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Sivaraj Sivaramakrishnan

Postdoctoral Fellow
Department of Biochemistry
Beckman Center, B419
Stanford University
Stanford, CA, 94025

Phone - (650)-725-6376
Fax - (650)-723-6783
Email - shivz@stanford.edu
URL - http://www.stanford.edu/people/shivz

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Education

Ph.D. Biomedical Engineering, Northwestern University [2006]
M.S. Mechanical Engineering, University of Illinois, Urbana-Champaign [2000]
B.E. Mechanical Engineering, University of Pune, India [1998]

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Research Interests

I am interested in single molecule imaging and manipulation with applications to understanding the protein function within cells. Currently, I am a postdoctoral fellow at the Spudich Lab where we study the molecular basis for cell motility. My research projects examine a unique actin-based molecular motor, Myosin VI, and its role in cellular endocytic pathway.

I received my Ph.D. from Northwestern University, where I was involved in a mutidisciplinary research effort examing the effects of mechanical forces on the keratin intermediate filament network in alveolar epithelial cells. This was done in collaboration with Dr. Karen Ridge at the Division of Pulmonary and Critical Care Medicine, Dr Robert Goldman at the Dept. of Cell and Molecular Biology and Dr. Matthew Glucksberg at the Dept. of Biomedical Engineering.

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Publications

‘Set up of a dual-beam optical trap to study the myosin family of molecular motors’, J. Sung, S. Sivaramakrishnan, A. Dunn, J.A. Spudich, Methods in Enzymology, Invited Article (submitted)
‘Revelations from myosin VI: the most innovative of molecular motors’, S. Sivaramakrishnan, J.A. Spudich, Nature Reviews: Molecular and Cellular Biology, Invited Review (In revision)
‘Combining single molecule optical trapping and small angle X-ray scattering measurements to compute the persistence length of a protein ER/K a-helix’, S. Sivaramakrishnan, J. Sung, M. Ali, S. Doniach, H. Flyvbjerg, J. A. Spudich, Biophysical Journal (In press, Dec 2009)
‘Coupled myosin VI motors facilitate unidirectional movement on an F-actin network’, S. Sivaramakrishnan, J.A. Spudich, Journal of Cell Biology, 2009 (In press, Oct 2, 2009)
‘Insights into human b-cardiac myosin function from single molecule and single cell studies’, S. Sivaramakrishnan, E. Ashley, L. Leinwand, J.A. Spudich, Journal of Translational Cardiac Research, Invited Review (In press)
'Dynamic charge interactions create surprising rigidity in the ER/K a-helical protein motif’, S. Sivaramakrishnan, B. J. Spink, A. Y. L. Sim, S. Doniach, J. A. Spudich, Proceedings of the National Academy of Sciences, USA, vol. 105, no. 36, 13356-61, Sep 9 2008
‘Bridging the Gap between the Structure and Function of Myosin VI’, B.J. Spink, S. Sivaramakrishnan, J. Lipfert, S. Doniach, J.A. Spudich, Nature: Structural and Molecular Biology, vol. 15, no. 6, 591-97, Jun 2008
‘Shear stress induced reorganization of the keratin intermediate filament network requires phosphorylation of K18Ser33 via PKC z and 14-3-3’, S. Sivaramakrishnan, J.L. Schneider, A. Sitikov, R.D. Goldman, K.M. Ridge, Molecular Biology of the Cell, 2007, (In Revision)
‘The Keratin Intermediate Filament Network in Alveolar Epithelial Cells Behaves as a Stiff Solid-Like Material’, S. Sivaramakrishnan, J.V. DeGuilio, R.D. Goldman, J.N. Schneider, K.M. Ridge, Proceedings of the National Academy of Sciences, USA, vol. 105, no. 3, 889-894, Jan 22 2008
Computational and Experimental Study of Turbulent Flow in a 0.4-Scale Water Model of a Continuous Steel Caster – Q. Yuan, S. Sivaramakrishnan, S.P. Vanka, B.G. Thomas, Metallurgical and Materials Transactions B, 1 October 2004, vol. 35, no. 5, pp. 967-982(16)
Comparison of four methods to evaluate fluid velocities in a continuous slab casting mold, B.G. Thomas, Q. Yuan, S. Sivaramakrishnan, T. Shi, S.P. Vanka and M.B. Assar, ISIJ Int., Vol. 41 (2001) No. 10, pp. 1262-1271

Publications – Commentaries

Journal of Cell Biology, Oct 2nd, 2009, In focus highlight
'The soft framework of the cellular machine.' D.A. Weitz, P.A. Janmey, Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1105-6. Epub 2008, Jan 23.
Journal of Cell Biology - ASCB Meeting research roundup (2008)

