---
_id: '1781'
abstract:
- lang: eng
text: Microwave cavities with high quality factors enable coherent coupling of distant
quantum systems. Virtual photons lead to a transverse interaction between qubits
when they are nonresonant with the cavity but resonant with each other. We experimentally
investigate the inverse scaling of the interqubit coupling with the detuning from
a cavity mode and its proportionality to the qubit-cavity interaction strength.
We demonstrate that the enhanced coupling at higher frequencies is mediated by
multiple higher-harmonic cavity modes. Moreover, we observe dark states of the
coupled qubit-qubit system and analyze their relation to the symmetry of the applied
driving field at different frequencies.
acknowledgement: This work was supported by the Swiss National Science Foundation
(SNF), the Austrian Science Foundation (FWF), and ETH Zurich
author:
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Filipp S, Göppl M, Fink JM, et al. Multimode mediated qubit-qubit coupling
and dark-state symmetries in circuit quantum electrodynamics. Physical Review
A - Atomic, Molecular, and Optical Physics. 2011;83(6). doi:10.1103/PhysRevA.83.063827
apa: Filipp, S., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Steffen, L.,
& Wallraff, A. (2011). Multimode mediated qubit-qubit coupling and dark-state
symmetries in circuit quantum electrodynamics. Physical Review A - Atomic,
Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.063827
chicago: Filipp, Stefan, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti,
L. Steffen, and Andreas Wallraff. “Multimode Mediated Qubit-Qubit Coupling and
Dark-State Symmetries in Circuit Quantum Electrodynamics.” Physical Review
A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011.
https://doi.org/10.1103/PhysRevA.83.063827.
ieee: S. Filipp et al., “Multimode mediated qubit-qubit coupling and dark-state
symmetries in circuit quantum electrodynamics,” Physical Review A - Atomic,
Molecular, and Optical Physics, vol. 83, no. 6. American Physical Society,
2011.
ista: Filipp S, Göppl M, Fink JM, Baur M, Bianchetti R, Steffen L, Wallraff A. 2011.
Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum
electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 83(6).
mla: Filipp, Stefan, et al. “Multimode Mediated Qubit-Qubit Coupling and Dark-State
Symmetries in Circuit Quantum Electrodynamics.” Physical Review A - Atomic,
Molecular, and Optical Physics, vol. 83, no. 6, American Physical Society,
2011, doi:10.1103/PhysRevA.83.063827.
short: S. Filipp, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, L. Steffen, A. Wallraff,
Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011).
date_created: 2018-12-11T11:53:58Z
date_published: 2011-06-22T00:00:00Z
date_updated: 2021-01-12T06:53:09Z
day: '22'
doi: 10.1103/PhysRevA.83.063827
extern: 1
intvolume: ' 83'
issue: '6'
month: '06'
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5335'
quality_controlled: 0
status: public
title: Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit
quantum electrodynamics
type: journal_article
volume: 83
year: '2011'
...
---
_id: '1815'
abstract:
- lang: eng
text: Many membrane channels and receptors exhibit adaptive, or desensitized, response
to a strong sustained input stimulus, often supported by protein activity-dependent
inactivation. Adaptive response is thought to be related to various cellular functions
such as homeostasis and enlargement of dynamic range by background compensation.
Here we study the quantitative relation between adaptive response and background
compensation within a modeling framework. We show that any particular type of
adaptive response is neither sufficient nor necessary for adaptive enlargement
of dynamic range. In particular a precise adaptive response, where system activity
is maintained at a constant level at steady state, does not ensure a large dynamic
range neither in input signal nor in system output. A general mechanism for input
dynamic range enlargement can come about from the activity-dependent modulation
of protein responsiveness by multiple biochemical modification, regardless of
the type of adaptive response it induces. Therefore hierarchical biochemical processes
such as methylation and phosphorylation are natural candidates to induce this
property in signaling systems.
author:
- first_name: Tamar
full_name: Tamar Friedlander
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Naama
full_name: Brenner, Naama
last_name: Brenner
citation:
ama: Friedlander T, Brenner N. Adaptive response and enlargement of dynamic range.
