Recommended Readings: Gerard Karsenty, M.D., Ph.D., January 16

Friday Lecture Series
Friday, January 16, 2015
3:45 p.m., Caspary Auditorium

Gerard Karsenty, M.D., Ph.D.
Paul A. Marks, M.D., Professor and Chairman
Department of Genetics & Development
Columbia University Medical Center

The Contribution of Bone to Whole Organism Physiology

Recommended Readings

Empirical Articles

Ducy, P., Amling, M., Takeda, S., Priemel, M., Schilling, A. F., Beil, F. T., … Karsenty, G. (2000). Leptin inhibits bone formation through a hypothalamic relay : A central control of bone mass. Cell, 100(2), 197–207. doi:10.1016/S0092-8674(00)81558-5

Lee, N. K., Sowa, H., Hinoi, E., Ferron, M., Ahn, J. D., Confavreux, C., … Karsenty, G. (2007). Endocrine regulation of energy metabolism by the skeleton. Cell, 130(3), 456–469. doi:10.1016/j.cell.2007.05.047

Takeda, S., Elefteriou, F., Levasseur, R., Liu, X., Zhao, L., Parker, K. L., … Karsenty, G. (2002). Leptin regulates bone formation via the sympathetic nervous system. Cell, 111(3), 305–317. doi:10.1016/S0092-8674(02)01049-8

Review Papers

Karsenty, G., & Ferron, M. (2012). The contribution of bone to whole-organism physiology. Nature, 481(7381), 314–20. doi:10.1038/nature10763

Karsenty, G., & Oury, F. (2012). Biology without walls: the novel endocrinology of bone. Annual Review of Physiology, 74, 87–105. doi:10.1146/annurev-physiol-020911-153233

Recommended Readings: Ronald M. Evans, Ph.D., December 19

Friday Lecture Series
Friday, December 19, 2014
3:45 p.m, Caspary Auditorium

Ronald M. Evans, Ph.D.,
Professor and Director,
Gene Expression Laboratory,
March of Dimes Chair in Molecular and Developmental Biology,
Salk Institute for Biological Studies
Investigator, Howard Hughes Medical Institute

Nuclear Receptors and Diabesity: a Roadmap to Human Health

Recommended Readings

Empirical Articles

Jonker, J. W., Suh, J. M., Atkins, A. R., Ahmadian, M., Li, P., Whyte, J., … Evans, R. M. (2012). A PPARγ-FGF1 axis is required for adaptive adipose remodelling and metabolic homeostasis. Nature, 485(7398), 391–394. doi:10.1038/nature10998

Suh, J. M., Jonker, J. W., Ahmadian, M., Goetz, R., Lackey, D., Osborn, O., … Evans, R. M. (2014). Endocrinization of FGF1 produces a neomorphic and potent insulin sensitizer. Nature, 513(7518), 436–439. doi:10.1038/nature13540

Review Papers

Evans, R. M., & Mangelsdorf, D. J. (2014). Nuclear Receptors, RXR, and the Big Bang. Cell, 157(1), 255–66. doi:10.1016/j.cell.2014.03.012

Hong, S.-H., Ahmadian, M., Yu, R. T., Atkins, A. R., Downes, M., & Evans, R. M. (2014). Nuclear receptors and metabolism: from feast to famine. Diabetologia, 57(5), 860–867. doi:10.1007/s00125-014-3209-9

Recommended Readings: Kivanc Birsoy, Ph.D., January 14

Special Lecture
Friday, January 14, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Kivanc Birsoy, Ph.D.
Jane Coffin Childs Medical Fund Fellow,
Whitehead Institute for Biomedical Research
Broad Institute of Harvard and MIT

Systematic Approaches to Study Metabolic Plasticity of Cancer Cells

Recommended Readings

Empirical Articles

Birsoy, K., Possemato, R., Lorbeer, F. K., Bayraktar, E. C., Thiru, P., Yucel, B., … Sabatini, D. M. (2014). Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides. Nature, 508(7494), 108–112. doi:10.1038/nature13110

Birsoy, K., Wang, T., Possemato, R., Yilmaz, O. H., Koch, C. E., Chen, W. W., … Sabatini, D. M. (2013). MCT1-mediated transport of a toxic molecule is an effective strategy for targeting glycolytic tumors. Nature Genetics, 45(1), 104–108. doi:10.1038/ng.2471

