Recommended Readings: Tania Baker Ph.D. Friday, November 18, 2016

Friday Lectures

Friday, November 18, 2016   3:45 p.m.

Caspary Auditorium

Tania Baker, Ph.D.

Edwin C. Whitehead Professor of Biology, MIT

Investigator, HHMI

Operations of AAA+ Unfoldase Motors:

Powerful Destroyers and Activators of Protein Function

Selected Publications:

Baker, Tania A.; Sauer, Robert T.  ClpXP, an ATP-powered unfolding and protein-degradation machine.    BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH.   1823(Special Issue SI): 15-28     JAN 2012

Stinson, Benjamin M.; Nager, Andrew R.; Glynn, Steven E.; et al.  Nucleotide Binding and Conformational Switching in the Hexameric Ring of a AAA plus Machine. CELL   153(3):628-639    APR 25 2013

Glynn, Steven E.; Nager, Andrew R.; Baker, Tania A.; et al.   Dynamic and static components power unfolding in topologically closed rings of a AAA plus proteolytic machine.   NATURE STRUCTURAL & MOLECULAR BIOLOGY.  19(6):616-+   JUN 2012

Cordova, Juan Carlos; Olivares, Adrian O.; Shin, Yongdae; et al.    Stochastic but Highly Coordinated Protein Unfolding and Translocation by the ClpXP Proteolytic Machine.  CELL    158(3): 647-658     JUL 31 2014

Olivares, Adrian O.; Nager, Andrew R.; Iosefson, Ohad; et al.   Mechanochemical basis of protein degradation by a double-ring AAA plus machine.   NATURE STRUCTURAL & MOLECULAR BIOLOGY    21(10): 871-875    OCT 2014


Recommended Readings: Michael O’Donnell Ph.D. Monday December 12, 2016

Monday Lectures

 December 12, 2016

4:00 p.m.  Carson Family Auditorium  CRC

Michael O’Donnell  Ph.D.

HHMI Investigator, and Anthony and Judith Evnin Professor
Laboratory of DNA Replication

The Rockefeller University

The Eukaryotic Replisome

Recommended Readings:

O’Donnell, Mike; Li, Huilin   The Eukaryotic Replisome Goes Under the Microscope.  CURRENT BIOLOGY  26(6): R247-R256      MAR 21 2016

Yuan, Zuanning; Bai, Lin; Sun, Jingchuan; et al.   Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation.  NATURE STRUCTURAL & MOLECULAR BIOLOGY   23(3): 217-224     MAR 2016

Sun, Jingchuan; Shi, Yi; Georgescu, Roxana E.; et al.   The architecture of a eukaryotic replisome.   NATURE STRUCTURAL & MOLECULAR BIOLOGY    22(12): 976-982 DEC 2015

Georgescu, Roxana E.; Schauer, Grant D.; Yao, Nina Y.; et al.  Reconstitution of a eukaryotic replisome reveals suppression mechanisms that define leading/lagging strand operation.      ELIFE    4: e04988     APR 14 2015

O’Donnell, Michael; Langston, Lance; Stillman, Bruce  Principles and Concepts of DNA Replication in Bacteria, Archaea, and Eukarya .   COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY    5(7): a010108

Recommended Readings: Jennifer A. Zallen Ph.D. Friday November 11, 2016

Friday Lectures

Frfday, November 11, 2016   3:45 p.m.

Caspary Auditorium

Jennifer A. Zallen, Ph.D.

