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Macro Molecular
Machines |
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Since the beginning of my scientific
career, my research has focused on 3D electron microscopy and computer-assisted
image processing to study the structure, function and dynamics of molecular
assemblies involved in fundamental biological processes such as protein
folding and transcription. Cryo-EM and more specifically cryo-negative
staining, which I helped develop during my thesis work in Prof. Jacques
Dubochet's lab in Lausanne (De
Carlo et al., 2002), have fostered substantial progress in studies
of large biological assemblies. This is especially true in the important
topic of gene regulation, upon which I have focused during the past
5 years. Using single-particle 3-D reconstruction techniques based on
electron microscopy data, my colleagues and I were able to describe
large flexible domains in both yeast RNA polymerase I (De Carlo et al.,
2003) and human RNA polymerase II (Kostek et al., 2006).
Using the newly
developed cryo-negative staining technique, we were able to solve the
structure of a very small human transcription factor, (hTFIIE, Jawhari
et al., 2006) whose molecular weight (110kDa) is twice as small as what
is still considered the detectable size-limit for cryo-EM of single
molecular species. This work demonstrates for the first time that the
structure of such relatively small molecules can be obtained by cryo-EM. Recently we also showed that cryo-negative staining allows high-resolution single particles analysis: indeed, GroEL could be resonstructed at 10Å resolution (De Carlo et al., 2007). |
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From Chen
et al (2007). Structure 15(4), 429-440 |
Recent work has focused on elucidating
transcription initiation and regulatory mechanisms in Archaea (with D. Taatjes,
Univ. of Colorado) and Bacteria (with Tracy
Nixon, Penn State; and with Dave Wemmer, UC Berkeley). The latter efforts are devoted to understanding
a family of molecular motors that are involved in bacterial transcription
activation, the enhancer-binding proteins (EBP) of the NtrC family (NtrC,
NtrC1, NtrC4). We have made substantial progress in understanding
the structural basis of the regulated assembly and function of NtrC (EM DataBase entry 1218)
and gained insight about the interaction of EBP with the sigma (σ54)
factor.
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Another long-term goal of my research is to study the structural basis of cellular communication mechanisms affecting gene expression in response to fluctuations in the environment. An example is phosphorelays signal transduction systems that are widely used for quorum sensing [i.e. efficiency sensing] in Bacteria.
They are somehow more complicated than two-component systems and the molecular details of the signal propagation are still poorly understood. It is fascinating how the ability to communicate allows Bacteria to coordinate gene expression and therefore their behavior leading to some interesting theories of social evolution among microorganisms.
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My
Ph.D thesis "Cryo-negative staining: advantages & applications
for three-dimensional electron microscopy of biological macromolecules",
Université de Lausanne (2002) is available online for download:
or go here... on-line
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Curriculum
vitae (  resume) |
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| I keep my "Curriculum
vitae" up to date, please feel free to download the PDF versions -------> |
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| Education, obtained
degrees |
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| 1989-1993:
High-school living certificate, opt. sciences |
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| 1993-1998:
B. Sc. Biology & Physics |
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| 1998-1999:
Biology Diploma |
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| 1999-2002:
PhD, opt. Biophysics |
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| Awards and honors |
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| 2006 BioCAT Research Highlight, by the Advanced Photon
Source, Argonne National Laboratory, United States |
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| PhD work awarded by the Société
Académique Vaudoise Lausanne, Switzerland |
2003 |
| Previous
labs I've been |
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| 1996-1997:
Laboratoire d'Analyse Ultrastructurale, Lausanne, Switzerland |
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| 1996-1997:
Insititut de Génétique et Biologie Microbiennes, Lausanne,
Switzerland |
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| 1998-2002:
Laboratoire d'Analyse Ultrastructurale, Lausanne, Switzerland |
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| 2002-2003:
Institut de Génétique et de Biologie Moléculaire et
Cellulaire, Strasbourg, France |
IGBMC,
Uni Strasbourg, France |
| 2004-2006:
Nogales Lab, Molecular and Cell Biology Dept., University of California
at Berkeley, USA |
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| 2006-2008:
Hoenger Lab, Molecular, Cellular and Develop. Biology Dept., University of Colorado at Boulder, USA |
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Find my
publications on PubMed
...or check
out the list here below |
De Carlo S., Taatjes D., and A. Hoenger (2008). Molecular Architecture of the Archaeal Transcription Pre-Initiation and Elongation Complexes. |
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J. Batchelor, M. Doucleff, C. Lee, K. Matsubara, S. De Carlo, E. Nogales, C. J. Heideker, M. Lamers, J. G. Pelton, D. E. Wemmer (2008). Structure and regulatory mechanism of A. aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation. |
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S. De Carlo,
N. Boisset and A. Hoenger (2008). High-resolution single-particle 3D analysis
on GroEL prepared by cryo-negative staining. Micron. e-pub ahead of print. |
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De Carlo S. Cryo-electron microscopy: plunge freezing. In: Handbook of Cryopreparation Methods for Electron Microscopy. Ed. CRC Press (2008). ISBN: 9780849372278. |
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De Carlo S. Cryo-negative staining. In: Handbook of Cryopreparation Methods for Electron Microscopy. Ed. CRC Press (2008). ISBN: 9780849372278. |
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Chen B.,
Doucleff M., Wemmer D., De Carlo S., Huang H., Nogales E., Hoover T., Kondrashkina
E., Guo L. and B. T. Nixon (2007). ATP Ground- and Transition States of
Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with their
Target Protein, σ54. Structure 15,
429-440. (See cover) |
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Kostek
S., Grob P., De Carlo S., Lipscomb S., Garczarek F. and E. Nogales. (2006).
