Recommended Readings: Tom Maniatis, Ph.D., Friday October 6th, 2017

Friday Lectures

Friday, October 06, 2017  3:45 p.m.

Caspary Auditorium

Tom Maniatis, Ph.D.

Isidore S. Edelman Professor and Chair

Department of Biochemistry and Molecular Biophysics

Columbia University Medical Center

The Generation and Function of Protocadherin Cell Surface Diversity in Mammalian Neural Circuit Assembly

Recommended Readings:

Technology Networks Wrong Wiring Causes Depression. Apr 28, 2017

Rubinstein, Rotem; Goodman, Kerry Marie; Maniatis, Tom; et al. (2017). Structural origins of clustered protocadherin-mediated neuronal barcoding. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 69 (SI): 140-150. PLEASE REQUEST FROM MARKUS LIBRARY.

Chen, Weisheng V.; Nwakeze, Chiamaka L.; Denny, Christine A.; et al. (2017). Pcdh alpha c2 is required for axonal tiling and assembly of serotonergic circuitries in mice. SCIENCE. 356 (6336): 406-410

Mountoufaris, George; Chen, Weisheng V.; Hirabayashi, Yusuke; et al. (2017). Multicluster Pcdh diversity is required for mouse olfactory neural circuit assembly. SCIENCE. 356 (6336): 411-413  

Goodman, Kerry Marie; Rubinstein, Rotem; Thu, Chan Aye; et al. (2016). gamma-Protocadherin structural diversity and functional implications. ELIFE. 5: e20930  

Chen, Weisheng V.; Maniatis, Tom (2013). Clustered protocadherins. DEVELOPMENT. 140 (16): 3297-3302

Lefebvre, Julie L.; Kostadinov, Dimitar; Chen, Weisheng V.; et al. (2012). Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. NATURE. 488 (7412): 517-+

Recommended Readings: Sue Biggins, Ph.D., Friday May 5th, 2017

Friday Lectures

Friday, May 5th, 2017   3:45 p.m.

Caspary Auditorium

Sue Biggins, Ph.D.

Member and Associate Director

Division of Basic Sciences

Fred Hutchinson Cancer Research Center

Sensing Tension at Kinetochores

Recommended Readings: 

Miller, Matthew P.; Asbury, Charles L.; Biggins, Sue (2016). A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments. CELL. 165(6): 1428-1439

Musacchio, Andrea (2015). The Molecular Biology of Spindle Assembly Checkpoint Signaling Dynamics. CURRENT BIOLOGY.  25(20): R1002-R1018

Biggins, Sue (2015). Under tension: Kinetochores and Basic Research. GENETICS. 200(3): 681-682

London, Nitobe; Biggins, Sue (2014). Signalling dynamics in the spindle checkpoint response. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 15 (11): 735-747

Sarangapani, Krishna K.; Duro, Eris; Deng, Yi; et al. (2014). Sister kinetochores are mechanically fused during meiosis I in yeast. SCIENCE. 346(6206): 248-251

Biggins, Sue (2013). The Composition, Functions, and Regulation of the Budding Yeast Kinetochore. GENETICS. 194(4): 817-846

Gonen, Shane; Akiyoshi, Bungo; Iadanza, Matthew G.; et al. (2012). The structure of purified kinetochores reveals multiple microtubule-attachment sites. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 19( 9): 925-929







Recommended Readings: Shixin Liu Ph.D. Monday November 14 2016

Monday Lectures

Monday November 14, 2016   3:45 p.m.

Caspary Auditorium

Shixin Liu   Ph.D.