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Honors

American Cancer Society (ACS) Postdoctoral Fellowship (2008- )
American Heart Association (AHA) Predoctoral Fellowship (Percentile Rank = 1.16) (2004-06)
Walter P. Murphy Fellowship, Biomedical Engineering Department, Northwestern University (2002-03)
Computational Science and Engineering Program, University of Illinois Urbana-Champaign (2000)

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Conference Presentations

‘Coupled myosin VI motors facilitate 10 mm long unidirectional movement on a dense interlaced F-actin network’, S. Sivaramakrishnan, J. A. Spudich, Invited Speaker, American Society of Cell Biology (ASCB) annual meeting, San Diego, CA, 2009
‘From structure to cellular function of mechanoenzymes: Lessons learned from Myosin VI’, S. Sivaramakrishnan, J. A. Spudich, Paper presentation, Biomedical Engineering Society Meeting (BMES), Oct, 2009, Pittsburg, PA
‘Stability and Rigidity of Isolated ER/K a-helices’, S. Sivaramakrishnan, J. A. Spudich, Invited Speaker, American Society of Cell Biology (ASCB) annual meeting, San Francisco, CA, 2008
‘Unusual protein structural elements involving myosin motors’, S. Sivaramakrishnan, B. J. Spink, A. Y. L. Sim, S. Doniach, J. A. Spudich, Paper Presentation, Gordon Research Conference, Muscle and Molecular Motors, Colby-Sawyer College, New London, NH, 2008
‘The tale of the tail: The role of Myosin VI Tail Domains in Shaping the Processive Step’, B. J. Spink, S. Sivaramakrishnan, J. Lipfert, S. Doniach, J. A. Spudich, Paper Presentation, Biophysical Society Meeting, Long Beach, CA, 2008
‘Shear Stress Induced Remodeling of the Keratin Filament Network in Alveolar Epithelial Cells’, S. Sivaramakrishnan, F.W. Flitney, R.D. Goldman, K.M. Ridge, Paper Presentation, Biomedical Engineering Society (BMES) Conference, Chicago, 2006
‘PKCz is Required for the Shear Stress-Induced Structural Reorganization of Keratin Intermediate Filaments in Alveolar Epithelial Cells’, S. Sivaramakrishnan, N. Na, R.D. Goldman, K.M. Ridge, American Society of Cell Biology annual meeting, San Francisco, 2005
‘New Dimensions in Intermediate Filament Dynamics: Quantitative Analysis of Vimentin Speckles by Cross Correlation of Intensity Profiles Reveals Non-random Movement of Speckles Along Individual Fibers’, L. Chang, S. Sivaramakrishnan, C. M. Waterman-Storer, T. Wittmann, R. D. Goldman, American Society of Cell Biology Conference, San Francisco, 2005
‘Effects of Shear Stress on the Alveolar Epithelial Cell Cytoskeleton’, S. Sivaramakrishnan, R.D. Goldman, K.M. Ridge, Biomedical Engineering Society (BMES) conference, Philadelphia, 117, October 2004
Computational and Experimental Study of Turbulent Flow in a 0.4-Scale Water Model of a Continuous Steel Caster S. Sivaramakrishnan, S.P. Vanka, B.G. Thomas, Paper Presentation, The Metallurgical, Materials and Minerals Society (TMS) Annual Meeting, Nashville, TN, March 2000.

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Research/Work Experience

Technical Sales/Support Engineer - Fluent Inc. (2000-2002) - I worked with the BIO-team at Fluent Inc. on a variety of projects studying the flow and aerosol particle distribution in upper lung airways, drug diffusion from coronary stents and flow design of biomedical devices such as genome chips, catheters, drug dispensers (inhalers), valves/piping and centrifuges.

Marine Biological Laboratories (2005-2007) - I was a student at the Physiology Course at MBL in the summer of 2005. MBL, especially the Physiology course, is an excellent environment for interdisciplinary research and innovative thinking. I was invited back in 2006 and 2007 as a Teaching Assistant for an intense one-week Introduction to Computational Biology Session.

Visiting Scholar, National Center for Biological Sciences, India (2007-) - Visiting Scholar at NCBS, as part of an interdisciplinary research effort, initiated by my mentor Dr. James Spudich, towards collaborative research across continents. Our current collaborators include Dr. Satyajit Mayor and Dr. R. Sowdhamini

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Teaching Experience

Course Assistant/Speaker, Stanford University, Spring 2008 – Dynamics of Cellular Architecture

Teaching Assistant – Marine Biological Laboratories, Woods Hole, MA – Summer 2006, 2007

Lecturer – One week Computational Biology Course for Graduate Students in Cell Biology, University of California San Francisco, September 2006

Teaching Assistant – Intermediate Fluid Mechanics, Biomedical Eng. Dept., Northwestern University, Evanton, IL

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