Boudarene, Lydia

Cissé, Ibrahim

Dahan, Maxime

Darzacq, Claire

Darzacq, Xavier

Izzedine, Ignacio

Lagoutte, Emilie

Normanno, Davide

Récamier, Vincent

Elsevier - Publisher Connector 

288a Monday, February 27, 20121467-Pos Board B237
Irreversible Thermodynamics of Transcriptional Regulation
Maria D. Correa-Rodriguez1,2, Enrique Hernandez-Lemus1,3.
1Computational Genomics Department, National Institute of Genomic
Medicine, Mexico City, Mexico, 2School of Sciences, National Autonomous
University of Mexico, Mexico City, Mexico, 3Center for Complexity
Sciences, National Autonomous University of Me´xico, Mexico City, Mexico.
In this work we studied memory and irreversible transport phenomena in a non-
equilibrium thermodynamically model for genomic transcriptional regulation.
Transcriptional regulation possess an extremely complex phenomenology, and
it is, of course, of foremost importance in organismal cell development and in
the pathogenesis of complex diseases. A better understanding of the way in
which these processes occur is mandatory to optimize the construction of gene
regulatory networks, but also to connect these networks with multi-scale phe-
nomena (e.g.metabolism, signaling pathways, etc.) under an integrative Systems
Biology-like vision. We analyzed three simple mechanisms of genetic stimula-
tion: an instant pulse, a periodic biochemical signal and a saturation processwith
sigmoidal kinetics and from these we derived the system’s thermodynamical re-
sponse, in the form of, for example, anomalous transcriptional bursts.
1468-Pos Board B238
Stochastic Hopf Bifurcation in Transcription Networks with Delayed
Feedback
Jorge Vinals1, John Wentworth1, Mathieu Gaudreault2.
1University of Minnesota, Minneapolis, MN, USA, 2McGill University,
Montreal, QC, Canada.
Transcriptional regulation is an intrinsically stochastic process. There is in-
creasing evidence, for example, of stochastic stabilization of biological clocks
and oscillators relative to their classical description based on macroscopic rate
equations. Elucidating the effect of randomness on biological oscillation is cen-
tral to understanding the design principles of robust oscillators, or to the design
of synthetic networks. We study the oscillatory instabilities of two model sys-
tems that rely on delayed negative feedback to induce oscillation: a single gene
auto repressor system, and a dimer negative autoregulation system. We focus
on fluctuations of intrinsic origin in the range of low copy number. The bifur-
cation diagram is obtained for these stochastic models, and shown to differ sig-
nificantly from that of a macroscopic description that neglects fluctuations.
Bifurcation lines remain sharp under fluctuations, but their location is a function
of the relative size of the fluctuations. Shifts in the stability threshold of the os-
cillators can be traced back to the interplay between statistical correlations and
delayed feedback. We finally show that there results cannot be captured by
weak noise approximations (the diffusion limit), but instead result from strong
fluctuations associated with low copy numbers.
1469-Pos Board B239
Transcription Factor Target Search Strategy at the Single Molecule Level
in Eukaryotic Cells
Lydia Boudarene, Vincent Re´camier, Davide Normanno, Ignacio Izzedine,
Ibrahim Cisse´, Emilie Lagoutte, Claire Darzacq, Xavier Darzacq,
Maxime Dahan.
Ecole Normale Supe´rieure, Paris, France.
Transcription is the mechanism by which information encoded in genes is
transmitted to an mRNA template. This process is initiated by the binding of
a transcription factor (TF) to a gene promoter. TFs have to find their specific
gene promoters (~20bp) within a 3.2 billion bps genome in a fast and efficient
manner. A key challenge is thus to understand by which mechanisms do TFs
execute target search in a crowded nucleus?
To address this question, we use a non-native doxycycline-deactivable Tet Re-
pressor (TetR) DNA-binding domain integrated into a human cell line (U2OS).
By transfecting cells with TetR tagged with the photo-convertible DENDRA2,
we are able to visualize their dynamics in the nuclei of live cells using
a sptPALM technique. Low UV irradiation causes stochastic conversion of
DENDRA2 from the green to the red, with an event probability low enough
to detect single molecules.
The nuclear dynamics of TetR exhibits three different behaviours: (I)trajecto-
ries that cross the entire nucleus, screening it predominantly with a fast motion
(16mm2/s); (II)quasi-immobile molecules(0,1mm2/s), and (III)an intermediate
behaviour, with medium motion(1,4mm2/s) confined in subparts of the nucleus.
When doxycycline is added, disabling TetR DNA-binding properties, there is
a drastic decrease of quasi-immobile molecules and a 50% decrease of the
medium-motion ones.
This suggests that the quasi-immobile molecules are unspecifically bound on
DNA. Their slow motion suggests a 1dimensional screening of DNA as seen
in in vitro experiments. The medium motion population shows transiant
DNA unspecific binding combined with 3dimentional jumps, allowing a local