HHMI Investigator / Member, Sloan Kettering Institute

Signals and Forces that Control Multicellular

Organization in the Embryo

Recommended Readings:

Mao, Qiyan; Lecuit, Thomas    Mechanochemical Interplay Drives Polarization in Cellular and Developmental Systems.  Book Series: Current Topics in Developmental Biology   Volume:116   Pages: 633-+    2016   Edited by: Wassarman, PM

Gouti, Mina; Metzis, Vicki; Briscoe, James.  The route to spinal cord cell types: a tale of signals and switches.TRENDS IN GENETICS   31(6): 282-289   Published: JUN 2015

Uriu, Koichiro; Morelli, Luis G.; Oates, Andrew C.  Interplay between intercellular signaling and cell movement in development.  SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY    35: 66-72      NOV 2014

Neijts, Roel; Simmini, Salvatore; Giuliani, Fabrizio; et al   Region-Specific Regulation of Posterior Axial Elongation During Vertebrate Embryogenesis.  DEVELOPMENTAL DYNAMICS   243(1. Special Issue: SI): 88-98    JAN 2014

 Zallen, Jennifer A.; Blankenship, J. Todd   Multicellular dynamics during epithelial elongation.  SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY.   19(3): 263-270 : JUN 2008

Recommended Readings: Elaine Fuchs PhD October 24, 2016

Monday Lecture Series

Monday October 24, 2016   3:45 p.m.

Caspary Auditorium

Elaine Fuchs, Ph.D.

Rebecca Lancefield Professor

Laboratory of Mammalian Cell Biology and Development

Skin Stem Cells in Silence, Action and Cancer

Recommended Readings:

Quist, S. R.; Eckardt, M.; Kriesche, A.; et al.  Expression of epidermal stem cell markers in skin and adnexal malignancies. BRITISH JOURNAL OF DERMATOLOGY   175(3):520-530     SEP 2016

 Holland, Jane D.; Klaus, Alexandra; Garratt, Alistair N.; et al.  Wnt signaling in stem and cancer stem cells.  CURRENT OPINION IN CELL BIOLOGY    25(2):254-264  APR 2013

Arwert, Esther N.; Hoste, Esther; Watt, Fiona M.    Epithelial stem cells, wound healing and cancer.  NATURE REVIEWS CANCER   12(3):170-180   MAR 2012

Blanpain, Cedric; Fuchs, Elaine  STEM CELL PLASTICITY Plasticity of epithelial stem cells in tissue regeneration.  SCIENCE   344(6189):1243-+  ( Article Number: 1242281)  JUN 13 2014

Hsu, Ya-Chieh; Li, Lishi; Fuchs, Elaine  Transit-Amplifying Cells Orchestrate Stem Cell Activity and Tissue Regeneration. CELL   157(4):935-949     MAY 8 2014

Fuchs, Elaine; Chen, Ting  A matter of life and death: self-renewal in stem cells.  EMBO REPORTS   14 (1): 39-48   JAN 2013 

Oshimori, Naoki; Fuchs, Elaine   The Harmonies Played by TGF-beta in Stem Cell Biology.    CELL STEM CELL   11(6):751-764    DEC 7 2012

Recommended Readings: Nicole King Ph.D. October 7 2016

Friday Lecture Series

Friday October 7, 2016   3:45 p.m.

The Fairfield Osborn Memorial Lecture

Caspary Auditorium

Nicole King

Professor, and HHMI Investigator

Dept.of Molecular and Cell Biology, Division of Genetics, Genomics and Development

University of California Berkeley

Bacteria as Master Regulators and Aphrodisiacs

Recommended Readings:

Anderson, Douglas P.; Whitney, Dustin S.; Hanson-Smith, Victor; et al.  Evolution of an ancient protein function involved in organized multicellularity in animals. ELIFE                   5: e10147    JAN 7 2016

Alegado, Rosanna A.; King, Nicole  Bacterial Influences on Animal OriginsCOLD SPRING HARBOR PERSPECTIVES IN BIOLOGY    6(11): a016162  NOV 2014

King, Nicole.  Evolutionary Transitions to Multicellular Life Principles and Mechanisms Forrward.  EVOLUTIONARY TRANSITIONS TO MULTICELLULAR LIFE: PRINCIPLES AND MECHANISMS   Book Series:Advances in Marine Genomics   Volume: 2   Pages: V-VI    2015

King, Nicole; Mueller, Susann.  Environmental microbiology: Revisiting the physiology of microorganisms on the single cell scale. CURRENT OPINION IN MICROBIOLOGY     Volume: 25   Pages: V-VI   Published: JUN 2015

