Recommended Readings: Mark Schnitzer, Ph.D.

Special Seminar Series: Neurobiology and Behavior

Of mice, men, and microscopes: watching the brain dynamics of motor control at the cellular scale in behaving subjects

Mark Schnitzer, Ph.D.

Assistant Professor, Departments of Biological Sciences and Applied Physics

Stanford School of Medicine

Investigator, HHMI

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Deisseroth, K., G. Feng, A. K. Majewska, G. Miesenböck, A. Ting, and M. J. Schnitzer. 2006. Next-generation optical technologies for illuminating genetically targeted brain circuits. Journal of Neuroscience. 26(41):10380-10386.

Flusberg, B. A., E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer. 2005. Fiber-optic fluorescence imaging. Nature Methods. 2(12):941-950.

Flusberg, B. A., J. C. Jung, E. D. Cocker, E. P. Anderson, and M. J. Schnitzer. 2005. In vivo brain imaging using a portable 3.9 gram two-photon fluorescence microendoscope. Optics Letters. 30(17):2272-2274.
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Flusberg, B. A., A. Nimmerjahn, E. D. Cocker, E. A. Mukamel, R. P. J. Barretto, T. H. Ko, L. D. Burns, J. C. Jung, and M. J. Schnitzer. 2008. High-speed, miniaturized fluorescence microscopy in freely moving mice. Nature Methods5: 935 – 938 .

Jung, J. C., A. D. Mehta, E. Aksay, R. Stepnoski, and M. J. Schnitzer. 2004. In vivo mammalian brain imaging using one- and two-photon fluorescence microendoscopy. Journal of Neurophysiology. 92(5):3121-3133.

Llewellyn, M. E., R. P. J. Barretto, S. L. Delp, and M. J. Schnitzer. 2008. Minimally invasive high-speed imaging of sarcomere contractile dynamics in mice and humans. Nature. 454(7205):784-788.

Mehta, A. D., J. C. Jung, B. A. Flusberg, and M. J. Schnitzer. 2004. Fiber optic in vivo imaging in the mammalian nervous system. Current Opinion in Neurobiology. 14(5):617-628.

Miyawaki, A., and M. J. Schnitzer. 2007. New technologies for neuroscience. Current Opinion in Neurobiology. 17(5):565-566.

New Evidence for Influence of Epigenetics

 Scientists at the Centre for Addiction and Mental Health (CAMH) have found evidence that a secondary molecular mechanism called epigenetics may also account for some inherited traits and diseases.  Epigenetic factors may help explain currently unclear issues in human disease, such as the presence of a disease in only one monozygotic twin, the different susceptibility of males (e.g. to autism) and females (e.g. to lupus), significant fluctuations in the course of a disease (e.g. bipolar disorder, inflammatory bowel disease, multiple sclerosis), among numerous others.   These factors represent a new way to look for the molecular cause of disease, and eventually may lead to improved diagnostics and treatment.   See the research reported in Nature Genetics advance online publication January 2009.

Recommended Readings: Sandeep R. Datta MD PhD

Monday Lecture Series

From Odors to Behavior: Visualizing Sensory Circuits in Flies and Mice

Sandeep Robert Datta  MD, PhD

Post-doctoral Fellow, Department of Neurobiology

Columbia University, New York

Monday, February 2, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Review Article:


Sato T,  Hirono J,  Hamana H, et al.  2008.  Architecture of odor information processing in the olfactory system.    Anatomical science international    83(4):195-206   



Recommended Readings:

Dickson BJ.  2008.  Wired for Sex: the neurobiology of Drosophila mating decisions .  Science  322(5903): 904-909


Katz DB, Matsunami H, Rinberg D, et al.  2008. Receptors, circuits, and behaviors: new directions in chemical senses.  Journal of neuroscience.   28(46): 11802-11805


Sambandan D, Carbone MA, Anholt RRH, et al.  2008. Phenotypic plasticity and genotype by environment interaction for olfactory behavior in Drosophila melanogaster.
Genetics.   179(2):1079-1088   


Datta SR, Vasconcelos ML  Ruta V, et al.   2008.  The Drosophila pheromone cVA activates a sexually dimorphic neural circuit.   Nature (London). 452(7186):473-477


Schlief ML, Wilson RI.  2007.  Olfactory processing and behavior downstream from highly selective receptor neurons.  Nature Neuroscience.    10(5):623-630   


 Sambandan D, Yamamoto A, Fanara JJ, et al.  2006.  Dynamic genetic interactions determine odor-guided behavior in Drosophila melanogaster.  Genetics.  174(3):1349-1363   







Recommended Readings: Robert Froemke, Ph.D.

