Download The Biology and Physics of Bacterial Chromosome Organization

The Biology and Physics
of Bacterial Chromosome
Organization
BIOPHYCHROM2016
5-8th Sept 2016
Collège de France
(Paris, France)
The Biology and Physics of Bacterial Chromosome Organization
5-8th Sept 2016, Collège de France (Paris, France)
Organizing committee
Olivier Espeli (Collège de France, Paris, France)
Remus Dame (University of Leiden, The Netherlands)
David Grainger (Univeristy of Birmingham, UK)
Paul Wiggins (Washington University, Seattle, USA)
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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BIOPHYCHROM2016
Program
Monday 5th
* 12h00 - 14h00 Registration
(Lobby of the College de France, 11 place Marcelin Berthelot, 75005 Paris)
14h00 welcome
Session 1 Multiscale structuring of bacterial chromosomes
* 14h15 - 14h40 Romain Koszul
Multilayer control of the spatial organization of the E. coli chromosome.
* 14h40 - 15h00 Andrew Jewett
Analysis and modeling of nucleoids seen by electron-cryo-tomography.
* 15h00 - 15h20 David Walker
Mapping Bacterial Nucleoid Topology with Bacteriophage Mu.
* 15h20 - 15h40 Mathia Arens
Bacterial chromosome compaction by Dps, the major stationary-phase DNA-binding protein, does not
affect transcription.
* 15h40 - 16h00 Wlodarski Michal
Escherichia coli challenged with sublethal antibiotic doses shows changes in chromosomal loci
compaction.
Coffee Break (Foyer)
Session 2 Chromosome condensation
* 16h35 - 17h00 Tung Le
Divorcing chromosomes still need rings: the role of an ancestral SMC protein in bacterial chromosome
segregation.
* 17h00 - 17h20 Michael Feig
Modeling and Simulation of C. crescentus chromosomes.
* 17h20 - 17h40 Ramon Van der Valk
Environmentally driven conformational changes modulate H-NS DNA bridging activity.
* 17h40 - 18h00 Chris Brackley
Polymer simulations of clusters, loops and domains : implications for chromosome organisation.
19h30 Welcome Party
at “Le Nouvel Institut”, 1 Boulevard Saint-Germain, 75005 Paris
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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Tuesday 6th
Session 3 Interplay between gene expression and chromosome structuring
* 9h00 - 9h25 Achillefs Kapanidis
Single-molecule tracking of transcription in the bacterial nucleoid.
* 9h25 - 9h45 Karin Schnetz
Interference of transcription and H-NS/StpA repression in Escherichia coli.
* 9h45 - 10h05 Jie Xiao
Spatial organization of transcription in bacterial cells.
* 10h05 - 10h25 Alfonso Soler Bistue
Location of ribosomal protein genes impacts Vibrio cholerae in absence of simultaneous replication
rounds.
Coffee Break (Foyer)
Session 4 Genome organization
* 11h00 - 11h25 François Xavier Barre
TBA
* 11h25 - 11h45 Lisa Lamberte
A molecular explanation for the toxicity of AT-rich DNA in bacteria.
* 11h45 - 12h05 Parul Singh
Unravelling cross talk between global transcriptional regulators Fis and CRP in Escherichia coli.
* 12h05 - 12h25 Jelena Repar
Selection and mutation bias shape inversion landscapes across prokaryotic genomes.
Lunch (Foyer)
Session 5 DNA topology
* 14h00 - 14h25 Andrew Spakowitz
Multi-scale modeling of chromosomal DNA from the base pair to the genome.
* 14h25 - 14h45 Bianca Sclavi
Effects of genome position on supercoiling-dependent promoter activity.
* 14h45 - 15h05 Aleksandre Japaridze
Hyperplectonemes: a new type of DNA self-organisation.
* 15h05 - 15h25 Elise Vickridge
SOS induced sister chromatid cohesion switch: from pre-catenanes to cohesion links.
* 15h25 - 15h45 Maria Panlilio
Growth and gene expression dynamics in Escherichia coli under non-equilibrium environmental
conditions.