search. The fast population screens in a global way the nucleus.TFs seem to have a well established target search strategy by unspecifically
binding on DNA and combining 1Dimentional and 3Dimentional motions, as
suggested by previous target search theories.
1470-Pos Board B240
Breaking the Code of Bacteria Decision Making
Trevor Stavropoulos1, Daniel Schultz2, Jose´ N. Onuchic1, Eshel Ben Jacob3.
1Center for Theoretical Biological Physics, UCSD, La Jolla, CA, USA,
2Harvard Medical School, Boston, MA, USA, 3School of Physics and
Astronomy, Tel Aviv University, Tel Aviv, Israel.
To enhance fitness in complex and changing environments, identical bacteria
cells in isogenic populations have the capacity to stochastically differentiate
into various phenotypes with special attributes. Stochastic fate determination
guarantees variability, as it provides each cell with the freedom to choose its
own fate. This hedge survival strategy allows the population to continuously
deploy specialized cells in anticipation of possible drastic changes in condi-
tions. Recently, we introduced and analyzed a novel integrative model devel-
oped for the complete decision-making signal transduction system that
determines the cell fate between sporulation and competence. Here I will focus
our current studies of the core decision circuit - the AbrB circuit. This circuit
regulates the interplay between the sporulation master regulator, which acts
as an adjustable timer whose clock rate is adjusted by the past and present
stress normalized by the mean-field stress of the other cells, and the
competence master regulator, which acts as a stochastic switch whose switch-
ing rate is adjusted by the normalized cell density. The decision circuit is com-
posed of a cascade of three inhibitory genes generating oscillatory dynamics of
opening the stochastic switch. The decision circuits of the individual bacteria
are coupled by inter-cell signaling such that the decision-making circuits of
the different cells work in coordination and amplify the noise and differences
between the cells. This ingenious scheme describes how individual bacteria
weigh their decisions carefully, taking into account the stress they are facing,
the situation of their peers, and the statistics of how many cells are sporulating
and how many are choosing competence.Membrane Physical Chemistry II
1471-Pos Board B241
Anesthetic Concentrations of Halothane Change the Domain Structure of
Mixed Lipid Membranes
Hirsh Nanda1, Michael Weinrich2, Charles F. Majkrzak1,
Brian B. Maranville1, David L. Worcester1, Sergey M. Bezrukov1.
1National Institute of Standards and Technology, Gaithersburg, MD, USA,
2National Institute of Health, Bethesda, MD, USA.
Binary and ternary mixtures of lipids that form separate phases (gel, fluid-
ordered, and fluid disordered) may provide useful insights into the complex
physics of real biological membranes. Here, we examine the mixing versus
temperature of DPPC:DLPC and DPPC:DOPC:Cholesterol phase separated
systems using neutron and x-ray diffraction methods. We also report the affects
of inhalation anesthetics on the phase behavior of these lipid mixtures. Phase
co-existence was measured by lamellar x-ray diffraction from multi-layer sam-
ples. Two distinct series of lamellar Bragg diffraction were observed demon-
strating separation into distinct 3D phases. We observe a broad transition in
which one phase diminishes as a function of temperature resulting in a single
homogenous phase. We used isotopic contrast from chain deuterated lipids to
show compositional changes in the fluid phase during the mixing transition.
The changes seen in the proportion of lipids in the lamellar diffraction studies
correspond to physical mixing of the lipid species shown by examining the
chain diffraction at wide angles produced by deuterated lipids. Finally, we
show that the anesthetic halothane shifts the temperature mixing curves and
sharpens the transition of these mixtures.
1472-Pos Board B242
The Phase Diagram for the Four-Component DSPC/DOPC/POPC/CHOL
Mixture
Tatyana Konyakhina, James Mastroianni, Gerald Feigenson.
Cornell University, Ithaca, NY, USA.
When liquid-ordered (Lo) and liquid-disordered (Ld) phases coexist in mix-
tures of DSPC/DOPC/Chol, phase domains appear as large round domains in
giant unilamellar vesicles (GUVs) examined by fluorescence microscopy.
However, when liquid-ordered and liquid-disordered phases coexist in
DSPC/POPC/Chol mixtures, domain size is too small to be detected by fluores-
cence microscopy. The phase diagram of the four-component DSPC/DOPC/
POPC/Chol mixture allows for the exploration of the transition from
macroscopic-to-nanoscopic domains. We have found complex shapes (modu-
lated phase morphology) in a particular region of composition within the


Transcription Factor Target Search Strategy at the Single Molecule Level in Eukaryotic Cells 

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Transcription Factor Target Search Strategy at the Single Molecule Level in Eukaryotic Cells

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