Publications
Brambilla, E., Yousuf, M., Zhang, Q., Mbemba, G., Oeuvray, C., Mektepbayeva, D., Olliver, A., Lagomarsino, M.C., and Sclavi, B. (2024). Insulation of ribosomal promoter activity by Fis, H-NS or a divergent promoter within the packed E. coli genome. Preprint at bioRxiv, 10.1101/2024.03.27.586983 10.1101/2024.03.27.586983.
Iuliani, I., Mbemba, G., Lagomarsino, M.C., and Sclavi, B. (2023). Direct single-cell observation of a key E. coli cell cycle oscillator. bioRxiv 2023.03.30.533363. 10.1101/2023.03.30.533363.
Si, Y., Grazon, C., Clavier, G., Audibert, J.-F., Sclavi, B., and Méallet-Renault, R. (2022). FRET-mediated quenching of BODIPY fluorescent nanoparticles by methylene blue and its application to bacterial imaging. Photochem Photobiol Sci 21, 1249–1255. doi: 10.1007/s43630-022-00215-1.
Sclavi, B. (2021). CHAPTER 8: Transcription–Replication Conflicts, Resolution and Coregulation. In RNA Polymerases as Molecular Motors, (Robert Landick, Terence Strick and Jue Wang Editors) Royal Society of Chemistry, pp. 176–195.
Panlilio, M., Grilli, J., Tallarico, G., Iuliani, I., Sclavi, B., Cicuta, P., and Lagomarsino, M.C. (2021). Threshold accumulation of a constitutive protein explains E. coli cell-division behavior in nutrient upshifts. PNAS May 4, 2021 118 (18) e2016391118.
Wlodarski, M., Mancini, L., Raciti, B., Sclavi, B., Lagomarsino, M.C., and Cicuta, P. (2020). Cytosolic Crowding Drives the Dynamics of Both Genome and Cytosol in Escherichia coli Challenged with Sub-lethal Antibiotic Treatments. IScience 23, 101560. doi: 10.1016/j.isci.2020.101560
Cristofalo, M., Marrano, C.A., Salerno, D., Corti, R., Cassina, V., Sclavi, B., Gherardi, M., Mammola, A., Cosentino Lagomarsino, M., Mantegazza, F. (2020), Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers, BBA - General Subjects, 1864, (12), 129725.
Si Y, Grazon C, Clavier G, Rieger J, Tian Y, Audibert JF, Sclavi B, Meallet-Renault R. (2020) Fluorescent copolymers for bacterial bioimaging and viability detection. ACS Sens. 2020 Aug 3. doi: 10.1021/acssensors.0c00981. Online ahead of print. PMID: 32786389
Qing Zhang, Elisa Brambilla, Rui Li, Hualin Shi, Marco Cosentino Lagomarsino, Bianca Sclavi (2020) A decrease in transcription capacity limits growth rate upon translation inhibition. mSystems, mSystems 5:e00575-20. https://doi.org/10.1128/mSystems.00575-20.
Crozat E, Tardin C, Salhi M, Rousseau P, Lablaine A, Bertoni T, Holcman D, Sclavi B, Cicuta P, Cornet F. (2020) Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP. Nat Commun. 2020 Jul 30;11(1):3796. doi: 10.1038/s41467-020-17606-6.
Yousuf M, Iuliani I, Veetil RT, Seshasayee ASN, Sclavi B, Cosentino Lagomarsino M. (2020) Early fate of exogenous promoters in E. coli. Nucleic Acids Res. 2020 Mar 18;48(5):2348-2356. doi: 10.1093/nar/gkz1196. PMID: 31960057
Sclavi, B., and Herrick, J. (2019). Genome size variation and species diversity in salamanders. J. Evol. Biol. 32(3):278-286.
Yu, S., Sheats, J., Cicuta, P., Sclavi, B., Lagomarsino, M.C., and Dorfman, K.D. (2018). Subdiffusion of loci and cytoplasmic particles are different in compressed Escherichia coli cells. Communications Biology 1, 176.
Piña-Iturbe, A., Ulloa-Allendes, D., Pardo-Roa, C., Coronado-Arrázola, I., Salazar-Echegarai, F.J., Sclavi, B., González, P.A., and Bueno, S.M. (2018). Comparative and phylogenetic analysis of a novel family of Enterobacteriaceae -associated genomic islands that share a conserved excision/integration module. Scientific Reports 8, 10292.
Wurihan, W., GeZi, G., Brambilla, E., Wang, S., Sun, H., Fan, L., Shi, Y., Sclavi, B.,*, Morigen M.* (2018) DnaA and LexA proteins regulate transcription of the uvrB gene in Escherichia coli: the role of DnaA in the control of the SOS regulon, Front. Microbiol. | doi: 10.3389/fmicb.2018.01212
Leh, H. Khodra, A., Bouger, M-C., Sclavi, B., Rimsky, S., Bury-Moné, S., (2017) Bacterial-Chromatin Structural Proteins Regulate the Bimodal Expression of the Locus of Enterocyte Effacement (LEE) Pathogenicity Island in Enteropathogenic Escherichia coli. mBio vol. 8 no. 4 e00773-17.
