ACS Chemical Biology 2:606-609.
Singh, S. K., Yamashita, A. and Gouaux, E. (2007). Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature 448:952-956.
Yamashita, A., Singh, S. K., Kawate, T., Jin, Y. and Gouaux, E. (2005). Crystal structure of a bacterial homologue of Na+/Cl–dependent neurotransmitter transporters. Nature 437:215-223.
Zhou, Z., Zhen, J., Karpowich, N. K., Goetz, R. M., Law, C. J., Reith, M. E. A. and Wang, D. N. (2007). LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake. Science 317:1390-1393.

Related Readings – Frederick W. Alt, Ph.D.

IgH Class Switching, DNA Breaks, Translocations and Cancer

Friday, February 15, 2008

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

Figure 1 Chaudhuri and Alt (2004) Nature Reviews Immunology 4:541-552.

Figure 1. Rearrangement at the immunoglobulin heavy-chain locus. From Chaudhuri and Alt (2004) Nature Reviews Immunology 4:541-552.

Recommended Review Article

Chaudhuri, J. and Alt, F. W. (2004). Class-switch recombination: Interplay of transcription, DNA deamination and DNA repair. Nature Reviews Immunology 4:541-552.

Further Reading

Dudley, D. D., Chaudhuri, J., Bassing, C. H. and Alt, F. W. (2005). Mechanism and control of V(D)J recombination versus class switch recombination: Similarities and differences. Advances in Immunology 86:43-112.

Related Articles

Franco, S., Alt, F. W. and Manis, J. P. (2006). Pathways that suppress programmed DNA breaks from progressing to chromosomal breaks and translocations. DNA Repair 5:1030-1041.
Jankovic, M., Nussenzweig, A. and Nussenzweig, M. C. (2007). Antigen receptor diversification and chromosome translocations. Nature Immunology 8:801-808.
Wuerffe, R., Wang, L., Grigera, F., Manis, J., Selsing, E., Perlot, T., Alt, F. W., Cogne, M., Pinaud, E. and Kenter, A. L. (2007). S-S synapsis during class switch recombination is promoted by distantly located transcriptional elements and activation-induced deaminase. Immunity 27:711-722.
Yan, C. T., Boboila, C., Souza, E. K., Franco, S., Hickernell, T. R., Murphy, M., Gumaste, S., Geyer, M., Zarrin, A. A., Manis, J. P., Rajewsky, K. and Alt, F. W. (2007). IgH class switching and translocations use a robust non-classical end-joining pathway. Nature 449:478-482.
Zarrin, A. A., Del Vecchio, C., Tseng, E., Gleason, M., Zarin, P., Tian, M. and Alt, F. W. (2007). Antibody class switching mediated by yeast endonuclease-generated DNA breaks. Science 315:377-381.

Related Readings – Danica Galonic Fujimori, Ph.D.

Halogenation of Unactivated Carbon Centers in Natural Products Biosynthesis

Monday, February 11, 2008
Welch Hall (2nd Floor)

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

Figure 1 from Fujimori et al. (2007) Journal of the American Chemical Society 129:13408-13409.

Figure 1. The 4.2-K Mössbauer spectra of a sample of the CytC3 Fe(II) αKG L-Aba-S-CytC2 Br complex that was reacted with O2 for 2 s. From Fujimori at al. (2007) Journal of the American Chemical Society 129:13408-13409.

Recommended Review Article

Vaillancourt, F. H., Yeh, E., Vosburg, D. A., Garneau-Tsodikova, S. and Walsh, C. T. (2006). Nature’s inventory of halogenation catalysts: Oxidative strategies predominate. Chemical Reviews 106:3364-3378.

Related Articles

Fujimori, D. G., Barr, E. W., Matthews, M. L., Koch, G. M., Yonce, J. R., Walsh, C. T., Bollinger, J. M., Krebs, C. and Riggs-Gelasco, P. J. (2007). Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the alpha-ketoglutarate-dependent halogenase CytC3 from Streptomyces. Journal of the American Chemical Society 129:13408-13409.
Fujimori, D. G., Hrvatin, S., Neumann, C. S., Strieker, M., Marahiel, M. A. and Walsh, C. T. (2007). Cloning and characterization of the biosynthetic gene cluster for kutznerides. Proceedings of the National Academy of Sciences 104:16498-16503.
Fujimori, D. G. and Walsh, C. T. (2007). What’s new in enzymatic hallogenations. Current Opinion in Chemical Biology 11:553-560.
Galonic, D. P., Barr, E. W., Walsh, C. T., Bollinger, J. M. and Krebs, C. (2007). Two interconverting Fe(IV) intermediates in aliphatic chlorination by the halogenase CytC3. Nature Chemical Biology 3:113-116.
Galonic, D. P., Vaillancourt, F. H. and Walsh, C. T. (2006). Halogenation of unactivated carbon centers in natural product biosynthesis: Trichlorination of leucine during barbamide biosynthesis. Journal of the American Chemical Society 128:3900-3901.

