Recommended Readings: Thomas Walz, Ph.D. Monday December 11th, 2017

Monday Lectures

Monday, December 11, 2017  3:45 p.m.

Carson Family Auditorium

Thomas Walz, Ph.D.

Professor and Head

Laboratory of Molecular Electron Microscopy

The Rockefeller University

An Experimental Look at Hydrophobic Mismatch

Recommended Readings:

Empirical Articles

Mi, Wei; Li, Yanyan; Yoon, Sung Hwan; et al. (2017). Structural basis of MsbA-mediated lipopolysaccharide transport. NATURE. Volume: 549 (7671): 233-+

Saboe, Patrick O.; Rapisarda, Chiara; Kaptan, Shreyas; et al. (2017). Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0. BIOPHYSICAL JOURNAL. 112 (5): 953-965

Hite, Richard K.; Yuan, Peng; Li, Zongli; et al. (2015). Cryo-electron microscopy structure of the Slo2.2 Na+-activated K+ channel.  NATURE. 527 (7577): 198-+

Shen, Yue-xiao; Si, Wen; Erbakan, Mustafa; et al. (2015). Highly permeable artificial water channels that can self-assemble into two-dimensional arrays. PNAS. 112 (32):9810-9815

Gonen, T; Cheng, YF; Sliz, P; et al. (2005). Lipid-protein interactions in double-layered two-dimensional AQPO crystals. NATURE. 438 (7068): 633-638

Gonen, T; Sliz, P; Kistler, J; et al. (2004).  Aquaporin-0 membrane junctions reveal the structure of a closed water pore. NATURE. 429 (6988): 193-197


Review Paper

Hite, Richard K.; Raunser, Stefan; Walz, Thomas (2007). Revival of electron crystallography. CURRENT OPINION IN STRUCTURAL BIOLOGY. 17 (4): 389-395

Gonen, Tamir; Walz, Thomas (2006). The structure of acquaporins. QUARTERLY REVIEWS OF BIOPHYSICS. 39 (4): 361-396

Book Chapter

Schenk, Andreas D.; Hite, Richard K.; Engel, Andreas; et al. (2010). ELECTRON CRYSTALLOGRAPHY AND AQUAPORINS. METHODS IN ENZYMOLOGY. Book Series: Methods in Enzymology. 483: 91-119

Raunser, Stefan; Walz, Thomas (2009). Electron Crystallography as a Technique to Study the Structure on Membrane Proteins in a Lipidic Environment. ANNUAL REVIEW OF BIOPHYSICS. Book Series: Annual Review of Biophysics. 38: 89-105



Recommended Readings: Ali H. Brivanlou, Ph.D. Monday November 20th, 2017

Monday Lectures

Monday, November 20, 2017  3:45 p.m.

Carson Family Auditorium

Ali H. Brivanlou, Ph.D.

Robert and Harriet Heilbrunnand Professor and Head

Laboratory of Stem Cell Biology and Molecular Embryology

The Rockefeller University


Self-organization of Spatial Patterns in Artificial Human Embryos and Organoids

Recommended Readings:


Patrick Monahan.

Empirical Articles

Deglincerti, Alessia; Croft, Gist F.; Pietila, Lauren N.; et al. (2016). Self-organization of the in vitro attached human embryo. NATURE.  533 (7602): 251-+

Etoc, Fred; Metzger, Jakob; Ruzo, Albert; et al. (2016). A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization. DEVELOPMENTAL CELL. 39 (3): 302-315  

Haremaki, Tomomi; Deglincerti, Alessia; Brivanlou, Ali H. (2015). Huntingtin is required for ciliogenesis and neurogenesis during early Xenopus development. DEVELOPMENTAL BIOLOGY. 408 (2): 305-315

Warmflash, Aryeh; Sorre, Benoit; Etoc, Fred; et al. (2014). A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. NATURE METHODS. 11 (8): 847-854

Bedzhov, Ivan; Leung, Chuen Yan; Bialecka, Monika; et al. (2014). In vitro culture of mouse blastocysts beyond the implantation stages. NATURE PROTOCOLS.  9 (12): 2732-2739

Review Paper

Simunovic, Mijo; Brivanlou, Ali H. (2017). Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis.  DEVELOPMENT. 144 (6): 976-985

Clevers, Hans (2016). Modeling Development and Disease with Organoids. CELL. 165 (7): 1586-1597


Recommended Readings: Gregory M. Alushin, Ph.D. Monday November 13th, 2017

Monday Lectures

Monday, November 13, 2017  3:45 p.m.