Monday Lecture Series

A Synaptic Memory Trace for Cortical Receptive Field Plasticity

Robert Froemke, Ph.D.

Post-doctoral Research Fellow, Department of Otolaryngology

University of California, San Francisco

Monday, January 26, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Froemke, R. C., and Y. Dan. 2002. Spike-timing-dependent synaptic modification induced by natural spike trains. Nature. 416(6879):433-438.

Froemke, R. C., M. M. Merzenich, and C. E. Schreiner. 2007. A synaptic memory trace for cortical receptive field plasticity. Nature. 450(7168):425-429.

Froemke, R. C., M. -M Poo, and Y. Dan. 2005. Spike-timing-dependent synaptic plasticity depends on dendritic location. Nature. 434(7030):221-225.

Froemke, R. C., I. A. Tsay, M. Raad, J. D. Long, and Y. Dan. 2006. Contribution of individual spikes in burst-induced long-term synaptic modification. Journal of Neurophysiology. 95(3):1620-1629.

Kenet, T., R. C. Froemke, C. E. Schreiner, I. N. Pessah, and M. M. Merzenich. 2007. Perinatal exposure to a noncoplanar polychlorinated biphenyl alters tonotopy, receptive fields, and plasticity in rat primary auditory cortex. Proceedings of the National Academy of Sciences of the United States of America. 104(18):7646-7651.

Urakubo, H., M. Honda, R. C. Froemke, and S. Kuroda. 2008. Requirement of an allosteric kinetics of NMDA receptors for spike timing-dependent plasticity. Journal of Neuroscience. 28(13):3310-3323.

Recommended Readings: Patrick Seale, Ph.D.

Monday Lecture Series (note: held on Tuesday 2.17.09)

The Transcriptional Regulator PRDM16 Controls a Brown Fat/Skeletal Muscle Development Switch

Patrick Seale, Ph.D.

Post-doctoral Research Fellow, Department of Cancer Biology

Dana-Farber Cancer Institute and Harvard Medical School

Tuesday, February 17, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Cannon, B., and J. Nedergaard. 2008. Developmental biology: Neither fat nor flesh. Nature. 454(7207):947-948.

Cooper, M. P., M. Uldry, S. Kajimura, Z. Arany, and B. M. Spiegelman. 2008. Modulation of PGC-1 coactivator pathways in brown fat differentiation through LRP130. Journal of Biological Chemistry. 283(46):31960-31967.

Kajimura, S., P. Seale, T. Tomaru, H. Erdjument-Bromage, M. P. Cooper, J. L. Ruas, S. Chin, P. Tempst, M. A. Lazar, and B. M. Spiegelman. 2008. Regulation of the brown and white fat gene programs through a PRDM16/CtBP transcriptional complex. Genes and Development. 22(10):1397-1409.

Lazar, M. A. 2008. Developmental biology: How now, brown fat? Science. 321(5892):1048-1049.

Seale, P., B. Bjork, W. Yang, S. Kajimura, S. Chin, S. Kuang, A. Scimè, et al. 2008. PRDM16 controls a brown fat/skeletal muscle switch. Nature. 454(7207):961-967.

Seale, P., S. Kajimura, W. Yang, S. Chin, L. M. Rohas, M. Uldry, G. Tavernier, D. Langin, and B. M. Spiegelman. 2007. Transcriptional control of brown fat determination by PRDM16. Cell Metabolism. 6(1):38-54.

 Uldry, M., W. Yang, J. St-Pierre, J. Lin, P. Seale, and B. M. Spiegelman. 2006. Complementary action of the PGC-1 coactivators in mitochondrial biogenesis and brown fat differentiation. Cell Metabolism. 4(1):97.

Recommended Readings: David M. Smith, Ph.D.

Monday Lecture Series

The Proteasomal ATPases: Regulating a Protein Degradation Machine

David M. Smith, Ph.D.

Instructor, Department of Cell Biology

Harvard Medical School

Monday, February 9, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Smith, D. M., N. Benaroudj, and A. Goldberg. 2006. Proteasomes and their associated ATPases: A destructive combination. Journal of Structural Biology. 156(1):72-83.

