Recommended Readings: Irving Weissman, M.D.

Friday Lecture Series

The Philip Levine Memorial Lecture

Normal and Neoplastic Stem Cells

Irving Weissman, M.D., director,

Institute of Stem Cell Biology and Regenerative Medicine;

V&D Ludwig Professor of Clinical Cancer Research; and professor, departments of

developmental biology, pathology and neurosurgery and biology,

Stanford University School of Medicine

November 1, 2013

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

Caspary Auditorium

Recommended Readings

Chao, M. P., Majeti, R., & Weissman, I. L. (2012). Programmed cell removal: A new obstacle in the road to developing cancer. Nature Reviews Cancer, 12(1), 58-67

Jan, M., Snyder, T. M., Corces-Zimmerman, M. R., Vyas, P., Weissman, I. L., Quake, S. R., & Majeti, R. (2012). Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Science Translational Medicine, 4(149)

Lu, R., Neff, N. F., Quake, S. R., & Weissman, I. L. (2011). Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nature Biotechnology, 29(10), 928-934

Pang, W. W., Pluvinage, J. V., Price, E. A., Sridhar, K., Arber, D. A., Greenberg, P. L., . . . Weissman, I. L. (2013). Hematopoietic stem cell and progenitor cell mechanisms in myelodysplastic syndromes. Proceedings of the National Academy of Sciences of the United States of America, 110(8), 3011-3016

Pang, W. W., Price, E. A., Sahoo, D., Beerman, I., Maloney, W. J., Rossi, D. J., . . . Weissman, I. L. (2011). Human bone marrow hematopoietic stem cells are increased in frequency and myeloid-biased with age. Proceedings of the National Academy of Sciences of the United States of America, 108(50), 20012-20017

Uchida, N., Chen, K., Dohse, M., Hansen, K. D., Dean, J., Buser, J. R., . . . Back, S. A. (2012). Human neural stem cells induce functional myelination in mice with severe dysmyelination. Science Translational Medicine, 4(155)

Weissman, I. (2012). Stem cell therapies could change medicine… if they get the chance. Cell Stem Cell, 10(6), 663-665


Recommended Readings: Juleen R. Zierath, Ph.D.

Friday Lecture Series

Nicholson Lecture

Molecular Mechanisms for the Health-promoting Effects of Exercise: Why Muscle Matters!

Juleen R. Zierath, Ph.D., professor of physiology, department of molecular

medicine and surgery, Section for Integrative Physiology, Karolinska Institutet;

professor of integrative physiology and scientific director,

Novo Nordisk Foundation Center for Basic Metabolic Research,

Copenhagen University

October 25, 2013

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

Caspary Auditorium

Recommended Readings

Barrès, R., Yan, J., Egan, B., Treebak, J. T., Rasmussen, M., Fritz, T., . . . Zierath, J. R. (2012). Acute exercise remodels promoter methylation in human skeletal muscle. Cell Metabolism, 15(3), 405-411

Cantó, C., Jiang, L. Q., Deshmukh, A. S., Mataki, C., Coste, A., Lagouge, M., . . . Auwerx, J. (2010). Interdependence of AMPK and SIRT1 for metabolic adaptation to fasting and exercise in skeletal muscle. Cell Metabolism, 11(3), 213-219

Egan, B., Carson, B. P., Garcia-Roves, P. M., Chibalin, A. V., Sarsfield, F. M., Barron, N., . . . O’Gorman, D. J. (2010). Exercise intensity-dependent regulation of peroxisome proliferator-activated receptor γ coactivator-1α mRNA abundance is associated with differential activation of upstream signalling kinases in human skeletal muscle. Journal of Physiology, 588(10), 1779-1790

Egan, B., O’Connor, P. L., Zierath, J. R., & O’Gorman, D. J. (2013). Time course analysis reveals gene-specific transcript and protein kinetics of adaptation to short-term aerobic exercise training in human skeletal muscle. PLoS ONE, 8(9)

Egan, B., & Zierath, J. R. (2013). Exercise metabolism and the molecular regulation of skeletal muscle adaptation. Cell Metabolism, 17(2), 162-184