Assistant Professor, The Rockefeller University

Laboratory of Nanoscale Biophysics and Biochemistry

Watching Biological Machines in Action

Recommended Readings:

 Liu, Shixin; Chistol, Gheorghe; Hetherington, Craig L.; et al.  A Viral Packaging Motor Varies Its DNA Rotation and Step Size to Preserve Subunit Coordination as the Capsid Fills.  CELL    157 (3):702-713     APR 24 2014

Chemla, Yann R.  High-Resolution, Hybrid Optical Trapping Methods, and Their Application to Nucleic Acid Processing Proteins.  BIOPOLYMERS   105(10): 704-714    OCT 2016

Ha, Taekjip.  Single-molecule methods leap aheadNATURE METHODS    11(10)1015-1018    OCT 2014

Guo, Peixuan; Grainge, Ian; Zhao, Zhengyi; et al.  Two classes of nucleic acid translocation motors: rotation and revolution without rotation. CELL AND BIOSCIENCE  4:54     SEP 16 2014

Casjens, Sherwood R.  The DNA-packaging nanomotor of tailed bacteriophages.  NATURE REVIEWS MICROBIOLOGY   9(9):647-657   SEP 2011

Chemla, YR; Aathavan, K; Michaelis, J; et al.  Mechanism of force generation of a viral DNA packaging motor. CELL   122(5 ): 683-692   : SEP 9 2005 

Recommended Readings: David Baker, Ph.D., April 29

Special Lecture Series
Wednesday, April 29, 2015
3:45 p.m., Carson Family Auditorium (CRC)

David Baker, Ph.D.,
Professor of Biochemistry,
University of Washington
Investigator, Howard Hughes Medical Institute

Post-Evolutionary Biology: Design of Novel Protein Structures, Functions and Assemblies

Recommended Readings

Empirical Articles

Bradley, P., Misura, K. M., & Baker, D. (2005). Toward high-resolution de novo structure prediction for small proteins. Science, 309(5742), 1868-1871.

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., … & Popović, Z. (2010). Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. doi:10.1038/nature09304

Eiben, C. B., Siegel, J. B., Bale, J. B., Cooper, S., Khatib, F., Shen, B. W., … & Baker, D. (2012). Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology, 30(2), 190-192. doi:10.1038/nbt.2109

Jiang, L., Althoff, E. A., Clemente, F. R., Doyle, L., Röthlisberger, D., Zanghellini, A., … & Baker, D. (2008). De novo computational design of retro-aldol enzymes. Science, 319(5868), 1387-1391. doi:10.1126/science.1152692

Review Papers

Adams, P. D., Baker, D., Brunger, A. T., Das, R., DiMaio, F., Read, R. J., … & Terwilliger, T. C. (2013). Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics, 42, 265-287.doi: 10.1146/annurev-biophys-083012-130253

Das, R., & Baker, D. (2008). Macromolecular modeling with Rosetta. Annual Review of Biophysics, 77, 363-382. doi:10.1146/annurev.biochem.77.062906.171838

Recommended Readings: Jue Chen, Ph.D., February 27

Friday Lecture Series / Ph.D. Recruitment Lecture
Friday, February 25, 2015
3:45 p.m., Caspary Auditorium

Jue Chen, Ph.D.,
Head of Laboratory of Membrane Biology and Biophysics,
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Understanding Molecular Pumps: Insights from Structural BiologyRecommended Readings

Empirical Articles

Chen, S., Oldham, M. L., Davidson, A. L., & Chen, J. (2013). Carbon catabolite repression of the maltose transporter revealed by X-ray crystallography. Nature, 499(7458), 364-368. doi:10.1038/nature12232

Jin, M. S., Oldham, M. L., Zhang, Q., & Chen, J. (2012). Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans. Nature. 490(7421), 566-569. doi:10.1038/nature11448

Oldham, M. L., Chen, S., & Chen, J. (2013). Structural basis for substrate specificity in the Escherichia coli maltose transport system. Proceedings of the National Academy of Sciences, 110(45), 18132-18137. doi:10.1073/pnas.1311407110

Review Papers

Chen, J. (2013). Molecular mechanism of the Escherichia coli maltose transporterCurrent Opinion in Structural Biology, 23(4), 492-498. doi: 10.1016/

Recommended Readings: Amédée des Georges, Ph.D. October 20

Special Lecture Series
Monday, October 20, 2014
4:00 p.m., Carson Family Auditorium