Coffee Break (Foyer)
16h00 - 19h00 posters session 1 (rooms 7 and 8)
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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BIOPHYCHROM2016
Wednesday 7th
Session 6 Nucleoid dynamics
* 9h00 - 9h25 Marcelo Nollmann
Chromosome structure and dynamics at high resolution.
* 9h25 - 9h45 Rodrigo Arias-Cartin
Induction of DNA damage response by loss of novel Nucleoid associated protein in Caulobacter
crescentus.
* 9h45 - 10h05 Marco Cosentino Lagomarsino
New puzzles on the physical nature of the nucleoid.
* 10h05 - 10h25 Hugo Brandao
Elucidating the role of transcription in shaping the 3D structure of the bacterial genome.
Coffee Break (Foyer)
Session 7 Molecular machines
* 11h00 - 11h25 Nynke Dekker
Dynamics of the replisome in live E. Coli
* 11h25 - 11h45 Phillipe Rousseau
FtsK differentially recognizes Xer/dif recombination complexes promoting vertical and horizontal
genetic transfer.
* 11h45 - 12h05 Beth Boudreau
StpA and Hha stimulate bridging within H-NS filaments and pausing by elongating RNA polymerase.
* 12h05 - 12h25 Meriem El Karoui
DNA double strand break repair in single Escherichia coli cells.
Lunch (Foyer)
Session 8 Damaged Nucleoids
* 14h00 - 14h25 David Bates
DNA topology-mediated replication fork stalling and reversal at protein barriers.
* 14h25 - 14h45 Susan Lovett
Replication difficulties and mutational hotspots
* 14h45 - 15h05 Bénédicte Michel
Mutations affecting potassium import restore the viability of the Escherichia coli DNA Polymerase III
holD mutant.
* 15h05 - 15h25 Shelley Lusetti
The role of the cohesin-like RecN protein in the presynaptic, long-range homology search of the
chromosome by the RecA recombinase.
Coffee Break (Foyer)
16h00 - 19h00 posters session 2 (rooms 7 and 8)
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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Thursday 8th
Session 9 Chromosome segregation and cell cycle
* 9h00 - 9h25 Daniela Barilla
Borrowing building blocks from bacteria and eukarya: a three-component DNA segregation machine
in archaea.
* 9h25 - 9h45 Isabelle Vallet Gely
Interplay of partition system, condensin and DNA replication contributes to Pseudomonas aeruginosa chromosome organization.
* 9h45 - 10h05 Roxane Diaz
Stochastic self-assembly mechanism of ParB-parS partition complex is conserved on bacterial chromosomes and plasmids.
* 10h05 - 10h25 Paul Wiggins
Replication conflicts and segregation dynamics in E. coli.
Coffee Break (Foyer)
* 11h00 - 11h20 Jean Charles Walter
Physical modeling of the active bacterial DNA segregation.
* 11h20 - 11h40 Ivan Junier
Basal coordination of transcription in bacteria: what do we know?
* 11h40 - 12h00 Sean Murray
Cells can find their middle and quarter positions using a self-positioning Turing pattern.
* 12h00 - 12h20 Torsten Waldminghaus
Synthetic secondary chromosomes to study chromosome maintenance in Escherichia coli.
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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BIOPHYCHROM2016
List of posters
Session 1 Tuesday 6th
1
Tove ATLUNG
2
Anthony BIRNIE
3
Marina BOGUE
4
Julie CASS
5
Aoife COLGAN
6
Axel COURNAC
7
Frédéric CRÉMAZY
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Estelle CROZAT-BRENDON
Jean-Michel DESFONTAINES
Stéphane DUIGOU
Gemma FISHER
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Elena GUZMÁN
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Investigating the effect on bacterial fitness of repositioning fis and dps
genes on the Salmonella Typhimurium chromosome.
Escherichia coli chromosomal loci segregate from midcell with universal
dynamics.
The effects of re-wiring the chromosomal position of the genes encoding the nucleoid associated proteins, H NS and StpA, on the physiology
of Salmonella enterica serovar Typhimurium.
Biological and physical contrains of the Escherichia coli genome.
Unveiling genomic loop formation mediated by the H-NS protein using
high resolution chromosome conformation capture.
Understanding the short-time dynamics of the bacterial chromosome.