Russell, A. P., Lamon, S., Boon, H., Wada, S., Güller, I., Brown, E. L., . . . Akimoto, T. (2013). Regulation of miRNAs in human skeletal muscle following acute endurance exercise and short-term endurance training. Journal of Physiology, 591(18), 4637-4653

Szekeres, F., Chadt, A., Tom, R. Z., Deshmukh, A. S., Chibalin, A. V., Björnholm, M., . . . Zierath, J. R. (2012). The rab-GTPase-activating protein TBC1D1 regulates skeletal muscle glucose metabolism. American Journal of Physiology – Endocrinology and Metabolism, 303(4), E524-E533


Recommended Readings: Nathaniel Heintz, Ph.D. Monday, Oct. 21

Understanding Neuronal Diversity: TRAP, Molecular Phenotyping and 5-hydroxymethylcytosine
Nathaniel Heintz, Ph.D.
Investigator, Howard Hughes Medical Institute
James and Marilyn Simons Professor
Laboratory of Molecular Biology
The Rockefeller University
4:00 p.m., Carson Family Auditorium

Recommended Readings

Review Paper

Branco, M. R., Ficz, G., & Reik, W. (2012). Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nature reviews. Genetics, 13(1), 7–13. doi:10.1038/nrg3080

Empirical Articles

Doyle, J. P., Dougherty, J. D., Heiman, M., Schmidt, E. F., Stevens, T. R., Ma, G., … Heintz, N. (2008). Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell, 135(4), 749–762. doi:10.1016/j.cell.2008.10.029

Gong, S., Zheng, C., Doughty, M. L., Losos, K., Didkovsky, N., Schambra, U. B., … Heintz, N. (2003). A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature, 425(6961), 917–925. doi:10.1038/nature02033

Heiman, M., Schaefer, A., Gong, S., Peterson, J. D., Day, M., Ramsey, K. E., … Heintz, N. (2008). A translational profiling approach for the molecular characterization of CNS cell types. Cell, 135(4), 738–748. doi:10.1016/j.cell.2008.10.028

Heintz, N. (2004). Gene expression nervous system atlas (GENSAT). Nature neuroscience, 7(5), 483. doi:10.1038/nn0504-483

Kriaucionis, S., & Heintz, N. (2009). The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 324(5929), 929–30. doi:10.1126/science.1169786

Recommended Readings: George Q. Daley, M.D., Ph.D.

Friday Lecture Series

Maclyn McCarty Memorial Lecture

Reprogramming Cell Identity

George Q. Daley, M.D., Ph.D., Samuel E. Lux, IV Professor of Hematology and

director,Stem Cell Transplantation Program, Boston Children’s Hospital;

investigator, Howard Hughes Medical Institute

October 18, 2013

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

Caspary Auditorium

Recommended Readings

Cherry, A. B. C., & Daley, G. Q. (2012). Reprogramming cellular identity for regenerative medicine. Cell, 148(6), 1110-1122

Morris, S. A., & Daley, G. Q. (2013). A blueprint for engineering cell fate: Current technologies to reprogram cell identity. Cell Research, 23(1), 33-48

Müller, L. U. W., Milsom, M. D., Harris, C. E., Vyas, R., Brumme, K. M., Parmar, K., . . . Williams, D. A. (2012). Overcoming reprogramming resistance of fanconi anemia cells. Blood, 119(23), 5449-5457

Onder, T. T., Kara, N., Cherry, A., Sinha, A. U., Zhu, N., Bernt, K. M., . . . Daley, G. Q. (2012). Chromatin-modifying enzymes as modulators of reprogramming. Nature, 483(7391), 598-602

Robinton, D. A., & Daley, G. Q. (2012). The promise of induced pluripotent stem cells in research and therapy. Nature, 481(7381), 295-305

Zhang, J., Nuebel, E., Daley, G. Q., Koehler, C. M., & Teitell, M. A. (2012). Metabolic regulation in pluripotent stem cells during reprogramming and self-renewal. Cell Stem Cell, 11(5), 589-595


Recommended Readings: Rob Knight, Ph.D. Wednesday, Oct. 30, 2013

Wednesday, October 30, 2013
4:00 p.m., Carson Family Auditorium

Rob Knight, Ph.D.
HHMI Early Career Scientist and Professor
Department of Chemistry & Biochemistry, Department of Computer Science, and BioFrontiers Institute
University of Colorado at Boulder

