Recommended Readings: Agata Smogorzewska, M.D., Ph.D., April 24

Friday Lecture Series
Friday, April 24, 2015
3:45 p.m., Caspary Auditorium

Agata Smogorzewska, M.D., Ph.D.
Assistant Professor and Head,
Laboratory of Genome Maintenance,
The Rockefeller University

DNA Interstrand Crosslink Repair: from Genetics to Mechanism

Recommended Readings

Empirical Articles

Flynn, E. K., Kamat, A., Lach, F. P., Donovan, F. X., Kimble, D. C., Narisu, N., … & Chandrasekharappa, S. C. (2014). Comprehensive analysis of pathogenic deletion variants in Fanconi anemia genes. Human Mutation, 35(11), 1342-1353. doi:10.1002/humu.22680

Kim, Y., Spitz, G. S., Veturi, U., Lach, F. P., Auerbach, A. D., & Smogorzewska, A. (2013). Regulation of multiple DNA repair pathways by the Fanconi anemia protein SLX4. Blood, 121(1), 54-63. doi:10.1182/blood-2012-07-441212

Ouyang, J., Garner, E., Hallet, A., Nguyen, H. D., Rickman, K. A., Gill, G., … & Zou, L. (2015). Noncovalent interactions with SUMO and ubiquitin orchestrate distinct functions of the SLX4 complex in genome maintenance. Molecular Cell, 57(1), 108-122. doi:10.1016/j.molcel.2014.11.015

Wang, R., Persky, N. S., Yoo, B., Ouerfelli, O., Smogorzewska, A., Elledge, S. J., & Pavletich, N. P. (2014). Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1. Science, 346(6213), 1127-1130. doi:10.1126/science.1258973

Review Paper

Kottemann, M. C., & Smogorzewska, A. (2013). Fanconi anaemia and the repair of Watson and Crick DNA crosslinks. Nature, 493(7432), 356-363. doi:10.1038/nature11863

Recommended Readings: A. James Hudspeth, M.D., Ph.D., April 27

Monday Lecture Series
Monday, April 27, 2015
4:00 p.m., Carson Family Auditorium (CRC)

A. James Hudspeth, M.D., Ph.D.
F.M. Kirby Professor and Head,
Laboratory of Sensory Neuroscience,
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Making an Effort to Listen: the Active Process of the Cochlea

Recommended Readings

Empirical Articles

Fisher, J. A., Nin, F., Reichenbach, T., Uthaiah, R. C., & Hudspeth, A. J. (2012). The spatial pattern of cochlear amplification. Neuron, 76(5), 989-997. doi:10.1016/j.neuron.2012.09.031

Jacobo, A., & Hudspeth, A. J. (2014). Reaction–diffusion model of hair-bundle morphogenesis. Proceedings of the National Academy of Sciences, 111(43), 15444-15449. doi:10.1073/pnas.1417420111

Maoiléidigh, D. Ó., & Hudspeth, A. J. (2013). Effects of cochlear loading on the motility of active outer hair cells. Proceedings of the National Academy of Sciences, 110(14), 5474-5479. doi:10.1073/pnas.1302911110

Nin, F., Reichenbach, T., Fisher, J. A., & Hudspeth, A. J. (2012). Contribution of active hair-bundle motility to nonlinear amplification in the mammalian cochlea. Proceedings of the National Academy of Sciences, 109(51), 21076-21080. doi:10.1073/pnas.1219379110

Review Papers

Hudspeth, A. J. (2015). The energetic ear. Daedalus, 144(1), 42-52. doi:10.1162/DAED_a_00316

Hudspeth, A. J. (2014). Integrating the active process of hair cells with cochlear function. Nature Reviews Neuroscience, 15(9), 600-614. doi:10.1038/nrn3786

Recommended Readings: Michael W. Young, Ph.D., April 20

Monday Lecture Series
Monday, April 20, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Michael W. Young, Ph.D.
Vice President for Academic Affairs,
Richard and Jeanne Fisher Professor and Head,
Laboratory of Genetics,
The Rockefeller University

Genes that Regulate Sleep and Circadian Rhythms

Recommended Readings

Empirical Articles

Levy, C., Zoltowski, B. D., Jones, A. R., Vaidya, A. T., Top, D., Widom, J., … & Leys, D. (2013). Updated structure of Drosophila cryptochrome. Nature, 495(7441), E3-E4. doi:10.1038/nature11995.

Rogulja, D., & Young, M. W. (2012). Control of sleep by cyclin A and its regulator. Science, 335(6076), 1617-1621. doi:10.1126/science.1212476.

Stavropoulos, N., & Young, M. W. (2011). insomniac and Cullin-3 regulate sleep and wakefulness in Drosophila. Neuron, 72(6), 964-976. doi:10.1016/j.neuron.2011.12.003.

Zoltowski, B. D., Vaidya, A. T., Top, D., Widom, J., Young, M. W., & Crane, B. R. (2011). Structure of full-length Drosophila cryptochrome. Nature, 480(7377), 396-399. doi:10.1038/nature10618.