Molecular architecture and conformational flexibility of human RNA polymerase
II. Structure 14, 1691-1700. |
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S.
De Carlo, B. Chen, T. R. Hoover, E. Kondrashkina, E. Nogales and B. T. Nixon
(2006). The Structural Basis of Regulated Assembly and Function of the Transcriptional
Activator NtrC. Genes & Development 20,1485-1495.(See cover) |
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Jawhari
A., Uhring M., De Carlo S., Crucifix C., Tocchini-Valentini G., Moras D.,
Schultz P. and A. Poterszman. (2006). Structure and oligomeric state of
human transcription factor TFIIE. EMBO Rep. 7,:500-505. |
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Jonić S., Sorzano C. O. S., Thévenaz P., El-Bez C., De Carlo S. and Unser M. (2005). Spline-based image-to-volume registration for three-dimensional electron microscopy. Ultramicroscopy 103: 303-317. |
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Unser M., Sorzano C. O. S., Jonić S., El-Bez C., De Carlo S., Thévenaz P., Conway J., Steven A. C. and Trus B. L. (2005). Spectral Signal-to-Noise Ratio and Resolution Assessment of 3-D Reconstructions. J. Struct. Biol. 149: 243-255. |
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De Carlo
S., Fiaux H. and A Marca-Martinet C. (2004). Electron cryo-microscopy reveals
mechanism of action of propranolol on artificial membranes. J. Lipo.
Res. 14, 61-76. |
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Spehner
D., De Carlo S., Drillien R., Weiland F., Mildner K., Hanau D. and Rziha
H.-J. (2004). Appearance of the bona fide spiral tubule of Orf virus is
dependent on an intact 10 kDa viral protein. J. Virol. 78,
8085-8093. |
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Sorzano C. O. S., Jonić S., El-Bez C., Carazo J. M., De Carlo S., Thévenaz P. and Unser M. (2004). A multiresolution approach to orientation assignment in 3-D electron microscopy of single particles. J. Struct. Biol. 146: 381-392. |
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De Carlo
S., Carles C., Riva M. and Schultz P. (2003). Cryo-negative staining reveals
conformational flexibility within yeast RNA Polymerase I. J. Mol. Biol. 329, 891-902. |
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| De
Carlo S., El-Bez C., Alvarez-Rúa C., Borge J. and Dubochet J. (2002).
Cryo-negative staining reduces electron beam sensitivity of vitrified biological
particles. J. Struct. Biol. 138, 216-226. (See cover) |
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Bellon P. L., Cantele F., De Carlo S. and Lanzavecchia S. (2002). A trajectory-based algorithm to determine and refine Euler angles of projections in three-dimensional microscopy: improvements and tests. Ultramicroscopy 93: 111-121. |
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Braissant O., Perez A., De Carlo S., Morel M., Borruat G. and Roten C.-A. (2001). CENTRIFUGE: A Microgravity Experiment realized by Lausanne University and Federal Institute of Technology in Lausanne students during the European Space Agency (ESA) Parabolic Flight Campaign. Bull. Soc. Vaud. Sc. Nat. 87: 203-209. |
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De
Carlo S., Adrian M., Kälin P., Mayer J. M. and Dubochet J. (1999).
Unexpected property of trehalose as observed by cryo-electron microscopy. J. Microsc. 196, 40-45. |
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Roten C.-A. [S. De Carlo: Micrographs]. (1999). Origine Extraterrestre? Pour la Science 261,29 [french edition of Scientific American]. |
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Roten C.-A., Galluser A., Borruat G., Udry S. D., Niederhäuser G., Croxatto A., Blanc O., De Carlo S. and Karamata D. (1998). Interplanetary biological transfer of bacteria entrapped in small meteorites: analysis of bacterial resistance to impact in ballistic experiments. In: Proc. Mars Soc. Found. Conv. Edited by Robert Zubrin, published by Univelt, California, USA. |
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