Mathematical Biosciences and Engineering. 2011;8(2):515-526. doi:10.3934/mbe.2011.8.515
apa: Friedlander, T., & Brenner, N. (2011). Adaptive response and enlargement
of dynamic range. Mathematical Biosciences and Engineering. Arizona State
University. https://doi.org/10.3934/mbe.2011.8.515
chicago: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement
of Dynamic Range.” Mathematical Biosciences and Engineering. Arizona State
University, 2011. https://doi.org/10.3934/mbe.2011.8.515.
ieee: T. Friedlander and N. Brenner, “Adaptive response and enlargement of dynamic
range,” Mathematical Biosciences and Engineering, vol. 8, no. 2. Arizona
State University, pp. 515–526, 2011.
ista: Friedlander T, Brenner N. 2011. Adaptive response and enlargement of dynamic
range. Mathematical Biosciences and Engineering. 8(2), 515–526.
mla: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of
Dynamic Range.” Mathematical Biosciences and Engineering, vol. 8, no. 2,
Arizona State University, 2011, pp. 515–26, doi:10.3934/mbe.2011.8.515.
short: T. Friedlander, N. Brenner, Mathematical Biosciences and Engineering 8 (2011)
515–526.
date_created: 2018-12-11T11:54:10Z
date_published: 2011-04-02T00:00:00Z
date_updated: 2021-01-12T06:53:23Z
day: '02'
doi: 10.3934/mbe.2011.8.515
extern: 1
intvolume: ' 8'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1003.2791
month: '04'
oa: 1
page: 515 - 526
publication: Mathematical Biosciences and Engineering
publication_status: published
publisher: Arizona State University
publist_id: '5291'
quality_controlled: 0
status: public
title: Adaptive response and enlargement of dynamic range
type: journal_article
volume: 8
year: '2011'
...
---
_id: '1863'
abstract:
- lang: eng
text: The Levene model is the simplest mathematical model to describe the evolution
of gene frequencies in spatially subdivided populations. It provides insight into
how locally varying selection promotes a population’s genetic diversity. Despite
its simplicity, interesting problems have remained unsolved even in the diallelic
case. In this paper we answer an open problem by establishing that for two alleles
at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first
present a proof for the case of stable monomorphisms and then show that the result
also holds for protected alleles. These findings allow us to prove that any odd
number (up to 2J−1) of equilibria is possible, before we extend the proof to even
numbers. We conclude with some numerical results and show that for J>2, the
proportion of parameter space affording this maximum is extremely small.
acknowledgement: FWF 21305
author:
- first_name: Sebastian
full_name: Sebastian Novak
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
citation:
ama: Novak S. The number of equilibria in the diallelic Levene model with multiple
demes. Theoretical Population Biology. 2011;79(3):97-101. doi:10.1016/j.tpb.2010.12.002
apa: Novak, S. (2011). The number of equilibria in the diallelic Levene model with
multiple demes. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2010.12.002
chicago: Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model
with Multiple Demes.” Theoretical Population Biology. Academic Press, 2011.
https://doi.org/10.1016/j.tpb.2010.12.002.
ieee: S. Novak, “The number of equilibria in the diallelic Levene model with multiple
demes,” Theoretical Population Biology, vol. 79, no. 3. Academic Press,
pp. 97–101, 2011.
ista: Novak S. 2011. The number of equilibria in the diallelic Levene model with
multiple demes. Theoretical Population Biology. 79(3), 97–101.
mla: Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with
Multiple Demes.” Theoretical Population Biology, vol. 79, no. 3, Academic
Press, 2011, pp. 97–101, doi:10.1016/j.tpb.2010.12.002.
short: S. Novak, Theoretical Population Biology 79 (2011) 97–101.
date_created: 2018-12-11T11:54:25Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:42Z
day: '01'
doi: 10.1016/j.tpb.2010.12.002
extern: 1
intvolume: ' 79'
issue: '3'
month: '05'
page: 97 - 101
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '5236'
quality_controlled: 0
status: public
title: The number of equilibria in the diallelic Levene model with multiple demes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 79
year: '2011'
...