Baudin, M., Cinquin, B., Sclavi, B., Pareau, D., Lopes, F. (2017) Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity. Journal of Microbiological Methods, 140, 47-57.
Julian Sheats, Bianca Sclavi, Marco Cosentino Lagomarsino, Pietro Cicuta, Kevin D. Dorfman (2017) Role of growth rate on the orientational alignment of Escherichia coli in a slit. Royal Society Open Science. Published 21 June 2017.DOI: 10.1098/rsos.170463
Bury-Moné, S., Sclavi, B. Stochasticity of gene expression as a motor of epigenetics in bacteria: from individual to collective behavior, Research in MIcrobiology (2017) 168(6), 503-514
Baud, A., Ayme, L., Gonnet, F., Salard, I., Gohon, Y., Jolivet, P., Brodolin, K., Da Silva, P., Giuliani, A., Sclavi, B., Chardot, T., Mercere, P., Roblin, P. & Daniel, R. (2017). SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline. J. Synchrotron Rad. 24.
Baud, A., Gonnet, F., Salard, I., Le Mignon, M., Giuliani,A., Mercère, P., Sclavi, B., Daniel, R., (2016) Probing the solution structure of factor H using Hydroxyl radical protein footprinting and cross-linking. Biochemical Journal, 473 (12) 1805-1819.
Scolari, V.F., Sclavi, B., Cosentino Lagomarsino, M., (2015). The nucleoid as a smart polymer. Frontiers in Microbiology, Frontiers, 2015, 6, pp.UNSP 424.
Si, Y., Grazon, C., Clavier, G., Rieger, J., Audibert, J.-F., Sclavi, B., Méallet-Renault, R. (2016) Rapid and accurate detection of Escherichia coli growth by fluorescent pH-sensitive organic nanoparticles for High-throughput screening applications. Biosens. Bioelectron, 75, 320-327.
Brambilla, E. and Sclavi, B. (2015) Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in E. coli. G3, Genes, Genomes, Genomics, 5, 605-614.
Long, Z., Olliver, A., Brambilla, E., Sclavi, B., Cosentino Lagomarsino, M., Dorfman, K.D. (2014) Measuring bacterial adaptation dynamics at the single-cell level using a microfluidic chemostat and time-lapse fluorescence microscopy, Analyst, 139, 5254-5262
Herrick, J., Sclavi, B., (2014) A new look at genome size, evolutionary duration and genetic variation in salamanders, Comptes Rendus Palevol, 13 (7), 611-621.
Thacker, VV., Bromek, K., Meijer, B., Kotar, J., Sclavi, B., Lagomarsino, M.C., Keyser, U.F., Cicuta, P.,(2014) Bacterial nucleoid structure probed by active drag and resistive pulse sensing. Integr Biol (Camb). 6(2):184-91.
Zarei, M., Sclavi,B. Cosentino Lagomarsino, M. (2013) Gene silencing and large-scale domain structure of the E. coli genome, Mol. BioSyst., 2013, 9 (4), 758 - 767
Long Z., Nugent, E. Javer, A., Cicuta, P., Sclavi, B., Cosentino Lagomarsino, M., Dorfman, K.D. (2013) Microfluidic chemostat for measuring single cell dynamics in bacteria. Lab Chip, 2013, 13 (5), 947 - 954
Yann-Važ Le Bihan, Beatrice Matot, Olivier Pietrement, Marie-Josephe Giraud-Panis, Sylvaine Gasparini, Eric Le Cam, Eric Gilson, Bianca Sclavi, Simona Miron and Marie-Helene Le Du (2013) "Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity" Acta Cryst. (2013). D69, 409419
Saggioro, C., Olliver, A., Sclavi, B., (2013) Temperature-dependence of the DnaA–DNA interaction and its effect on the autoregulation of dnaA expression. Biochem. J. 449 (333–341).
Zorman S, Seitz H, Sclavi B, Strick TR. (2012) Topological characterization of the DnaA-oriC complex using single-molecule nanomanipuation. Nucleic Acids Res. 1;40(15):7375-83
Grant MA, Saggioro C, Ferrari U, Bassetti B, Sclavi B, Cosentino Lagomarsino M. (2011) DnaA and the timing of chromosome replication in Escherichia coli as a function of growth rate. BMC Syst Biol. 5(1):201.
Scolari, V.F., Bassetti, B., Sclavi, B., Cosentino Lagomarsino, M. (2010) Gene clusters reflecting macrodomain structure respond to nucleoid perturbations. Molecular BioSystems, DOI: 10.1039/C0MB00213E.
Olliver A., Saggioro C., Herrick J., Sclavi B. (2010) DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. Mol Microbiol 76(6) : 1555-1571.
Rogozina, A., Zaychikov, E., Buckle, M., Heumann, H., Sclavi, B. (2009) DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37°C and results in the accumulation of an off-pathway intermediate. Nucleic Acids Research, 37(16):5390-404. Epub 2009 Jul 3
Evdokimov AA, Sclavi B, Zinoviev VV, Malygin EG, Hattman S, Buckle M.(2007). Study of Bacteriophage T4-encoded Dam DNA (Adenine-N6)-methyltransferase Binding with Substrates by Rapid Laser UV Cross-linking. J Biol Chem. 282(36), 26067-76.
