Recommended Readings: Madeline Lancaster, Ph.D. Monday, Dec. 11

Special Lecture
The Human Brain in a Dish: Using Cerebral Organoids to Model Development and Disease
Madeline A. Lancaster, Ph.D.
Postdoctoral Fellow
Institute of Molecular Biotechnology
4:00 p.m., Carson Family Auditorium

Recommended Readings

Review Papers

Eiraku, M., & Sasai, Y. (2012). Self-formation of layered neural structures in three-dimensional culture of ES cells. Current Opinion in Neurobiology, 22(5), 768–777. doi:10.1016/j.conb.2012.02.005

Gage, F. H., & Temple, S. (2013). Neural stem cells: generating and regenerating the brain. Neuron, 80(3), 588–601. doi:10.1016/j.neuron.2013.10.037

Han, S. S. W., Williams, L. a, & Eggan, K. C. (2011). Constructing and deconstructing stem cell models of neurological disease. Neuron, 70(4), 626–644. doi:10.1016/j.neuron.2011.05.003

Lui, J. H., Hansen, D. V, & Kriegstein, A. R. (2011). Development and evolution of the human neocortex. Cell, 146(1), 18–36. doi:10.1016/j.cell.2011.06.030

Empirical Articles

Espuny-Camacho, I., Michelsen, K. a, Gall, D., Linaro, D., Hasche, A., Bonnefont, J., … Vanderhaeghen, P. (2013). Pyramidal neurons derived from human pluripotent stem cells integrate efficiently into mouse brain circuits in vivo. Neuron, 77(3), 440–456. doi:10.1016/j.neuron.2012.12.011

Lancaster, M. a, Renner, M., Martin, C.-A., Wenzel, D., Bicknell, L. S., Hurles, M. E., … Knoblich, J. a. (2013). Cerebral organoids model human brain development and microcephaly. Nature, 501(7467), 373–379. doi:10.1038/nature12517

Mariani, J., Simonini, M. V., Palejev, D., Tomasini, L., Coppola, G., Szekely, A. M., … Vaccarino, F. M. (2012). Modeling human cortical development in vitro using induced pluripotent stem cells. Proceedings of the National Academy of Sciences of the United States of America, 109(31), 12770–12775. doi:10.1073/pnas.1202944109

Recommended Readings: Seth Darst, Ph.D. Monday, Dec. 9

Monday Lecture Series
Structural studies of bacterial transcription: Bacteriophage T7 Gp2 inhibition of Escherichia coli RNA polymerase
Seth Darst, Ph.D.
Jack Fishman Professor
Laboratory of Molecular Biophysics
The Rockefeller University
4:00 p.m., Carson Family Auditorium

Recommended Readings

Review Paper

Samson, J. E., Magadán, A. H., Sabri, M., & Moineau, S. (2013). Revenge of the phages: defeating bacterial defenses. Nature Reviews Microbiology, 11(10), 675–687. doi:10.1038/nrmicro3096

Empirical Articles

Bae, B., Davis, E., Brown, D., Campbell, E. a, Wigneshweraraj, S., & Darst, S. a. (In Press). Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1. Proceedings of the National Academy of Sciences of the United States of America. doi:10.1073/pnas.1314576110

Cámara, B., Liu, M., Reynolds, J., Shadrin, A., Liu, B., Kwok, K., … Wigneshweraraj, S. R. (2010). T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site. Proceedings of the National Academy of Sciences of the United States of America, 107(5), 2247–2252. doi:10.1073/pnas.0907908107

James, E., Liu, M., Sheppard, C., Mekler, V., Cámara, B., Liu, B., … Wigneshweraraj, S. (2012). Structural and mechanistic basis for the inhibition of Escherichia coli RNA polymerase by T7 Gp2. Molecular Cell, 47(5), 755–766. doi:10.1016/j.molcel.2012.06.013

Sheppard, C., Cámara, B., Shadrin, A., Akulenko, N., Liu, M., Baldwin, G., … Wigneshweraraj, S. R. (2011). Inhibition of Escherichia coli RNAp by T7 Gp2 protein: role of negatively charged strip of amino acid residues in Gp2. Journal of Molecular Biology, 407(5), 623–632. doi:10.1016/j.jmb.2011.02.013

Recommended Readings: Kevan Shokat, Ph.D.

