Publications

Single molecule studies of helicases with magnetic tweezers - Hodeib, Samar and Raj, Saurabh and Manosas, M. and Zhang, Weiting and Bagchi, Debjani and Ducos, Bertrand and Allemand, Jean-Francois and Bensimon, David and Croquette, Vincent
METHODS 105, 3-15 (2016)

Abstract : Helicases are a broad family of enzymes that perform crucial functions in DNA replication and in the maintenance of DNA and RNA integrity. A detailed mechanical study of helicases on DNA and RNA is possible using single molecule manipulation methods. Among those, magnetic tweezers (or traps) present a convenient, moderate throughput assay (tens of enzymes can be monitored simultaneously) that allow for high resolution (single base-pair) studies of these enzymes in various conditions and on various substrates (double and single stranded DNA and RNA). Here we discuss various implementation of the basic assay relevant for these studies. (C) 2016 Elsevier Inc. All rights reserved.

Single-molecule mechanical identification and sequencing - Ding, Fangyuan and Manosas, Maria and Spiering, Michelle M. and Benkovic, Stephen J. and Bensimon, David and Allemand, Jean-Francois and Croquette, Vincent
NATURE METHODS 9, 367-U74 (2012)

Abstract : High-throughput, low-cost DNA sequencing has emerged as one of the challenges of the postgenomic era. Here we present the proof of concept for a single-molecule platform that allows DNA identification and sequencing. In contrast to most present methods, our scheme is not based on the detection of the fluorescent nucleotides but on DNA hairpin length. By pulling on magnetic beads tethered by a DNA hairpin to the surface, the molecule can be unzipped. In this open state it can hybridize with complementary oligonucleotides, which transiently block the hairpin rezipping when the pulling force is reduced. By measuring from the surface to the bead of a blocked hairpin, one can determine the position of the hybrid along the molecule with nearly single-base precision. Our approach can be used to identify a DNA fragment of known sequence in a mix of various fragments and to sequence an unknown DNA fragment by hybridization or ligation.

Automated imaging of neuronal activity in freely behaving Caenorhabditis elegans - Ben Arous, Juliette and Tanizawa, Yoshinori and Rabinowitch, Ithai and Chatenay, Didier and Schafer, William R.
JOURNAL OF NEUROSCIENCE METHODS 187, 229-234 (2010)

Abstract : In order to understand how neuronal circuits control locomotory patterns it is necessary to record neuronal activity of freely behaving animals. Here, using a new automated system for simultaneous recording of behavior and neuronal activity in freely moving Caenorhabditis elegans on standard agar plates, we show that spontaneous reversals from forward to backward locomotion reflect precisely the activity of the AVA command interneurons. We also witness spontaneous activity transients in the PLM sensory neurons during free behavior of the worm in standard conditions. We show that these activity transients are coupled to short spontaneous forward accelerations of the worm. (C) 2010 Elsevier B.V. All rights reserved.

MATHEMATICS AND COMPLEXITY IN LIFE AND HUMAN SCIENCES - Bellomo, N. and Berestycki, H. and Brezzi, F. and Nadal, J. -P.
MATHEMATICAL MODELS \& METHODS IN APPLIED SCIENCES 20, 1391-1395 (2010)

DISCRETE CHOICES UNDER SOCIAL INFLUENCE: GENERIC PROPERTIES - Gordon, Mirta B. and Nadal, Jean-Pierre and Phan, Denis and Semeshenko, Viktoriya
MATHEMATICAL MODELS \& METHODS IN APPLIED SCIENCES 19, 1441-1481 (2009)

Abstract : We consider a model of socially interacting individuals that make a binary choice in a context of positive additive endogenous externalities. It encompasses as particular cases several models from the sociology and economics literature. We extend previous results to the case of a general distribution of idiosyncratic preferences, called here Idiosyncratic Willingnesses to Pay (IWP). When j, the ratio of the social influence strength to the standard deviation of the IWP distribution, is small enough, the inverse demand is a classical monotonic (decreasing) function of the adoption rate. However, even if the IWP distribution is mono-modal, there is a critical value of j above which the inverse demand is non-monotonic. Thus, depending on the price, there are either one or several equilibria. Beyond this first result, we exhibit the generic properties of the boundaries limiting the regions where the system presents different types of equilibria (unique or multiple). These properties are shown to depend only on qualitative features of the IWP distribution: modality ( number of maxima), smoothness and type of support (compact or infinite). The main results are summarized as phase diagrams in the space of the model parameters, on which the regions of multiple equilibria are precisely delimited. We also discuss the links between the model and the random field Ising model studied in the physics literature.

MATHEMATICS AND COMPLEXITY IN LIFE AND HUMAN SCIENCES - Bellomo, N. and Berestycki, H. and Brezzi, F. and Nadal, J-P.
MATHEMATICAL MODELS \& METHODS IN APPLIED SCIENCES 19, 1385-1389 (2009)