Review Papers

Boothroyd, C. E., & Young, M. W. (2008). The in (put)s and out (put)s of the Drosophila circadian clock. Annals of the New York Academy of Sciences, 1129(1), 350-357. doi:10.1196/annals.1417.006

Crane, B. R., & Young, M. W. (2014). Interactive features of proteins composing eukaryotic circadian clocks. Annual Review of Biochemistry, 83, 191-219. doi:10.1146/annurev-biochem-060713-035644

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: David Tollervey, Ph.D., April 10

Friday Lecture Series
Friday, April 10, 2015
3:45 p.m., Caspary Auditorium

David Tollervey, Ph.D.,
Wellcome Trust Centre for Cell Biology,
University of Edinburgh

Lighting Up RNA Interactions

Recommended Readings

Empirical Articles

Granneman, S., Kudla, G., Petfalski, E., & Tollervey, D. (2009). Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proceedings of the National Academy of Sciences, 106(24), 9613-9618. doi:10.1073/pnas.0901997106

Helwak, A., Kudla, G., Dudnakova, T., & Tollervey, D. (2013). Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153(3), 654-665. doi:10.1016/j.cell.2013.03.043

Helwak, A., & Tollervey, D. (2014). Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH). Nature Protocols, 9(3), 711-728. doi:10.1038/nprot.2014.043

Tuck, A. C., & Tollervey, D. (2013). A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell, 154(5), 996-1009. doi:10.1016/j.cell.2013.07.047

Review Papers

Schneider, C., & Tollervey, D. (2013). Threading the barrel of the RNA exosome. Trends in Biochemical Sciences, 38(10), 485-493. doi:10.1016/j.tibs.2013.06.013

Tuck, A. C., & Tollervey, D. (2011). RNA in pieces. Trends in Genetics, 27(10), 422-432. doi:10.1016/j.tig.2011.06.001

Recommended Readings: Marc Tessier-Lavigne, Ph.D., April 6

Monday Lecture Series
Monday, April 6, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Marc Tessier-Lavigne, Ph.D.,
Carson Family Professor and Head,
Laboratory of Brain Development and Repair,
The Rockefeller University

Sculpting Neuronal Connections: The Logic and Mechanisms of Axon Growth and Pruning

Recommended Readings

Empirical Articles

Leyva-Díaz, E., del Toro, D., Menal, M. J., Cambray, S., Susín, R., Tessier-Lavigne, M., … & López-Bendito, G. (2014). FLRT3 is a Robo1-interacting protein that determines Netrin-1 attraction in developing axons. Current Biology, 24(5), 494-508. doi:10.1016/j.cub.2014.01.042

Mire, E., Mezzera, C., Leyva-Díaz, E., Paternain, A. V., Squarzoni, P., Bluy, L., … & López-Bendito, G. (2012). Spontaneous activity regulates Robo1 transcription to mediate a switch in thalamocortical axon growth. Nature Neuroscience, 15(8), 1134-1143. doi:10.1038/nn.3160

Romi, E., Gokhman, I., Wong, E., Antonovsky, N., Ludwig, A., Sagi, I., … & Yaron, A. (2014). ADAM metalloproteases promote a developmental switch in responsiveness to the axonal repellant Sema3A. Nature communications, 5. doi:10.1038/ncomms5058

Xu, K., Wu, Z., Renier, N., Antipenko, A., Tzvetkova-Robev, D., Xu, Y., … & Nikolov, D. B. (2014). Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism. Science, 344(6189), 1275-1279. doi:10.1126/science.1255149

Review Papers

Kolodkin, A. L., & Tessier-Lavigne, M. (2011). Mechanisms and molecules of neuronal wiring: a primer. Cold Spring Harbor Perspectives in Biology, 3(6), a001727. doi:10.1101/cshperspect.a001727

Recommended Readings: Jos Jonkers, Ph.D., March 20

Friday Lecture Series
Friday, March 20, 2015
3:45 p.m., Caspary Auditorium

Jos Jonkers, Ph.D.
Head, Division of Molecular Pathology,
Netherlands Cancer Institute

Unraveling Therapy Response and Resistance in Mouse Models of Human Breast Cancer

Recommended Readings

Empirical Articles

Bouwman, P., Aly, A., Escandell, J. M., Pieterse, M., Bartkova, J., van der Gulden, H., … & Jonkers, J. (2010). 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nature Structural & Molecular Biology, 17(6), 688-695. doi:10.1038/nsmb.1831.