Friday Lecture Series

The William H. Stein Memorial Lecture

A New Druggable Pocket on K-Ras and a Neo-substrate for Activating the Kinase

PINK in Parkinson’s Disease

Kevan Shokat, Ph.D., professor and chair, department of cellular and molecular

pharmacology, University of California, San Francisco;

investigator, Howard Hughes Medical Institute

November 22, 2013

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Hertz, N. T., Berthet, A., Sos, M. L., Thorn, K. S., Burlingame, A. L., Nakamura, K., & Shokat, K. M. (2013). A neo-substrate that amplifies catalytic activity of parkinson’s-disease- related kinase PINK1. Cell, 154(4), 737-747

Larochelle, S., Amat, R., Glover-Cutter, K., Sansó, M., Zhang, C., Allen, J. J., . . . Fisher, R. P. (2012). Cyclin-dependent kinase control of the initiation-to-elongation switch of polymerase II. Nature Structural and Molecular Biology, 19(11), 1108-1115

Soskis, M. J., Ho, H. -. H., Bloodgood, B. L., Robichaux, M. A., Malik, A. N., Ataman, B., . . . Greenberg, M. E. (2012). A chemical genetic approach reveals distinct EphB signaling mechanisms during brain development. Nature Neuroscience, 15(12), 1645-1654

Statsuk, A. V., & Shokat, K. M. (2012). Covalent cross-linking of kinases with their corresponding peptide substrates. Methods in Molecular Biology 795 , pp. 179-190

Sun, Y., Miao, Y., Yamane, Y., Zhang, C., Shokat, K. M., Takematsu, H., . . . Drubin, D. G. (2012). Orm protein phosphoregulation mediates transient sphingolipid biosynthesis response to heat stress via the pkh-ypk and Cdc55-PP2A pathways. Molecular Biology of the Cell, 23(12), 2388-2398

Ultanir, S., Hertz, N., Li, G., Ge, W. -., Burlingame, A., Pleasure, S., . . . Jan, Y. -. (2012). Chemical genetic identification of NDR1/2 kinase substrates AAK1 and Rabin8 uncovers their roles in dendrite arborization and spine development. Neuron, 73(6), 1127-1142


Recommended Readings: S. Lawrence Zipursky, Ph.D.

Friday Lecture Series

Cell Recognition and the Assembly of Neural Circuits

S. Lawrence Zipursky, Ph.D., professor, biological chemistry,

David Geffen School of Medicine, University of California, Los Angeles;

investigator, Howard Hughes Medical Institute

November 15, 2013

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Hattori, D., Demir, E., Kim, H. W., Viragh, E., Zipursky, S. L., & Dickson, B. J. (2007). Dscam diversity is essential for neuronal wiring and self-recognition. Nature, 449(7159), 223-227

Hattori, D., Millard, S. S., Wojtowicz, W. M., & Zipursky, S. L. (2008). Dscam-mediated cell recognition regulates neural circuit formation. Annual Review of Cell and Developmental Biology 24 , pp. 597-620

Hummel, T., Vasconcelos, M. L., Clemens, J. C., Fishilevich, Y., Vosshall, L. B., & Zipursky, S. L. (2003). Axonal targeting of olfactory receptor neurons in drosophila is controlled by dscam. Neuron, 37(2), 221-231

Wojtowicz, W. M., Wu, W., Andre, I., Qian, B., Baker, D., & Zipursky, S. L. (2007). A vast repertoire of dscam binding specificities arises from modular interactions of variable ig domains. Cell, 130(6), 1134-1145

Zhu, Y., Nern, A., Zipursky, S. L., & Frye, M. A. (2009). Peripheral visual circuits functionally segregate motion and phototaxis behaviors in the fly. Current Biology, 19(7), 613-619

Zipursky, S. L., & Sanes, J. R. (2010). Chemoaffinity revisited: Dscams, protocadherins, and neural circuit assembly. Cell, 143(3), 343-353


Recommended Readings: Roland Beckmann, Ph.D. Monday, Nov 25

Monday, November 25, 2013
4:00 p.m., Carson Family Auditorium

Roland Beckmann, Ph.D.
Chair of Cellular Biochemistry
Gene Center Munich
Ludwig Maximilian University of Munich

Cryo-EM of ribosomal particles:
From ribosome biogenesis to protein translocation and quality control

Recommended Readings:

Empirical Articles

Anger, A. M., Armache, J.-P., Berninghausen, O., Habeck, M., Subklewe, M., Wilson, D. N., & Beckmann, R. (2013). Structures of the human and Drosophila 80S ribosome. Nature, 497(7447), 80–85. doi:10.1038/nature12104

Armache, J.-P., Jarasch, A., Anger, A. M., Villa, E., Becker, T., Bhushan, S., … Beckmann, R. (2010). Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proceedings of the National Academy of Sciences of the United States of America, 107(46), 19748–19753. doi:10.1073/pnas.1009999107

Beckmann, R., Spahn, C. M., Eswar, N., Helmers, J., Penczek, P. a, Sali, a, … Blobel, G. (2001). Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell, 107(3), 361–372.

Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., & Yusupov, M. (2011). The structure of the eukaryotic ribosome at 3.0 Å resolution. Science, 334(6062), 1524–1529. doi:10.1126/science.1212642

Leidig, C., Bange, G., Kopp, J., Amlacher, S., Aravind, A., Wickles, S., … Sinning, I. (2013). Structural characterization of a eukaryotic chaperone–the ribosome-associated complex. Nature structural & molecular biology, 20(1), 23–28. doi:10.1038/nsmb.2447

Review Papers

Klinge, S., Voigts-Hoffmann, F., Leibundgut, M., & Ban, N. (2012). Atomic structures of the eukaryotic ribosome. Trends in biochemical sciences, 37(5), 189–198. doi:10.1016/j.tibs.2012.02.007

Granneman, S., & Baserga, S. J. (2004). Ribosome biogenesis: of knobs and RNA processing. Experimental cell research, 296(1), 43–50. doi:10.1016/j.yexcr.2004.03.016

Schmeing, T. M., & Ramakrishnan, V. (2009). What recent ribosome structures have revealed about the mechanism of translation. Nature, 461(7268), 1234–1242. doi:10.1038/nature08403

Alfred Russel Wallace (8 January 1823 – 7 November 1913)

Alfred Russel Wallace (8 January 1823 – 7 November 1913) was a British naturalist, explorer, geographer, anthropologist, and biologist. He is best known for independently conceiving the theory of evolution through natural selection; his paper on the subject was jointly published with some of Charles Darwin’s writings in 1858. This prompted Darwin to publish his own ideas in On the Origin of Species. Wallace did extensive fieldwork, first in the Amazon River basin and then in the Malay Archipelago, where he identified the Wallace Line that divides the Indonesian archipelago into two distinct parts: a western portion in which the animals are largely of Asian origin, and an eastern portion where the fauna reflect Australasia.

He was considered the 19th century’s leading expert on the geographical distribution of animal species and is sometimes called the “father of biogeography”. Wallace was one of the leading evolutionary thinkers of the 19th century and made many other contributions to the development of evolutionary theory besides being codiscoverer of natural selection. These included the concept of warning coloration in animals, and the Wallace effect, a hypothesis on how natural selection could contribute to speciation by encouraging the development of barriers against hybridization.

Wallace was strongly attracted to unconventional ideas (such as evolution). His advocacy of spiritualism and his belief in a non-material origin for the higher mental faculties of humans strained his relationship with some members of the scientific establishment. In addition to his scientific work, he was a social activist who was critical of what he considered to be an unjust social and economic system in 19th-century Britain. His interest in natural history resulted in his being one of the first prominent scientists to raise concerns over the environmental impact of human activity.

In honor of the centennial of his death, this short film celebrates the extraordinary life and lasting scientific contributions of the other, arguably more colorful discoverer of natural selection.

‘The Animated Life of A.R. Wallace’

Recommended Readings: Pardis Sabeti M.D., Ph.D. Friday, Nov 8

Friday, November 8, 2013
3:45 p.m., Caspary Auditorium

Pardis Sabeti M.D., Ph.D.
Senior Associate Member, Broad Institute of MIT and Harvard;
Associate Professor, Center for Systems Biology, Harvard University Department of Organismic and Evolutionary Biology, and Department of Immunology and Infectious Disease at Harvard School of Public Health

Evolutionary Forces in Humans and Pathogens

Recommended Readings:

Empirical Articles

The 100 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061–1073. doi:10.1038/nature09534

The International MapMap Consortium. (2005). A haplotype map of the human genome. Nature, 437(7063), 1299–1320. doi:10.1038/nature04226

Grossman, S. R., Andersen, K. G., Shlyakhter, I., Tabrizi, S., Winnicki, S., Yen, A., … Sabeti, P. C. (2013). Identifying recent adaptations in large-scale genomic data. Cell, 152(4), 703–713. doi:10.1016/j.cell.2013.01.035

Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., … & Lander, E. S. (2002). Detecting recent positive selection in the human genome from haplotype structureNature419(6909), 832-837. doi:10.1038/nature01140

Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., … Gaudet, R. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164), 913–8. doi:10.1038/nature06250

Review Papers

Biswas, S., Akey, J. M. (2006) Genomic insights into positive selection. Trends in Genetics, 22(8), 437-445. doi:10.1016/j.tig.2006.06.005

Kreitman, M. (2000). Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics, 1, 539-559. doi: 10.1146/annurev.genom.1.1.539

Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C., & Clark, A. G. (2007). Recent and ongoing selection in the human genome. Nature Reviews Genetics,8(11), 857-868. doi:10.1038/nrg2187

Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., … & Lander, E. S. (2006). Positive natural selection in the human lineage .Science, 312(5780), 1614-1620. doi:10.1126/science.1124309

Vitti, J. J., Cho, M. K., Tichkoff, S. A., Sabeti, P. C. (2012). Human evolutionary genomics: ethical and interpretive issues. Trends in Genetics, 28(3), 137-145. doi:10.1016/j.tig.2011.12.001