Amédée des Georges, Ph.D.
Postdoctoral Associate,
Department of Biochemistry and Molecular Biophysics,
Columbia University

Structures of Eukaryotic Translation Initiation Complexes by Single-Particle Cryo-EM, a Powerful Tool for the Study of Heterogeneous Samples

Recommended Readings

Empirical Articles

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature, 503(7477), 539–543. doi:10.1038/nature12658

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell, 153(5), 1108–1119. doi:10.1016/j.cell.2013.04.036

Hashem, Y., des Georges, A., Fu, J., Buss, S. N., Jossinet, F., Jobe, A., … Frank, J. (2013). High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature, 494(7437), 385–389. doi:10.1038/nature11872

Review Papers

Jackson, R. J., Hellen, C. U. T., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology, 11(2), 113–127. doi:10.1038/nrm2838

Recommended Readings: Thomas Walz, Ph.D. June 23

Special Seminar 
Monday, June 23, 2014
4:00 p.m., Carson Family Auditorium

Thomas Walz, Ph.D
Professor, Department of Cell Biology
Harvard Medical School
Investigator, Howard Hughes Medical Institute

Using Two-dimensional Crystals of Aquaporin-0 to Investigate Lipid-Protein Interactions

Recommended Readings:

Empirical Articles

Aponte-Santamaría, C., Briones, R., Schenk, A. D., Walz, T., & de Groot, B. L. (2012). Molecular driving forces defining lipid positions around aquaporin-0. Proceedings of the National Academy of Sciences, 109(25), 9887–9892. doi:10.1073/pnas.1121054109

Gonen, T., Cheng, Y., Sliz, P., Hiroaki, Y., Fujiyoshi, Y., Harrison, S. C., & Walz, T. (2005). Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature, 438(7068), 633–638. doi:10.1038/nature04321

Gonen, T., Sliz, P., Kistler, J., Cheng, Y., & Walz, T. (2004). Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature, 429(6988), 193–197. doi:10.1038/nature02503

Hite, R. K., Li, Z., & Walz, T. (2010). Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals. The EMBO Journal, 29(10), 1652–1658. doi:10.1038/emboj.2010.68

Review Papers

Gonen, T., & Walz, T. (2006). The structure of aquaporins. Quarterly Reviews of Biophysics, 39(4), 361–396. doi:10.1017/S0033583506004458

Raunser, S., & Walz, T. (2009). Electron crystallography as a technique to study the structure on membrane proteins in a lipidic environment. Annual Review of Biophysics, 38, 89–105. doi:10.1146/annurev.biophys.050708.133649

Recommended Readings: Angeline Lyon, Ph.D. Monday, January 6

Monday, January 6, 2014
4:00 p.m., Carson Family Auditorium

Angeline Lyon, Ph.D.
American Heart Association Postdoctoral Fellow
Life Sciences Institute, University of Michigan

Molecular Mechanisms of Phospholipase Cβ Regulation

Recommended Readings:

Empirical Articles

Hicks, S. N., Jezyk, M. R., Gershburg, S., Seifert, J. P., Harden, T. K., & Sondek, J. (2008). General and versatile autoinhibition of PLC isozymes. Molecular Cell, 31(3), 383–394. doi:10.1016/j.molcel.2008.06.018

Lyon, A. M., Dutta, S., Boguth, C. A., Skiniotis, G., & Tesmer, J. J. G. (2013). Full-length Gα(q)-phospholipase C-β3 structure reveals interfaces of the C-terminal coiled-coil domain. Nature: Structural & Molecular Biology, 20(3), 355–362. doi:10.1038/nsmb.2497

Lyon, A. M., Tesmer, V. M., Dhamsania, V. D., Thal, D. M., Gutierrez, J., Chowdhury, S., … Tesmer, J. J. G. (2011). An autoinhibitory helix in the C-terminal region of phospholipase C-β mediates Gαq activation. Nature: Structural & Molecular Biology, 18(9), 999–1005. doi:10.1038/nsmb.2095