Jonkers, J., Meuwissen, R., van der Gulden, H., Peterse, H., van der Valk, M., & Berns, A. (2001). Synergistic tumor suppressor activity of BRCA2 and p53 in a conditional mouse model for breast cancer. Nature Genetics, 29(4), 418-425. doi:10.1038/ng747

Liu, X., Holstege, H., van der Gulden, H., Treur-Mulder, M., Zevenhoven, J., Velds, A., … & Jonkers, J. (2007). Somatic loss of BRCA1 and p53 in mice induces mammary tumors with features of human BRCA1-mutated basal-like breast cancer. Proceedings of the National Academy of Sciences, 104(29), 12111-12116. doi:10.1073/pnas.0702969104

Rottenberg, S., Jaspers, J. E., Kersbergen, A., van der Burg, E., Nygren, A. O., Zander, S. A., … & Jonkers, J. (2008). High sensitivity of BRCA1-deficient mammary tumors to the PARP inhibitor AZD2281 alone and in combination with platinum drugs. Proceedings of the National Academy of Sciences, 105(44), 17079-17084. doi:10.1073/pnas.0806092105

Review Papers

Bouwman, P., & Jonkers, J. (2014). Molecular Pathways: How can BRCA-mutated tumors become resistant to PARP inhibitors?. Clinical Cancer Research, 20(3), 540-547. doi:10.1158/1078-0432.CCR-13-0225

Klarenbeek, S., van Miltenburg, M. H., & Jonkers, J. (2013). Genetically engineered mouse models of PI3K signaling in breast cancer. Molecular Oncology, 7(2), 146-164. doi:10.1016/j.molonc.2013.02.003

Library Newsletter

The February 2015 edition of the library’s newsletter is now available!

Please follow this link to download our inaugural issue featuring:

  1. A tutorial on renewing library material online
  2. A list of new books in our scientific and recreational reading collections.
  3. Book recommendations from the library’s science informationist, John Borghi
  4. A description of select services offered by the library: Including Browzine, Mango Languages, and PubSubmit.
  5. A description of AHRQ’s new public access policy
  6. Answers to frequently asked questions: Including how to access library resources while off campus and accessing library materials available through the libraries at Weill Cornell and Memorial Sloan Kettering.

Thanks for reading!

Recommended Readings: Jef Boeke, Ph.D., March 13

Friday Lecture Series
Friday, March 13, 2015
3:45 p.m., Caspary Auditorium

Jef Boeke, Ph.D.
Department of Biochemistry and Molecular Pharmacology,
Director, Institute for systems genetics,
New York University

Synthesis of Designer Chromosomes from Scratch

Recommended Readings

Empirical Articles

Annaluru, N., Muller, H., Mitchell, L. a, Ramalingam, S., Stracquadanio, G., Richardson, S. M., … Chandrasegaran, S. (2014). Total synthesis of a functional designer eukaryotic chromosome. Science, 344(6179), 55–58. doi:10.1126/science.1249252

Dymond, J. S., Richardson, S. M., Coombes, C. E., Babatz, T., Muller, H., Annaluru, N., … Boeke, J. D. (2011). Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 477(7365), 471–476. doi:10.1038/nature10403

Mitchell, L. a., & Boeke, J. D. (2014). Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proceedings of the National Academy of Sciences, 111(48), 17003–17010. doi:10.1073/pnas.1414399111

Reviews and Protocols

Cooper, E. M., Müller, H., Chandrasegaran, S., Bader, J. S., & Boeke, J. D. (2012). The build-a-genome course. Methods in Molecular Biology, 852, 273–283. doi:10.1007/978-1-61779-564-0_20

Recommended Readings: Tom Muir, Ph.D., March 27

Friday Lecture Series
Friday, March 27, 2015
3:45 p.m., Caspary Auditorium

Tom Muir, Ph.D.
Van Zandt Williams Jr. Class of ‘65 Professor of Chemistry,
Chair, Department of chemistry
Princeton University

‘Houdini’ Proteins: Discovery and Applications of Ultrafast Inteins

Recommended Readings

Empirical Articles

Shah, N. H., Dann, G. P., Vila-Perelló, M., Liu, Z., & Muir, T. W. (2012). Ultrafast protein splicing is common among cyanobacterial split inteins: Implications for protein engineering. Journal of the American Chemical Society, 134(28), 11338–11341. doi:10.1021/ja303226x

Shah, N. H., Eryilmaz, E., Cowburn, D., & Muir, T. W. (2013). Naturally split inteins assemble through a “capture and collapse” mechanism. Journal of the American Chemical Society, 135(49), 18673–18681. doi:10.1021/ja4104364

Shah, N. H., Vila-Perelló, M., & Muir, T. W. (2011). Kinetic control of one-pot trans-splicing reactions by using a wild-type and designed split intein. Angewandte Chemie, 50(290, 6511–6515. doi:10.1002/anie.201102909

Vila-Perelló, M., Liu, Z., Shah, N. H., Willis, J. A., Idoyaga, J., & Muir, T. W. (2013). Streamlined expressed protein ligation using split inteins. Journal of the American Chemical Society, 135(1), 286–292. doi:10.1021/ja309126m

Review Papers

Eryilma, E., Shah, N. H., Muir, T. W., & Cowburn, D. (2014). Structural and dynamical features of Inteins and implications on protein splicing. Journal of Biological Chemistry, 289(21), 14506–14511. doi:10.1074/jbc.R113.540302

Shah, N. H., & Muir, T. W. (2014). Inteins: Nature’s Gift to Protein Chemists. Chemical Science, 5(1), 446–461. doi:10.1016/j.biotechadv.2011.08.021.Secreted