Carson Family Auditorium

Gregory M. Alushin, Ph.D.

Assistant Professor and Head

Laboratory of Structural Biophysics and Mechanobiology

The Rockefeller University

Cytoskeletal Structural Plasticity in Force Generation and Mechanosensation

Recommended Readings:

Empirical Articles

Omabegho T, Gurel PS, Cheng CY, Kim LY, Ruijgrok PV, Das R, Alushin GM, Bryant Z. (2017). Controllable molecular motors engineered from myosin and RNA. NATURE NANOTECHNOLOGY. PLEASE REQUEST FROM MARKUS LIBRARY.

Swaminathan V, Alushin GM, Waterman CM. (2017). Mechanosensation: A Catch Bond That Only Hooks One Way. CURRENT BIOLOGY. 27 (21):R1158–R1160

Kim, Laura Y.; Thompson, Peter M.; Lee, Hyunna T.; et al. (2016). The Structural Basis of Actin Organization by Vinculin and Metavinculin. JOURNAL OF MOLECULAR BIOLOGY.  428 (1): 10-25

Skau, Colleen T.; Fischer, Robert S.; Gurel, Pinar; et al. (2016). FMN2 Makes Perinuclear Actin to Protect Nuclei during Confined Migration and Promote Metastasis. CELL. 167 (6):1571-+

Review Papers

Thomas DG, Robinson DN. (2017). The fifth sense: Mechanosensory regulation of alpha-actinin-4 and its relevance for cancer metastasis. SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. PLEASE REQUEST FROM MARKUS LIBRARY.

Mishra, Mithilesh; Huang, Junqi; Balasubramanian, Mohan K. (2014). The yeast actin cytoskeleton. FEMS MICROBIOLOGY REVIEWS. 38 (2): 213-227

Book Chapter

Luo, Tianzhi; Robinson, Douglas N. (2011). The Role of the Actin Cytoskeleton in Mechanosensation. MECHANOSENSITIVITY AND MECHANOTRANSDUCTION. Mechanosensitivity in Cells and Tissues. 4: 25-65


Recommended Readings: Seth Darst, Ph.D. Monday November 6th, 2017

Monday Lectures

Monday, November 6, 2017  3:45 p.m.

Carson Family Auditorium

Seth Darst, Ph.D.

Jack Fishman Professor and Head

Laboratory of Molecular Biophysics

The Rockefeller University

Promoter Melting by Bacterial RNA Polymerase – One Step at a Time

Recommended Readings:

Feklistov, Andrey; Bae, Brian; Hauver, Jesse; et al. (2017). RNA polymerase motions during promoter melting. SCIENCE. 356 (6340): 863-866

Hubin, Elizabeth A.; Fay, Allison; Xu, Catherine; et al. (2017). Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. ELIFE. 6

Chen, James; Wassarman, Karen M.; Feng, Shili; et al. (2017). 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. MOLECULAR CELL. 68 (2): 388-+

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; et al. (2015). Structure of a bacterial RNA polymerase holoenzyme open promoter complex. ELIFE. 4

Davis, Elizabeth; Chen, James; Leon, Katherine; et al. (2015). Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD.  NUCLEIC ACIDS RESEARCH. 43 (1): 433-445

Chen, Jie; Darst, Seth A.; Thirumalai, D. (2010). Promoter melting triggered by bacterial RNA polymerase occurs in three steps. PNAS. 107 (28): 12523-12528


Recommended Readings: Timothy Ryan, Ph.D., Monday October 23th, 2017

Monday Lectures

Monday, October 23, 2017  3:45 p.m.

Carson Family Auditorium

Timothy Ryan, Ph.D.

Tri-Institutional Professor

Department of biochemistry

Weill Cornell Medical College

The Cost of Thinking: Metabolic Fitness at the Synapse Level

Recommended Readings:

Jaime de Juan Sanz (2017). The surprising metabolism of “exercising” neurons. Plos Blogs

Ashrafi, Ghazaleh; Ryan, Timothy A. (2017). Glucose metabolism in nerve terminals. CURRENT OPINION IN NEUROBIOLOGY. 45:156-161

Ashrafi, Ghazaleh; Wu, Zhuhao; Farrell, Ryan J.; et al. (2017). GLUT4 Mobilization Supports Energetic Demands of Active Synapses. NEURON. 93 (3): 606-+

Jang, SoRi; Nelson, Jessica C.; Bend, Eric G.; et al. (2016). Glycolytic Enzymes Localize to Synapses under Energy Stress to Support Synaptic Function. NEURON. 90 (2): 278-291

Magistretti, Pierre J.; Allaman, Igor (2015). A Cellular Perspective on Brain Energy Metabolism and Functional Imaging. NEURON. 86 (4): 883-901

Rangaraju, Vidhya; Calloway, Nathaniel; Ryan, Timothy A.(2014). Activity-Driven Local ATP Synthesis Is Required for Synaptic Function. CELL. 156 (4): 825-835

Recommended Readings: Thomas P. Sakmar, M.D., Monday May 22th, 2017

Monday Lectures

Monday, May 22, 2017  3:45 p.m.