Tadano, M., Edamatsu, H., Minamisawa, S., Yokoyama, U., Ishikawa, Y., Suzuki, N., … Kataoka, T. (2005). Congenital semilunar valvulogenesis defect in mice deficient in phospholipase C epsilon. Molecular and Cellular Biology, 25(6), 2191–2199. doi:10.1128/MCB.25.6.2191-2199.2005

Wang, H., Oestreich, E. A., Maekawa, N., Bullard, T. A., Vikstrom, K. L., Dirksen, R. T., … Smrcka, A. V. (2005). Phospholipase C epsilon modulates beta-adrenergic receptor-dependent cardiac contraction and inhibits cardiac hypertrophy. Circulation Research, 97(12), 1305–13. doi:10.1161/

Review Papers

Gresset, A., Sondek, J., & Harden, T. K. (2012). The phospholipase C isozymes and their regulationSub-Cellular Biochemistry58, 61–94. doi:10.1007/978-94-007-3012-0_3

Suh, P.-G., Park, J.-I., Manzoli, L., Cocco, L., Peak, J. C., Katan, M., … Ryu, S. H. (2008). Multiple roles of phosphoinositide-specific phospholipase C isozymesBMB Reports41(6), 415–434.

Woodcock, E. a, Kistler, P. M., & Ju, Y.-K. (2009). Phosphoinositide signalling and cardiac arrhythmiasCardiovascular Research82(2), 286–295. doi:10.1093/cvr/cvn283

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: Benjamin Judkewitz Ph.D. Monday September 16, 2013

Monday Seminar   September 16, 2013

Deep Tissue Fluorescence Imaging With Time-reversed Light

Benjamin Judkewitz, Ph.D.

Sir Henry Wellcome Postdoctoral Fellow

Departments of Bioengineering and Electrical Engineering

California Institute of Technology

4:00 p.m. Carson Family Auditorium

Recommended Readings:

Judkewitz, Benjamin; Wang, Ying Min; Horstmeyer, Roarke; et al.  2013.  Speckle-scale focusing in the diffusive regime with time reversal of variance-encoded light (TROVE).  NATURE PHOTONICS  7(4):300-305   DOI: 10.1038/NPHOTON.2013.31  

Wang, Ying Min; Judkewitz, Benjamin; DiMarzio, Charles A.; et al. 2012. Deep-tissue focal fluorescence imaging with digitally time-reversed ultrasound-encoded light.   NATURE COMMUNICATIONS   3(Article 928):   DOI: 10.1038/ncomms1925

Suzuki, Yuta; Xu, Xiao; Lai, Puxiang; et al   2012.  Energy enhancement in time-reversed ultrasonically encoded optical focusing using a photorefractive polymer.   JOURNAL OF BIOMEDICAL OPTICS   17(8): Article Number: 080507   DOI: 10.1117/1.JBO.17.8.080507  

Makale, Milan; McElroy, Michele; O’Brien, Peter; et al.  2009.  Extended-working-distance multiphoton micromanipulation microscope for deep-penetration imaging in live mice and tissue.   JOURNAL OF BIOMEDICAL OPTICS   14(2): Article Number 024032   DOI:10.1117/1.3103783  

Lai, Puxiang; Xu, Xiao; Liu, Honglin; et al.  2012.  Time-reversed ultrasonically encoded optical focusing in biological tissue.   JOURNAL OF BIOMEDICAL OPTICS   17(3): Article Number 030506   DOI: 10.1117/1.JBO.17.3.030506  

Liu, Honglin; Xu, Xiao; Wang, Lihong V.  2011. Focusing light into turbid media: time-reversed ultrasonically encoded (TRUE) focusing. Book Editor(s): Oraevsky, AA; Wang, LV.   Conference on Photons Plus Ultrasound – Imaging and Sensing  Location: San Francisco, CA Date: JAN 23-25,  Proceedings of SPIE   7899:Article Number 78991A   DOI: 10.1117/12.876956