---
_id: '1973'
abstract:
- lang: eng
text: Complex I is the first and largest enzyme of the respiratory chain, coupling
electron transfer between NADH and ubiquinone to the translocation of four protons
across the membrane. It has a central role in cellular energy production and has
been implicated in many human neurodegenerative diseases. The L-shaped enzyme
consists of hydrophilic and membrane domains. Previously, we determined the structure
of the hydrophilic domain. Here we report the crystal structure of the Esherichia
coli complex I membrane domain at 3.0 Ã. resolution. It includes six subunits,
NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold
of the homologous antiporter-like subunits L, M and N is novel, with two inverted
structural repeats of five transmembrane helices arranged, unusually, face-to-back.
Each repeat includes a discontinuous transmembrane helix and forms half of a channel
across the membrane. A network of conserved polar residues connects the two half-channels,
completing the proton translocation pathway. Unexpectedly, lysines rather than
carboxylate residues act as the main elements of the proton pump in these subunits.
The fourth probable proton-translocation channel is at the interface of subunits
N, K, J and A. The structure indicates that proton translocation in complex I,
uniquely, involves coordinated conformational changes in six symmetrical structural
elements.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Efremov R, Sazanov LA. Structure of the membrane domain of respiratory complex
i. Nature. 2011;476(7361):414-421. doi:10.1038/nature10330
apa: Efremov, R., & Sazanov, L. A. (2011). Structure of the membrane domain
of respiratory complex i. Nature. Nature Publishing Group. https://doi.org/10.1038/nature10330
chicago: Efremov, Rouslan, and Leonid A Sazanov. “Structure of the Membrane Domain
of Respiratory Complex I.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/nature10330.
ieee: R. Efremov and L. A. Sazanov, “Structure of the membrane domain of respiratory
complex i,” Nature, vol. 476, no. 7361. Nature Publishing Group, pp. 414–421,
2011.
ista: Efremov R, Sazanov LA. 2011. Structure of the membrane domain of respiratory
complex i. Nature. 476(7361), 414–421.
mla: Efremov, Rouslan, and Leonid A. Sazanov. “Structure of the Membrane Domain
of Respiratory Complex I.” Nature, vol. 476, no. 7361, Nature Publishing
Group, 2011, pp. 414–21, doi:10.1038/nature10330.
short: R. Efremov, L.A. Sazanov, Nature 476 (2011) 414–421.
date_created: 2018-12-11T11:54:59Z
date_published: 2011-08-25T00:00:00Z
date_updated: 2021-01-12T06:54:26Z
day: '25'
doi: 10.1038/nature10330
extern: 1
intvolume: ' 476'
issue: '7361'
month: '08'
page: 414 - 421
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5110'
quality_controlled: 0
status: public
title: Structure of the membrane domain of respiratory complex i
type: journal_article
volume: 476
year: '2011'
...
---
_id: '1974'
abstract:
- lang: eng
text: Complex I is the first enzyme of the respiratory chain and plays a central
role in cellular energy production. It has been implicated in many human neurodegenerative
diseases, as well as in ageing. One of the biggest membrane protein complexes,
it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously,
we have determined structures of the hydrophilic domain in several redox states.
Last year was marked by fascinating breakthroughs in the understanding of the
complete structure. We described the architecture of the membrane domain and of
the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme
has also been published. The core subunits of the bacterial and mitochondrial
enzymes have remarkably similar structures. The proposed mechanism of coupling
between electron transfer and proton translocation involves long-range conformational
changes, coordinated in part by a long α-helix, akin to the coupling rod of a
steam engine.
acknowledgement: The work in authors’ laboratory was funded by the Medical Research
Council.
author:
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Efremov R, Sazanov LA. Respiratory complex I: “steam engine” of the cell?