Sclavi, B., Beatty, C.M., Thach, D.S., Fredericks, C.E., Buckle, M., and Wolfe, A.J. (2007) The multiple roles of CRP at the complex acs promoter depend on activation region 2 and IHF. Molecular Microbiology 65(2), 425–440.
Herrick, J., Sclavi, B., (2007) Ribonucleotide reductase and the regulation of DNA replication: an old story and an ancient heritage. Molecular Microbiology, 63 (1), 22-34.
Sclavi, B .*, Zaychikov, E.*, Rogozina, A., Walther, F., Buckle, M., Heumann, H., (2005) Real time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. PNAS USA, 102, 4706-4711.
Malygin E. G., Sclavi B., Zinoviev V.V., Evdokimov A. A. Hattman S. and Buckle M. (2004) Bacteriophage T4Dam DNA-[adenine-N6] methyltransferase comparison of pre-steady state and single turnover methylation of 40mer duplexes containing two (un)modified target sites. J Biol Chem 279 (48):50012-8
Orsini G, Igonet S, Pene C, Sclavi B, Buckle M, Uzan M, Kolb A. (2004) Phage T4 early promoters are resistant to inhibition by the anti-sigma factor AsiA. Mol Microbiol. 52 (4):1013-28.
Recchi C, Sclavi B, Rauzier J, Gicquel B, Reyrat JM. (2003) Mycobacterium tuberculosis Rv1395 is a class III transcriptional regulator of the AraC family involved in cytochrome P450 regulation. J Biol Chem. 278 (36) : 33763-73.
Sclavi, B ., Sullivan, M., Chance, M.R., Brenowitz, M., Woodson, S.A. (1998) RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting. Science, 279, 1940-1943.
Sclavi, B ., Woodson, S., Sullivan, M., Chance, M., Brenowitz, M., (1997). Time-resolved synchrotron x-ray footprinting, a new approach to the study of nucleic acid structure and function: Application to protein-DNA interactions and RNA folding. Journal of Molecular Biology, 266, 144-159.
Chance, M.R., Miller, L., Fischetti, R., Scheuring, E., Huang, W.-X, Sclavi, B., Hai, Y., Sullivan, M., (1996) Global Mapping of Structural Solutions Provided by the Extended X-ray Absorption Fine Structure ad initio code FEFF 6.01: Structure of the Cryogenic Photoproduct of the Myoglobin-Carbon Monoxide Complex. Biochemistry, 35 (28), 9014-23.
Sclavi, B ., Peticolas, W.L., Powell, J.W., (1994) Fractal-like Patterns in DNA Films, B form at 0% Relative Humidity, and Heteronomous DNA: an IR Study. Biopolymers, 34 (8), p.1105-13.
Lee, S.A., Sclavi, B., Powell, J.W., Williamson III, W., Rupprecht, A., (1993) Vibrational Dynamics of Wet-spun films of the NaDNA-Netropsin Complex: A Raman and Infrared Study. Physical Review E, 48(3), p.2240-45.
Invited publications and reviews :
Sclavi B. (2008) Time-resolved footprinting for the study of the structural dynamics of DNA-protein interactions. Biochem Soc Trans. 2008 Aug; 36( Pt 4): 745-8.
Sclavi, B. (2008) Opening the DNA at the promoter; the energetic challenge. RNA Polymerases as molecular motors (Buc, H., Strick, T., eds) Royal Society of Chemistry Book Publishing, (in press).
Sclavi, B ., Roux, P., Buc, H. (2000) Kinetic analysis of enzyme-template interactions. Nucleotide incorporation by DNA-dependent RNA and DNA polymerases. DNA-Protein Interactions. Buckle, M and Travers, A. eds. Oxford University Press, Oxford, UK. p. 239-256.
Ralston, C.Y., Sclavi, B., Sullivan, M., Deras, M.L., Woodson, S.A., Chance, M.R , Brenowitz, M. (2000) Time-resolved synchrotron X-ray footprinting and its applications to RNA folding. Methods in Enzymology, 317, 353-368.
Ralston, C.Y., Sclavi, B., Brenowitz, M., Sullivan, M., Chance, M.R. (1999) The early folding intermediates of the Tetrahymena ribozyme are kinetically trapped. Journal of Biomolecular Structure and Dynamics, Conversation 11, Issue #2, Proceedings of the eleventh conversation. p. 195-200.
Sclavi, B ., Woodson, S. A., Sullivan, M., Chance, M. R. and Brenowitz, M. (1998). Following the Folding of RNA with Time-resolved Synchrotron X-Ray Footprinting. Methods in Enzymology, 295, 379-402.
Chance, MR., Sclavi, B, Woodson., S.A & Brenowitz, M. (1997). Examining the conformational dynamics of macromolecules with time-resolved synchrotron X-ray footprinting. Structure, 5, 865-869.