Related Readings – L. David Mech, Ph.D.

A Career in Wolf Research

Friday, February 8, 2008

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

Artic Wolf Howling
Artic Wolf Howling ©L. David Mech

Recommended Overview

Paquet, P. C., Zimen, E., and Boitani, L. (2007). Wolves. In: Macdonald, D. W., ed. The Encyclopedia of Mammals. [Oxford Reference Online; 7 February 2008]. New York: Oxford University Press.

Further Reading

Mech, L. D. and Boitani, L., eds. (2003). Wolves: Ecology, Behavior, and Conservation. Chicago: University of Chicago Press.

Related Articles

Harper, E. K., Paul, W. J. and Mech, L. D. (2005). Causes of wolf depredation increase in Minnesota from 1979-1998. Wildlife Society Bulletin 33:888-896.
Mech, L. D. Arctic wolves and their prey. [Internet]. National Oceanic and Atmospheric Administration (NOAA). Artic Theme Page: Essays on the Artic.
Mech, L. D. (1992). Daytime activity of wolves during winter in northeastern Minnesota. Journal of Mammology 73:570-571.
Mech, L. D., Smith, D. W., Murphy, K. M. and MacNulty, D. R. (2001). Winter severity and wolf predation on a formerly wolf-free elk herd. The Journal of Wildlife Management 65:998-1003.
Merrill, S. B. and Mech, D. L. (2003). The usefulness of GPS telemetry to study wolf circadian and social activity. Wildlife Society Bulletin 31:947-960.
Schmidt, P. A. and Mech, D. L. (1997). Wolf pack size and food acquisition. The American Naturalist 150:513-517.
Smith, D. W., Mech, L. D., Meagher, M., Clark, W. E., Jaffe, R., Phillips, M. K. and Mack, J. A. (2000). Wolf-bison interactions in Yellowstone National Park. Journal of Mammalogy 81:1128-1135.

Related Readings – David L. Stern, PhD

Special Seminar Series: Evolution, Ecology and Ethology

Dissecting the Genetic Causes of Morphological Differences Between Fly Species

Welch Hall Level 2 Wednesday February 6 4 p.m.

Recommended Review Article:

Frankino, W.A.; Zwaan, B.J.; Stern, D.L. and Brakefield, P.M. (2005) Natural selection and developmental constraints in the evolution of allometries. Science 307 (5710):718-720

Related Articles:

Orgogozo, V.; Muro, N.M.; Stern, D.L. (2007) Variation in fiber number of a male-specific muscle between Drosophila species: a genetic and developmental analysis. Evolution & Development 9 (4):368-377

McGregor, A. P.; Orgogozo, V.; Delon, I.; Zanet, J.; Srinivasen, D. G.; Payre, F.; Stern, D. L. (2007) Morphological evolution through multiple cis-regulatory mutations on a single gene. Nature 448 (7153):587-590

Kheradpour, P.; Stark, A.; Roy, S.; and Kellis, M. (2007) Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Research 17 (12):1919-1931

Orgogozo, V.; Broman, K. W.; Stern, D. L. (2006) High-resolution quantitative trait locus mapping reveals epistasis controlling ovariole number between two Drosophila species. Genetics 173 (1) :197-205

Orgogozo, V.; Grueber, W.B. (2005) FlyPNS, a database of the Drosophila embryonic and larval peripheral nervous system. BMC Developmental Biology 5 (article 4)

Related Readings – Daoyun Ji, Ph.D.

Searching for Memory Traces in the Brain: From the Hippocampus to Visual Cortex

Monday, February 4, 2008
Welch Hall (2nd Floor)

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

Figure 4 from Ji and Wilson (2007) Nature Neuroscience 10:100-107

Figure 4. Sleep frames replayed multicell firing sequences during RUN in both the visual cortex and the hippocampus. From Ji and Wilson (2007) Nature Neuroscience 10:100-107.

Recommended Review Article

Marshall, U. and Born, J. (2007). The contribution of sleep to hippocampus-dependent memory consolidation. Trends in Cognitive Sciences 11:442-450.

Related Articles

Hoffman, K. L., Battaglia, F. P., Harris, K., MacLean, J. N., Marshall, L. and Mehta, M. R. (2007). The upshot of up states in the neocortex: From slow oscillations to memory formation. Journal of Neuroscience 27:11838-11841.
Ji, D. Y. and Wilson, M. A. (2007). Coordinated memory replay in the visual cortex and hippocampus during sleep. Nature Neuroscience 10:100-107.
Mehta, M. R. (2007). Cortico-hippocampal interaction during up-down states and memory consolidation. Nature Neuroscience 10:13-15.