Gut Microbes and their Role in Malnutrition and Obesity

Recommended Readings:

Review Papers

Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012). The impact of the gut microbiota on human health: an integrative view. Cell, 148(6), 1258–1270. doi:10.1016/j.cell.2012.01.035

Gevers, D., Knight, R., Petrosino, J. F., Huang, K., McGuire, A. L., Birren, B. W., … Huttenhower, C. (2012). The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biology, 10(8), e1001377. doi:10.1371/journal.pbio.1001377

Hamady, M., & Knight, R. (2009). Microbial community profiling for human microbiome projects : Tools , techniques , and challenges, Genome Research, 19(7), 1141–1152. doi:10.1101/gr.085464.108.19

Ley, R. E., Lozupone, C. a, Hamady, M., Knight, R., & Gordon, J. I. (2008). Worlds within worlds: evolution of the vertebrate gut microbiotaNature Reviews Microbiology6(10), 776–788. doi:10.1038/nrmicro1978

Empirical Articles

Costello, E., Lauber, C., & Hamady, M. (2009). Bacterial community variation in human body habitats across space and time. Science, 326, 8–11.

The Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–14. doi:10.1038/nature11234

Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A, Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences of the United States of America, 102(31), 11070–5. doi:10.1073/pnas.0504978102

Lozupone, C. A., Stombaugh, J., Gonzalez, A., Ackermann, G., Jansson, J. K., Gordon, J. I., … Knight, R. (2013). Meta-analyses of studies of the human microbiota, Genome Research, 23,1704–1714. doi:10.1101/gr.151803.112

Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., … Gordon, J. I. (2009). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480–484. doi:10.1038/nature07540

Turnbaugh, P. J., Ley, R. E., Mahowald, M. a, Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027–31. doi:10.1038/nature05414

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., … Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–7. doi:10.1038/nature11053

Recommended Readings: Bonnie Bassler, Ph.D.

Friday Lecture Series

Manipulating Quorum Sensing to Control Bacterial Pathogenesis

Bonnie Bassler, Ph.D., Squibb Professor in Molecular Biology and director,

Council on Science and Technology,

Princeton University

October 11, 2013

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

Caspary Auditorium

Recommended Readings

Bassler, B., & Vogel, J. (2013). Bacterial regulatory mechanisms: The gene and beyond. Current Opinion in Microbiology, 16(2), 109-111

Chen, G., Swem, L., Swem, D., Stauff, D., O’Loughlin, C., Jeffrey, P., . . . Hughson, F. (2011). A strategy for antagonizing quorum sensing. Molecular Cell, 42(2), 199-209

Stauff, D. L., & Bassler, B. L. (2011). Quorum sensing in chromobacterium violaceum: DNA recognition and gene regulation by the CviR receptor. Journal of Bacteriology, 193(15), 3871-3878

Swem, L. R., Swem, D. L., O’Loughlin, C. T., Gatmaitan, R., Zhao, B., Ulrich, S. M., & Bassler, B. L. (2009). A quorum-sensing antagonist targets both membrane-bound and cytoplasmic receptors and controls bacterial pathogenicity. Molecular Cell, 35(2), 143-153

Teng, S. -., Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., . . . Wingreen, N. S. (2011). Active regulation of receptor ratios controls integration of quorum-sensing signals in vibrio harveyi. Molecular Systems Biology, 7


Recommended Readings: Leonard Zon, M.D.