Grabiner, B. C., Nardi, V., Birsoy, K., Possemato, R., Shen, K., Sinha, S., … Sabatini, D. M. (2014). A diverse array of cancer-associated MTOR mutations are hyperactivating and can predict rapamycin sensitivity. Cancer Discovery, 4(5), 554–563. doi:10.1158/2159-8290.CD-13-0929

Review Papers

Birsoy, K., Sabatini, D. M., & Possemato, R. (2012). Untuning the tumor metabolic machine: Targeting cancer metabolism: a bedside lesson. Nature Medicine, 18(7), 1022–1023. doi:10.1038/nm.2870

Recommended Readings: Liangcai Gu, Ph.D. January 7

Special Lecture
Wednesday, January 7, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Liangcai Gu, Ph.D.
Research Fellow,
Department of Genetics,
Harvard Medical School

In Situ Sequencing of Molecular Interactomes

Recommended Readings

Empirical Articles

Gu, L., Li, C., Aach, J., Hill, D. E., Vidal, M., & Church, G. M. (2014). Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature, 515(7528), 554–557. doi:10.1038/nature13761

Gu, L., Wang, B., Kulkarni, A., Geders, T. W., Grindberg, R. V, Gerwick, L., … Sherman, D. H. (2009). Metamorphic enzyme assembly in polyketide diversification. Nature, 459(7247), 731–735. doi:10.1038/nature07870

Li, J., Gu, L., Aach, J., & Church, G. M. (2014). Improved cell-free RNA and protein synthesis system. PLOS ONE, 9(9), e106232. doi:10.1371/journal.pone.0106232

Review Papers

Jones, A. C., Gu, L., Sorrels, C. M., Sherman, D. H., & Gerwick, W. H. (2009). New tricks from ancient algae: natural products biosynthesis in marine cyanobacteria. Current Opinion in Chemical Biology, 13(2), 216–23. doi:10.1016/j.cbpa.2009.02.019

Recommended Readings: Louis M. Staudt, M.D., Ph.D. January 9

Friday Lecture Series
Friday, January 9, 2015
3:45 p.m., Caspary Auditorium

Louis M. Staudt, M.D., Ph.D.
Director, Center for Cancer Genomics
Co-chief, Lymphoid Malignancies Branch
Head, Molecular Biology of Lymphoid Malignancies Section,
Center for Cancer Research,
National Cancer Institute at the National Institutes of Health

Therapy of Lymphoma Inspired by Functional and Structural Genomics

Recommended Readings

Empirical Articles

Alizadeh, A., Eisen, M., Davis, R., & Ma, C. (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403(6769), 503-511.

Ngo, V. N., Davis, R. E., Lamy, L., Yu, X., Zhao, H., Lenz, G., … Staudt, L. M. (2006). A loss-of-function RNA interference screen for molecular targets in cancer. Nature, 441(7089), 106–110. doi:10.1038/nature04687

Rosenwald, A., Wright, G., Chan, W. C., Connors, J. M., Campo, E., Fisher, R. I., … Staudt, L. M. (2002). The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. The New England Journal of Medicine, 346(25), 1937–1947. doi:10.1056/NEJMoa012914

Yang, Y., III, A. S., Emre, N., & Ceribelli, M. (2012). Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma. Cancer Cell, 21(6), 723–737. doi:10.1016/j.ccr.2012.05.024.Exploiting

Review Papers

Lenz, G., & Staudt, L. M. (2010). Aggressive lymphomas. The New England Journal of Medicine, 362(15), 1417–1429. doi:10.1056/NEJMra0807082

Shaffer, A. L., Young, R. M., & Staudt, L. M. (2012). Pathogenesis of human B cell lymphomas. Annual Review of Immunology, 30, 565–610. doi:10.1146/annurev-immunol-020711-075027

Recommended Readings: Rachel Green, Ph.D. December 10

Special Seminar Series
Wednesday, December 10, 2014
4:00 p.m., Carson Family Auditorium (CRC)

Rachel Green, Ph.D.
Professor,
Department of Molecular Biology and Genetics,
Johns Hopkins University School of Medicine
Investigator,
Howard Hughes Medical Institute