Recommended Readings: Hermann Steller, Ph.D May 5

Monday Lecture Series
Monday, May 5, 2014
4:00 p.m., Carson Family Auditorium

Hermann Steller, Ph.D
Strang Professor, Strang Laboratory of Apoptosis and Cancer Biology
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Regulation of Protein Degradation in Development, Aging and Disease

Recommended Readings:

Empirical Articles

Bader, M., Benjamin, S., Wapinski, O. L., Smith, D. M., Goldberg, A. L., & Steller, H. (2011). A conserved F box regulatory complex controls proteasome activity in Drosophila. Cell, 145(3), 371–382. doi:10.1016/j.cell.2011.03.021

Cho-Park, P. F., & Steller, H. (2013). Proteasome regulation by ADP-ribosylation. Cell, 153(3), 614–627. doi:10.1016/j.cell.2013.03.040

Review Papers

Finley, D. (2009). Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annual Review of Biochemistry, 78(1), 477–513. doi:10.1146/annurev.biochem.78.081507.101607

Glickman, M. H., & Ciechanover, A. (2002). The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiological Reviews, 82(2), 373–428. doi:10.1152/physrev.00027.2001

Murata, S., Yashiroda, H., & Tanaka, K. (2009). Molecular mechanisms of proteasome assembly. Nature Reviews Molecular Cell Biology, 10(2), 104–15. doi:10.1038/nrm2630

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: 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

HHMI News: Janelia Farm’s Newest Addition to HMMER

A few weeks after its release, the Janelia Farm’s Jackhmmer algorithm — an iterative search method in the HMMER package similar to the NCBI’s PSI-BLAST algorithm — is performing as expected.  The new algorithm takes advantage of the sophisticated probabilistic models that underpin profile Hidden Markov Models (HMMs).

Profile HMMs are the most sensitive tools to use, which is why many protein family databases use them. Bench biologists now have a fast method for discovering the likely structure of a sequence which can allow for the creation of functional hypothesis that can guide experiments.

Recommended Readings: Robert B. Darnell M.D., PhD March 14, 2011

Monday Lecture Series

Maps of the RNA World

Robert B. Darnell M.D. , PhD

Investigator, Howard Hughes Medical Institute

 Laboratory of  Molecular Neuro-oncology

March 14, 2011

4:00 p.m.-5:00 p.m. Caspary Auditorium

Recommended Readings

Brooks, A.N.; Yang, L.; Duff, M.O.  et al.  2011.  Conservation of an  RNA regulatory map between Drosophila and mammalsGenome Research.  21(2):193-101

Misquitta-Ali, C.M.; Cheng, E.; O’Hanlon, D. et al.  2011.  Global profiling and moelcualr characterization of alternative splicing events misregulated in lung cancerMolecular and Cellular Biology.   31(1):138-150

Licatalosi, D.D.; and R.B. Darnell.  2010.  Applications of next-generation sequencing RNA processing and its regulation: global insights into biological networks.   Nature Reviews Genetics.   11(1):75-87

Zhang, C.L.; Frias, M.A.; Mele, A. et al.  2010.  Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls.  Science.   329(5990):439-443

Yano, M.; Hayakawa-Yano, Y; Mele, A.  et al.  2010.  Nova2 regulates neuronal migration through an RNA switch in disabled-1 signaling.  Neuron.   66(6):848-858

Chi, S.W.; Sang, J.B.; Mele, A. et al.  2009.   Argonaute HITS-CLIP decodes microRNA-mRNA interactions mapsNATURE   460(7254):479-486

Lactalosi, D. D.; Mele A.; and J.J. Fak.  2008.  HITS-CLIP yields genome-wide insights into brain alternative RNA processing.  NATURE.   456(7221):464-U22

Darnell, R.B.  2006.  Developing global insight into RNA regulation.  Cold Spring Harbor Symposium on Quantitative Biology( May 31-June 5, 2006) Cold Spring, NY.   71:321-327.