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

Leonard Zon, M.D.
Director of the Stem Cell Program at Children’s Hospital Boston
Grousbeck Professor of Pediatric Medicine, Harvard Medical School
Investigator, Howard Hughes Medical Institute

Pathways that Stimulate Stem Cell Development and Self-Renewal

Recommended Readings:

Review Papers

De Jong, J. L. O., & Zon, L. I. (2005). Use of the zebrafish system to study primitive and definitive hematopoiesis. Annual Review of Genetics, 39, 481–501. doi:10.1146/annurev.genet.39.073003.095931

Orkin, S. H., & Zon, L. I. (2008). Hematopoiesis: an evolving paradigm for stem cell biologyCell132(4), 631–644. doi:10.1016/j.cell.2008.01.025

White, R., Rose, K., & Zon, L. (2013). Zebrafish cancer: the state of the art and the path forward. Nature Reviews Cancer, 13(9), 624–636. doi:10.1038/nrc3589

Zon, L. I. (2008). Intrinsic and extrinsic control of haematopoietic stem-cell self-renewal. Nature, 453(7193), 306–313. doi:10.1038/nature07038

Empirical Articles

Goessling, W., North, T. E., Loewer, S., Lord, A. M., Lee, S., Stoick-Cooper, C. L., … Zon, L. I. (2009). Genetic interaction of PGE2 and Wnt signaling regulates developmental specification of stem cells and regeneration. Cell, 136(6), 1136–1147. doi:10.1016/j.cell.2009.01.015

Lengerke, C., Schmitt, S., Bowman, T. V, Jang, I. H., Maouche-Chretien, L., McKinney-Freeman, S., … Daley, G. Q. (2008). BMP and Wnt specify hematopoietic fate by activation of the Cdx-Hox pathway. Cell Stem Cell, 2(1), 72–82. doi:10.1016/j.stem.2007.10.022

North, T. E., Goessling, W., Peeters, M., Li, P., Ceol, C., Lord, A. M., … Zon, L. I. (2009). Hematopoietic stem cell development is dependent on blood flow. Cell, 137(4), 736–748. doi:10.1016/j.cell.2009.04.023

North, T. E., Goessling, W., Walkley, C. R., Lengerke, C., Kopani, K. R., Lord, A. M., … Zon, L. I. (2007). Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature, 447(7147), 1007–1011. doi:10.1038/nature05883

Making (and Learning) History!

Those who don’t know history are doomed to reinvent wheels and miss out on great stories! A historian and a young scientist discuss the rewards and importance of learning about the history of science.

Dr. Carol Moberg, historian of science and Senior Research Associate at The Rockefeller University, shares some of the stories behind her book, Entering an Unseen World, about the history and development of modern cell biology. She’s joined by Rockefeller University Graduate Fellow Joseph Luna, who lends his perspective on the value of studying the history of science for students and young scientists.

Science & the City Podcast

Recommended Readings: Hironori Funabiki, Ph.D.

Friday Lecture Series

Spindle or Envelope: Building Right on Chromosomes in Mitosis

Hironori Funabiki, Ph.D.,

associate professor, Laboratory of Chromosome and Cell Biology,

The Rockefeller University

October 4, 2013

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

Caspary Auditorium

Recommended Readings

Carmena, M., Wheelock, M., Funabiki, H., & Earnshaw, W. C. (2012). The chromosomal passenger complex (CPC): From easy rider to the godfather of mitosis. Nature Reviews Molecular Cell Biology, 13(12), 789-803

Funabiki, H., & Murray, A. W. (2000). The xenopus chromokinesin xkid is essential for metaphase chromosome alignment and must be degraded to allow anaphase chromosome movement. Cell, 102(4), 411-424

Kelly, A. E., Ghenoiu, C., Xue, J. Z., Zierhut, C., Kimura, H., & Funabiki, H. (2010). Survivin reads phosphorylated histone H3 threonine 3 to activate the mitotic kinase aurora B. Science, 330(6001), 235-239

Rivera, T., Ghenoiu, C., Rodríguez-Corsino, M., Mochida, S., Funabiki, H., & Losada, A. (2012). Xenopus shugoshin 2 regulates the spindle assembly pathway mediated by the chromosomal passenger complex. EMBO Journal, 31(6), 1467-1479

Sampath, S. C., Ohi, R., Leismann, O., Salic, A., Pozniakovski, A., & Funabiki, H. (2004). The chromosomal passenger complex is required for chromatin-induced microtubule stabilization and spindle assembly. Cell, 118(2), 187-202

Tseng, B. S., Tan, L., Kapoor, T. M., & Funabiki, H. (2010). Dual detection of chromosomes and microtubules by the chromosomal passenger complex drives spindle assembly. Developmental Cell, 18(6), 903-91