Dou, Q. P., D. M. Smith, K. G. Daniel, and A. Kazi. 2003. Interruption of tumor cell cycle progression through proteasome inhibition: Implications for cancer therapy. Progress in cell cycle research. 5:441-446.
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Horwitz, A. A., A. Navon, M. Groll, D. M. Smith, C. Reis, and A. L. Goldberg. 2007. ATP-induced structural transitions in PAN, the proteasome-regulatory ATPase complex in archaea. Journal of Biological Chemistry. 282(31):22921-22929.

Nam, S., D. M. Smith, and Q. P. Dou. 2001. Ester bond-containing tea polyphenols potently inhibit proteasome activity in vitro and in vivo. Journal of Biological Chemistry. 276(16):13322-13330.

Rabl, J., D. M. Smith, Y. Yu, S. -C Chang, A. L. Goldberg, and Y. Cheng. 2008. Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Molecular Cell. 30(3):360-368.

Smith, D. M., S. -C Chang, S. Park, D. Finley, Y. Cheng, and A. L. Goldberg. 2007. Docking of the proteasomal ATPases’ carboxyl termini in the 20S proteasome’s α ring opens the gate for substrate entry. Molecular Cell. 27(5):731-744.

 Smith, D. M., K. G. Daniel, Z. Wang, W. C. Guida, T. -H Chan, and Q. P. Dou. 2004. Docking studies and model development of tea polyphenol proteasome inhibitors: Applications to rational drug design. Proteins: Structure, Function and Genetics. 54(1):58-70.

Smith, D. M., G. Kafri, Y. Cheng, D. Ng, T. Walz, and A. L. Goldberg. 2005. ATP binding to PAN or the 26S ATPases causes association with the 20S proteasome, gate opening, and translocation of unfolded proteins. Molecular Cell. 20(5):687-698.

Recommended Readings: Marc W. Kirschner, Ph.D.

Special Seminar Series: Systems Biology

Systems Questions in Cell Biology: Cell Growth and Protein Level Homeostasis

Marc W. Kirschner, Ph.D.

Professor and Chair, Department of Systems Biology

Harvard Medical School

Wednesday, February 4, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Kirschner, M. W. 2005. The meaning of systems biology. Cell. 121(4):503-504.

Odde, D. J., L. Ma, A. H. Briggs, A. DeMarco, and M. W. Kirschner. 1999. Microtubule bending and breaking in living fibroblast cells. Journal of Cell Science. 112(19):3283-3288.

Drubin, D., S. Kobayashi, D. Kellogg, and M. Kirschner. 1988. Regulation of microtubule protein levels during cellular morphogenesis in nerve growth factor-treated PC12 cells. Journal of Cell Biology. 106(5):1583-1591.

Fang, G., Y. Hongtao, and M. W. Kirschner. 1998. Direct binding of CDC20 protein family members activates the anaphase-promoting complex in mitosis and G1. Molecular Cell. 2(2):163-171.

Kothakota, S., T. Azuma, C. Reinhard, A. Klippel, J. Tang, K. Chu, T. J. McGarry, et al. 1997. Caspase-3-generated fragment of gelsolin: Effector of morphological change in apoptosis. Science. 278(5336):294-298.

Wolin, S. L., G. Krohne, and M. W. Kirschner. 1987. A new lamin in xenopus somatic tissues displays strong homology to human lamin A. EMBO Journal. 6(12):3809-3818.

Yew, P. R., and M. W. Kirschner. 1997. Proteolysis and DNA replication: The CDC34 requirement in the xenopus egg cell cycle. Science. 277(5332):1672-1676.

Recommended Readings: Rudolf Jaenisch, M.D.

Friday Lecture Series

Stem Cells, Pluripotency and Nuclear Reprogramming

 Rudolf Jaenisch, M.D.

Member, Whitehead Institute for Biomedical Research

Professor of Biology, Massachusetts Institute of Technology

Friday, January 30, 2009

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

Caspary Auditorium

Recommended Articles:

Brambrink, T., R. Foreman, G. G. Welstead, C. J. Lengner, M. Wernig, H. Suh, and R. Jaenisch. 2008. Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. Cell Stem Cell. 2(2):151-159.

Hanna, J., S. Markoulaki, P. Schorderet, B. W. Carey, C. Beard, M. Wernig, MennoP Creyghton, et al. 2008. Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell. 133(2):250-264.