Intimate Connections Between mRNA Decay and Translation

Recommended Readings

Empirical Articles

Djuranovic, S., Nahvi, A., & Green, R. (2012). miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science, 336(6078), 237–240. doi:10.1126/science.1215691

Koutmou, K. S., McDonald, M. E., Brunelle, J. L., & Green, R. (2014). RF3:GTP promotes rapid dissociation of the class 1 termination factor. RNA, 20(5), 609–620. doi:10.1261/rna.042523.113

Shoemaker, C. J., Eyler, D. E., & Green, R. (2010). Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay. Science, 330(6002), 369–372. doi:10.1126/science.1192430

Shoemaker, C. J., & Green, R. (2011). Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast. Proceedings of the National Academy of Sciences, 108(51), E1392–8. doi:10.1073/pnas.1113956108

Review Papers

Dever, T. E., & Green, R. (2012). The elongation, termination, and recycling phases of translation in eukaryotes. Cold Spring Harbor Perspectives in Biology, 4(7), a013706. doi:10.1101/cshperspect.a013706

Shoemaker, C. J., & Green, R. (2012). Translation drives mRNA quality control. Nature Structural & Molecular Biology, 19(6), 594–601. doi:10.1038/nsmb.2301

Recommended Readings: Rudolf Jaenisch, M.D. December 12

Friday Lecture Series
Friday, December 12, 2014
3:45 p.m., Caspary Auditorium

Rudolf Jaenisch, M.D.
Professor of Biology,
Massachusetts Institute of Technology
Member,
Whitehead Institute for Biomedical Research

iPS Cell Technology, Gene Editing and Disease Research

Recommended Readings

Empirical Articles

Chung, C. Y., Khurana, V., Auluck, P. K., Tardiff, D. F., Mazzulli, J. R., Soldner, F., … Lindquist, S. (2013). Identification and rescue of α-synuclein toxicity in Parkinson patient-derived neurons. Science, 342(6161), 983–987. doi:10.1126/science.1245296

Li, Y., Wang, H., Muffat, J., Cheng, A. W., Orlando, D. a, Lovén, J., … Jaenisch, R. (2013). Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons. Cell Stem Cell, 13(4), 446–458. doi:10.1016/j.stem.2013.09.001

Soldner, F., Laganière, J., Cheng, A. W., Hockemeyer, D., Gao, Q., Alagappan, R., … Jaenisch, R. (2011). Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell, 146(2), 318–331. doi:10.1016/j.cell.2011.06.019

Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013). One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell, 153(4), 910–918. doi:10.1016/j.cell.2013.04.025

Review Papers

Buganim, Y., Faddah, D. A., & Jaenisch, R. (2013). Mechanisms and models of somatic cell reprogramming. Nature Reviews Genetics, 14(6), 427–439. doi:10.1038/nrg3473

Theunissen, T. W., & Jaenisch, R. (2014). Molecular Control of Induced Pluripotency. Cell Stem Cell, 14(6), 720–734. doi:10.1016/j.stem.2014.05.002

Recommended Readings: Thomas Südhof, M.D. December 5

Friday Lecture Series
Friday, December 5, 2014
3:45 p.m., Caspary Auditorium

Thomas Südhof, M.D.
Avram Goldstein Professor,
Department of Molecular and Cellular Physiology,
Stanford School of Medicine
Investigator,
Howard Hughes Medical Institute

Cracking the Neurexin Code – Towards a Molecular Logic of Neural Circuits

Recommended Readings

Empirical Articles

Gokce, O., & Südhof, T. C. (2013). Membrane-tethered monomeric neurexin LNS-domain triggers synapse formation. The Journal of Neuroscience, 33(36), 14617–14628. doi:10.1523/JNEUROSCI.1232-13.2013

Rothwell, P. E., Fuccillo, M. V, Maxeiner, S., Hayton, S. J., Gokce, O., Lim, B. K., … Südhof, T. C. (2014). Autism-associated neuroligin-3 mutations commonly impair striatal circuits to boost repetitive behaviors. Cell, 158(1), 198–212. doi:10.1016/j.cell.2014.04.045