Current Opinion in Structural Biology. 2011;21(4):532-540. doi:10.1016/j.sbi.2011.07.002'
apa: 'Efremov, R., & Sazanov, L. A. (2011). Respiratory complex I: “steam engine”
of the cell? Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2011.07.002'
chicago: 'Efremov, Rouslan, and Leonid A Sazanov. “Respiratory Complex I: ‘steam
Engine’ of the Cell?” Current Opinion in Structural Biology. Elsevier,
2011. https://doi.org/10.1016/j.sbi.2011.07.002.'
ieee: 'R. Efremov and L. A. Sazanov, “Respiratory complex I: ‘steam engine’ of the
cell?,” Current Opinion in Structural Biology, vol. 21, no. 4. Elsevier,
pp. 532–540, 2011.'
ista: 'Efremov R, Sazanov LA. 2011. Respiratory complex I: ‘steam engine’ of the
cell? Current Opinion in Structural Biology. 21(4), 532–540.'
mla: 'Efremov, Rouslan, and Leonid A. Sazanov. “Respiratory Complex I: ‘steam Engine’
of the Cell?” Current Opinion in Structural Biology, vol. 21, no. 4, Elsevier,
2011, pp. 532–40, doi:10.1016/j.sbi.2011.07.002.'
short: R. Efremov, L.A. Sazanov, Current Opinion in Structural Biology 21 (2011)
532–540.
date_created: 2018-12-11T11:54:59Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T06:54:27Z
day: '01'
doi: 10.1016/j.sbi.2011.07.002
extern: 1
intvolume: ' 21'
issue: '4'
month: '08'
page: 532 - 540
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '5111'
quality_controlled: 0
status: public
title: 'Respiratory complex I: ''steam engine'' of the cell?'
type: journal_article
volume: 21
year: '2011'
...
---
_id: '1975'
abstract:
- lang: eng
text: 'Modern α-proteobacteria are thought to be closely related to the ancient
symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from
α-proteobacteria and mitochondria is well conserved at the level of the 14 "core"
subunits, consistent with that notion. Mitochondrial complex I contains the core
subunits, present in all species, and up to 31 "supernumerary" subunits,
generally thought to have originated only within eukaryotic lineages. However,
the full protein composition of an α-proteobacterial complex I has not been established
previously. Here, we report the first purification and characterization of complex
I from the α-proteobacterium Paracoccus denitrificans. Single particle electron
microscopy shows that the complex has a well defined L-shape. Unexpectedly, in
addition to the 14 core subunits, the enzyme also contains homologues of three
supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine
nomenclature). This finding suggests that evolution of complex I via addition
of supernumerary or "accessory" subunits started before the original
endosymbiotic event that led to the creation of the eukaryotic cell. It also provides
further confirmation that α-proteobacteria are the closest extant relatives of
mitochondria.'
acknowledgement: 'This work was supported by the Medical Research Council. '
author:
- first_name: Chui
full_name: Yip, Chui Y
last_name: Yip
- first_name: Michael
full_name: Harbour, Michael E
last_name: Harbour
- first_name: Kamburapola
full_name: Jayawardena, Kamburapola G
last_name: Jayawardena
- first_name: Ian
full_name: Fearnley, Ian M
last_name: Fearnley
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. Evolution of respiratory
complex I "Supernumerary" subunits are present in the α-proteobacterial
enzyme. Journal of Biological Chemistry. 2011;286(7):5023-5033. doi:10.1074/jbc.M110.194993
apa: Yip, C., Harbour, M., Jayawardena, K., Fearnley, I., & Sazanov, L. A. (2011).
Evolution of respiratory complex I "Supernumerary" subunits
are present in the α-proteobacterial enzyme. Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M110.194993
chicago: Yip, Chui, Michael Harbour, Kamburapola Jayawardena, Ian Fearnley, and
Leonid A Sazanov. “Evolution of Respiratory Complex I "Supernumerary"
Subunits Are Present in the α-Proteobacterial Enzyme.” Journal of Biological
Chemistry. American Society for Biochemistry and Molecular Biology, 2011.
https://doi.org/10.1074/jbc.M110.194993.
ieee: C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, and L. A. Sazanov, “Evolution
of respiratory complex I "Supernumerary" subunits are present
in the α-proteobacterial enzyme,” Journal of Biological Chemistry, vol.