Chromosome segregation in Vibrio cholerae.
Long range chromosome organization in E.coli: the origin of replication
defined Right and Left Macrodomain.
High-resolution whole genome mapping of the proximity of sister
Baptiste GUILHAS
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The dynamics and structure of DNA in strong confinement.
Elena ESPINOSA ALFARO chromatids.
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Response of E. coli replication time and fidelity to changes in nucleotide
pool size.
David GRAINGER
Flemming HANSEN
James HAYCOCKS
The C-terminal domain of ParB enables DNA binding and bridging interactions to condense the bacterial centromere.
Control of lifestyle switching in Vibrio cholerae.
Architecture and dynamics of bacterial partition systems.
Transcription from Ribosomal Genes rrn Modulates Thymineless Death
(TLD) in Escherichia coli.
A new fluorescent H-NS E. coli strain with wild type phenotype and
normal nucleoid.
Control of lifestyle switching in Vibrio cholerae.
Emily HELGESEN
Stabilization of E. coli replication forks by dynamic SeqA structures.
Bram HENNEMAN
Dynamic loop formation along the bacterial genome.
Andreas HOFMANN
Chris MERRIKH
The influence of loops on the genome organization.
Transcription causes pervasive replication fork collapse during every
cell cycle.
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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List of posters
Session 2 Wednesday 7th
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Marie-Eve KENNEDY-VAL
Valentine LAGAGE
w
Organisation and segregation of Pseudomonas aeruginosa chromosome.
Otmane LAMRABET
Long-term evolution of the CRP regulon in Escherichia coli.
Antoine LE GALL
Imaging DNA organization and transport at super-resolution.
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Thibault LEPAGE
Polymer model of supercoiled molecules including multiple structural
forms of DNA.
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Alessia LEPORE
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Szu-Ning LIN
Virginia LIOY
Cesar LOPEZ PASTRANA
Florilene MAIRE
Céline MATHIEU-DEMAZIÈRE
Sam MEYER
Christophe POSSOZ
Liang QIN
Quantifying bacterial DNA double-strand break repair in real time.
The interplay between a bacterial chromatin protein and DNA polymerase.
Chromosome organization in Pseudomonas aeruginosa.
The C-terminal domain of ParB: structure and function in bacterial centromere condensation.
Gene Synthesis - Sure Vector.
Molecular mechanism of partition in Escherichia coli: deciphering the role
of ParAF oscillations in plasmid F segregation.
ThreaDNA: simple and efficient estimation of DNA mechanical contribution
to protein sequence preferences at the genomic scale.
The role of the MukB condensin in Vibrio cholerae.
The integrated response of genome organization and activity to environmental cues.
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Bruno ROBERT
A New Approach to Super-resolution Microscopy for bacterial chromosome studies.
37
Maria ROJEC
The impact of archaeal histones on gene regulation in a naïve bacterial
system.
38
Vittore SCOLARI
Quantitative assessment of irreversible crosslink effect on cromatine structure.
39
Uliana SHVYREVA
More “gears” in the dps gene regulation.
40
Jacopo SOLARI
Super resolution and in vivo studies of nucleoid spatial organization in
relation to crowding and transcription.
41
Stella STYLIANIDOU
SuperSegger : an automated image processing suite for analysis of highthroughput cell-cycle imaging of bacteria.
42
Sho TAKAMORI
Towards the Understanding of Colloidal Properties of Bacterial Nucleoid.
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Maria TUTUKINA
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Sravani K. RAMISETTY
Interplay of nucleoid proteins and cAMP-CRP in regulation of the yjjM gene
coding for transcription factor involved in the control of cell motility and
biofilm formation.
Experimental evidence showing synergism of macromolecular crowding
and DNA-bridging protein/surfactant in DNA condensation.
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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BIOPHYCHROM2016
Sponsors
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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Collège de France
11 place Marcelin Berthelot
75005 Paris, France
M Maubert - Mutualité
M Cluny - La Sorbonne
M Saint-Michel
RER
M Saint-Michel - Notre-Dame
The Biology and Physics of Bacterial Chromosome Organization 5-8th Sept 2016, Paris (France)
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Collège de France
11 place Marcelin Berthelot
75005 Paris, France