Treutlein, B., Gokce, O., Quake, S. R., & Südhof, T. C. (2014). Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Proceedings of the National Academy of Sciences, 111(13), E1291–E1299. doi:10.1073/pnas.1403244111

Tsetsenis, T., Boucard, a. a., Arac, D., Brunger, a. T., & Sudhof, T. C. (2014). Direct visualization of trans-synaptic neurexin-neuroligin interactions during synapse formation. Journal of Neuroscience, 34(45), 15083–15096. doi:10.1523/JNEUROSCI.0348-14.2014

Review Articles

Südhof, T. C. (2008). Neuroligins and neurexins link synaptic function to cognitive disease. Nature, 455(7215), 903–911. doi:10.1038/nature07456

Südhof, T. C. (2014). The molecular machinery of neurotransmitter release (Nobel Lecture). Angewandte Chemie, 53(47), 12696–12717. doi:10.1002/anie.201406359

Recommended Readings: Charles D. Gilbert, M.D., Ph.D. December 15

Monday Lecture Series
Monday, December 15, 2014
4:00 p.m., Carson Family Auditorium

Charles D. Gilbert, M.D., Ph.D.
Arthur and Janet Ross Professor and Head,
Laboratory of Neurobiology,
The Rockefeller University

The Dynamic Brain

Recommended Readings

Empirical Articles

Piëch, V., & Li, W., & Gilbert, C. D. (2013). Network model of top-down influences on local gain and contextual interactions in visual cortex. Proceedings of the National Academy of Sciences. 110(43), E4108-E4117. doi:10.1073/pnas.1317019110

Ramalingam, N., McManus, J. N. J., Li, W., & Gilbert, C. D. (2013). Top-down modulation of lateral interactions in visual cortex. The Journal of Neuroscience, 33(5), 1773–1789. doi:10.1523/JNEUROSCI.3825-12.2013

Yamahachi, H., Marik, S., McManus, J., Denk, W., & Gilbert, C. D. (2009). Rapid axonal sprouting and pruning accompany functional reorganization in primary visual cortex. Neuron, 64(5), 719-729. doi:10.1016/j.neuron.2009.11.026

Review Papers

Gilbert, C. D., & Li, W. (2013). Top-down influences on visual processing. Nature Reviews Neuroscience, 14(5), 350–363. doi:10.1038/nrn3476

Gilbert, C., & Li, W. (2012). Adult visual cortical plasticity. Neuron, 75(2), 250–264. doi:10.1016/j.neuron.2012.06.030

Recommended Readings: Ali H. Brivanlou, Ph.D. November 24

Monday Lecture Series
Monday, November 24, 2014
4:00 p.m., Carson Family Auditorium

Ali H. Brivanlou, Ph.D.
Robert and Harriet Heilbrunn Professor and Head,
Laboratory of Stem Cell Biology and Molecular Embryology,
The Rockefeller University

Dynamic Patterns: Self-Organization of Human Embryonic Cells

Recommended Readings

Empirical Articles

Arduini, B., & Brivanlou, A. (2012). Modulation of FOXD3 activity in human embryonic stem cells directs pluripotency and paraxial mesoderm fates. Stem Cells, 30(10), 2188–2198. doi:10.1002/stem.2012

Ozair, M., Noggle, S., & Warmflash, A. (2013). SMAD7 directly converts human embryonic stem cells to telencephalic fate by a default mechanism. Stem Cells, 31(1), 35–47. doi:10.1002/stem.1246.SMAD7

Rosa, A., Papaioannou, M. D., Krzyspiak, J. E., & Brivanlou, A. H. (2014). miR-373 is regulated by TGFβ signaling and promotes mesendoderm differentiation in human embryonic stem cells. Developmental Biology, 391(1), 81–88. doi:10.1016/j.ydbio.2014.03.020

Warmflash, A., Sorre, B., Etoc, F., Siggia, E. D., & Brivanlou, A. H. (2014). A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nature Methods, 11(8). doi:10.1038/nmeth.3016

Review Article

Muñoz-Sanjuán, I., & Brivanlou, A. H. (2002). Neural induction, the default model, and embryonic stem cells. Nature Reviews Neuroscience, 3(4), 271–280. doi:10.1038/nrn786