Carson Family Auditorium

Thomas P. Sakmar, M.D.

Richard M. and Isabel P. Furlaud Professor and Head,

Laboratory of Chemical Biology and Signal Transduction

The Rockefeller University

Uveal Melanoma: Case History of a Mutant GPCR

Recommended Readings:

Chua V, Lapadula D, Randolph C, Benovic JL, Wedegaertner PB, Aplin AE. (2017). Dysregulated GPCR Signaling and Therapeutic Options in Uveal Melanoma. MOLECULAR CANCER RESEARCH. 15(5):501-506

Moore, Amanda R.; Ceraudo, Emilie; Sher, Jessica J.; et al. (2016). Recurrent activating mutations of G-protein-coupled receptor CYSLTR2 in uveal melanoma. NATURE GENETICS. 48(6): 675-+

Shoushtari, Alexander N.; Carvajal, Richard D. (2014). GNAQ and GNA11 mutations in uveal melanoma. MELANOMA RESEARCH. 24(6): 525-534. PLEASE REQUEST FROM MARKUS LIBRARY.

Harbour, J. William (2012). The genetics of uveal melanoma: an emerging framework for targeted therapy. PIGMENT CELL & MELANOMA RESEARCH. 25(2)

Periole, Xavier; Knepp, Adam M.; Sakmar, Thomas P.; et al. (2012). Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 134(26): 10959-10965



Recommended Readings: Michael P. Rout, Ph.D., Monday May 15th, 2017

Monday Lectures

Monday, May 15, 2017  3:45 p.m.

Carson Family Auditorium

Michael P. Rout, Ph.D.

 Professor and Head,

Laboratory of Cellular and Structural Biology

The Rockefeller University

Getting the Hole Picture: Structure-Function Mapping of the Nuclear Pore Complex

Recommended Readings:

Timney, Benjamin L.; Raveh, Barak; Mironska, Roxana; et al. (2016). Simple rules for passive diffusion through the nuclear pore complex. JOURNAL OF CELL BIOLOGY. 215(1): 57-76

Raveh, Barak; Karp, Jerome M.; Sparks, Samuel; et al. (2016). Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA . 113(18): E2489-E2497

Fernandez-Martinez, Javier; Kim, Seung Joong; Shi, Yi; et al. (2016). Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. CELL. 167(5): 1215-+

Tu, Li-Chun; Fu, Guo; Zilman, Anton; et al. (2013). Large cargo transport by nuclear pores: implications for the spatial organization of FG-nucleoporins.EMBO JOURNAL. 32(24): 3220-3230

Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D.; et al. (2012). Structure-function mapping of a heptameric module in the nuclear pore complex. JOURNAL OF CELL BIOLOGY. 196(4): 419-434

Grossman, Einat; Medalia, Ohad; Zwerger, Monika (2012). Functional Architecture of the Nuclear Pore Complex. ANNUAL REVIEW OF BIOPHYSICS. 41: 557-584

Recommended Readings: Alipasha Vaziri, Ph.D., Monday May 1, 2017

Monday Lectures

Monday, May 1, 2017  3:45 p.m.

Carson Family Auditorium

Alipasha Vaziri, Ph.D.

Associate Professor and Head,

Laboratory of Neurotechnology and Biophysics

The Rockefeller University

Optical Tools for Unraveling Whole-brain Neuronal Circuit Dynamics Underlying Behavior

Recommended Readings:

Prevedel, Robert; Verhoef, Aart J.; Pernia-Andrade, Alejandro J.; et al. (2016).  Fast volumetric calcium imaging across multiple cortical layers using sculpted light. NATURE METHODS. 13(12): 1021-U215

Rupprecht, Peter; Prevedel, Robert; Groessl, Florian; et al. (2015). Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience. BIOMEDICAL OPTICS EXPRESS. 6(2): 353-368