Hochedlinger, K., and R. Jaenisch. 2006. Nuclear reprogramming and pluripotency. Nature. 441(7097):1061-1067.

Hockemeyer, D., F. Soldner, E. G. Cook, Q. Gao, M. Mitalipova, and R. Jaenisch. 2008. A drug-inducible system for direct reprogramming of human somatic cells to pluripotency. Cell Stem Cell. 3(3):346-353.

Jaenisch, R., and R. Young. 2008. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell. 132(4):567-582.

Lewitzky, M., and S. Yamanaka. 2007. Reprogramming somatic cells towards pluripotency by defined factors. Current Opinion in Biotechnology. 18(5):467-473.

Mikkelsen, T. S., J. Hanna, X. Zhang, M. Ku, M. Wernig, P. Schorderet, B. E. Bernstein, R. Jaenisch, E. S. Lander, and A. Meissner. 2008. Dissecting direct reprogramming through integrative genomic analysis. Nature. 454(7200):49-55.

Wernig, M., C. J. Lengner, J. Hanna, M. A. Lodato, E. Steine, R. Foreman, J. Staerk, S. Markoulaki, and R. Jaenisch. 2008. A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types. Nature Biotechnology. 26(8):916-924.

Wernig, M., J. -P Zhao, J. Pruszak, E. Hedlund, D. Fu, F. Soldner, V. Broccoli, M. Constantine-Paton, O. Isacson, and R. Jaenisch. 2008. Neurons derived from reprogrammed fibroblasts functionally integrate into the fetal brain and improve symptoms of rats with parkinson’s disease. Proceedings of the National Academy of Sciences of the United States of America. 105(15):5856-5861.

Yamanaka, S. 2008. Pluripotency and nuclear reprogramming. Philosophical Transactions of the Royal Society B: Biological Sciences. 363(1500):2079-2087.

Recommended Readings: Uri Alon, Ph.D.

Special Seminar Series

Design Principles of Biological Circuits/on Science and Nurturing

Uri Alon, Ph.D.

Principal Investigator, Depts. of Molecular Cell Biology and Physics of Complex Systems

Weizmann Institute of Science

Wednesday, January 28, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Book and Journal Articles:

Alon, Uri.  An Introduction to Systems Biology: Design Principles of Biological Circuits.  Boca Raton, FL: Chapman & Hall/CRC, 2007.  (2 copies of this book are available at the Markus Library Circulation Desk.

Geva-Zatorsky, N., N. Rosenfeld, S. Itzkovitz, R. Milo, A. Sigal, E. Dekel, T. Yarnitzky, et al. 2006. Oscillations and variability in the p53 system. Molecular systems biology [electronic resource]. 2.
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Kalir, S., S. Mangan, and U. Alon. 2005. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Molecular systems biology [electronic resource]. 1.
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Kalisky, T., E. Dekel, and U. Alon. 2007. Cost-benefit theory and optimal design of gene regulation functions. Physical Biology. 4(4):229-245.

Kaplan, S., A. Bren, E. Dekel, and U. Alon. 2008. The incoherent feed-forward loop can generate non-monotonic input functions for genes. Molecular Systems Biology. 4.

Mangan, S., and U. Alon. 2003. Structure and function of the feed-forward loop network motif. Proceedings of the National Academy of Sciences of the United States of America. 100(21):11980-11985.

Mangan, S., S. Itzkovitz, A. Zaslaver, and U. Alon. 2006. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. Journal of Molecular Biology. 356(5):1073-1081.

Rosenfeld, N., J. W. Young, U. Alon, P. S. Swain, and M. B. Elowitz. 2007. Accurate prediction of gene feedback circuit behavior from component properties. Molecular Systems Biology. 3. article #3.

Rosenfeld, N., Young, J.W., Alon, U., Swain, P.S., and Elowitz, M.B. 2005. Gene regulation at the single-cell level. Science. 307(5717):1962-1965.

Novel Odor Detecting Proteins: Vosshall Lab Research Highlighted in CELL

A new class of olfactory proteins, labelled ‘ionotropic’ olfactory receptors may be key in finding ways to better control agricultural pests and to prevent insect borne disease.    The existence of ionotropic receptors has been known, but their role in communicating information from the environment to the brain had not been explored.    Read the details in today’s issue of Cell.