Prevedel, Robert; Yoon, Young-Gyu; Hoffmann, Maximilian; et al. (2014). Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. NATURE METHODS. 11(7): 727-U161

Schrodel, Tina; Prevedel, Robert; Aumayr, Karin; et al. (2013). Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light. NATURE METHODS. 10(10)1013-+

Fenno, Lief; Yizhar, Ofer; Deisseroth, Karl. (2011). The Development and Application of Optogenetics.  ANNUAL REVIEW OF NEUROSCIENCE. 34: 389-412

Andrasfalvy, Bertalan K.; Zemelman, Boris V.; Tang, Jianyong; et al. (2010).Two-photon single-cell optogenetic control of neuronal activity by sculpted light. PNAS. 107(26): 11981-11986







Recommended Readings: Vincent A. Fischetti, Ph.D. April 24, 2017

Monday Lectures

Monday, April 17, 2017  3:45 p.m.

Carson Family Auditorium

Vincent A. Fischetti, Ph.D.

Professor and Head,

Laboratory of Bacterial Pathogenesis and Immunology

The Rockefeller University

Exploiting phage evolution for the development of novel therapeutics

Recommended Readings:

David Bautz. March 20th 2017. CFRX: Phase 2 Trial of CF-301 to Initiate in mid-2017.

Czaplewski, Lloyd; Bax, Richard; Clokie, Martha; et al. (2016). Alternatives to antibiotics-a pipeline portfolio review. LANCET INFECTIOUS DISEASES. 16(2): 239-251

Diez-Martinez, Roberto; De Paz, Hector D.; Garcia-Fernandez, Esther; et al. (2015). A novel chimeric phage lysin with high in vitro and in vivo bactericidal activity against Streptococcus pneumoniae. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. 70(6): 1763-1773

Bikard, David; Euler, Chad W.; Jiang, Wenyan; et al. (2014). Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. NATURE BIOTECHNOLOGY. 32(11): 1146-1150

Schuch, Raymond; Lee, Han M.; Schneider, Brent C.; et al. (2014). Combination Therapy With Lysin CF-301 and Antibiotic Is Superior to Antibiotic Alone for Treating Methicillin-Resistant Staphylococcus aureus-Induced Murine Bacteremia. JOURNAL OF INFECTIOUS DISEASES. 209(9): 1469-1478

Pastagia, Mina; Schuch, Raymond; Fischetti, Vincent A.; et al. (2013). Lysins: the arrival of pathogen-directed anti-infectives. JOURNAL OF MEDICAL MICROBIOLOGY. 62:1506-1516

Gilmer, Daniel B.; Schmitz, Jonathan E.; Euler, Chad W.; et al. (2013). Novel Bacteriophage Lysin with Broad Lytic Activity Protects against Mixed Infection by Streptococcus pyogenes and Methicillin-Resistant Staphylococcus aureus. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY. 57(6): 2743-2750


Recommended Readings: Stuart H. Orkin M.D. January 6 2017

Friday Lectures

Friday, January 6,  3:45 p.m.

Caspary Auditorium

Stuart H. Orkin   M.D.

David G. Nathan Distinguished Professor of Pediatrics, Dana Farber Institute

The Human Fetal Globin Switch:

A Paradigm for Disease-related Common Genetic Variation in Regulatory Elements

Recommended Readings:

Bauer, Daniel E.; Kamran, Sophia C.; Lessard, Samuel; et al.  An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level.  SCIENCE  342(6155): 253-257    OCT 11 2013  

Galarneau, Genevieve; Palmer, Cameron D.; Sankaran, Vijay G.; et al.  Fine-mapping at three loci known to affect fetal hemoglobin levels explains additional genetic variation.  NATURE GENETICS   42(12): 1049-1051   DEC 2010

Menzel, Stephan; Thein, Swee Lay.   Genetic architecture of hemoglobin F control. CURRENT OPINION IN HEMATOLOGY   16(3): 179-186   MAY 2009  PLEASE REQUEST FROM MARKUS LIBRARY

He, Yunyan; Lin, Weixiong; Luo, Jianming.  Influences of Genetic Variation on Fetal Hemoglobin. PEDIATRIC HEMATOLOGY AND ONCOLOGY   Volume: 28   Issue: 8   Pages: 708-717   Published:  NOV 2011   PLEASE REQUEST FROM MARKUS LIBRARY.

Orkin, Stuart H.  Recent advances in globin research using genome-wide association studies and gene editing. Annals of the New York Academy of Sciences   1368 : 5-10    2016