286, no. 7. American Society for Biochemistry and Molecular Biology, pp. 5023–5033,
2011.
ista: Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. 2011. Evolution of
respiratory complex I "Supernumerary" subunits are present in
the α-proteobacterial enzyme. Journal of Biological Chemistry. 286(7), 5023–5033.
mla: Yip, Chui, et al. “Evolution of Respiratory Complex I "Supernumerary"
Subunits Are Present in the α-Proteobacterial Enzyme.” Journal of Biological
Chemistry, vol. 286, no. 7, American Society for Biochemistry and Molecular
Biology, 2011, pp. 5023–33, doi:10.1074/jbc.M110.194993.
short: C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, L.A. Sazanov, Journal of
Biological Chemistry 286 (2011) 5023–5033.
date_created: 2018-12-11T11:55:00Z
date_published: 2011-02-18T00:00:00Z
date_updated: 2021-01-12T06:54:27Z
day: '18'
doi: 10.1074/jbc.M110.194993
extern: 1
intvolume: ' 286'
issue: '7'
month: '02'
page: 5023 - 5033
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '5112'
quality_controlled: 0
status: public
title: Evolution of respiratory complex I "Supernumerary" subunits are present
in the α-proteobacterial enzyme
type: journal_article
volume: 286
year: '2011'
...
---
_id: '1985'
abstract:
- lang: eng
text: |2-
In Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation.
acknowledgement: This work was also supported by the Max Planck Society (M.L., E.F.-F.,
P.S.).
author:
- first_name: Martin
full_name: Martin Loose
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Elisabeth
full_name: Fischer-Friedrich, Elisabeth
last_name: Fischer Friedrich
- first_name: Christoph
full_name: Herold, Christoph
last_name: Herold
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Petra
full_name: 'Schwille, Petra '
last_name: Schwille
citation:
ama: Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. Min protein patterns
emerge from rapid rebinding and membrane interaction of MinE. Nature Structural
and Molecular Biology. 2011;18(5):577-583. doi:10.1038/nsmb.2037
apa: Loose, M., Fischer Friedrich, E., Herold, C., Kruse, K., & Schwille, P.
(2011). Min protein patterns emerge from rapid rebinding and membrane interaction
of MinE. Nature Structural and Molecular Biology. Nature Publishing Group.
https://doi.org/10.1038/nsmb.2037
chicago: Loose, Martin, Elisabeth Fischer Friedrich, Christoph Herold, Karsten Kruse,
and Petra Schwille. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane
Interaction of MinE.” Nature Structural and Molecular Biology. Nature Publishing
Group, 2011. https://doi.org/10.1038/nsmb.2037.
ieee: M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, and P. Schwille, “Min
protein patterns emerge from rapid rebinding and membrane interaction of MinE,”
Nature Structural and Molecular Biology, vol. 18, no. 5. Nature Publishing
Group, pp. 577–583, 2011.
ista: Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. 2011. Min protein
patterns emerge from rapid rebinding and membrane interaction of MinE. Nature
Structural and Molecular Biology. 18(5), 577–583.
mla: Loose, Martin, et al. “Min Protein Patterns Emerge from Rapid Rebinding and
Membrane Interaction of MinE.” Nature Structural and Molecular Biology,
vol. 18, no. 5, Nature Publishing Group, 2011, pp. 577–83, doi:10.1038/nsmb.2037.
short: M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, P. Schwille, Nature
Structural and Molecular Biology 18 (2011) 577–583.
date_created: 2018-12-11T11:55:03Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2021-01-12T06:54:31Z
day: '01'
doi: 10.1038/nsmb.2037
extern: 1
intvolume: ' 18'
issue: '5'
month: '05'
page: 577 - 583
publication: Nature Structural and Molecular Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5098'
quality_controlled: 0
status: public
title: Min protein patterns emerge from rapid rebinding and membrane interaction of
MinE
type: journal_article
volume: 18
year: '2011'
...
---
_id: '1986'
abstract:
- lang: eng
text: One of the most fundamental features of biological systems is probably their
ability to self-organize in space and time on different scales. Despite many elaborate
theoretical models of how molecular self-organization can come about, only a few
experimental systems of biological origin have so far been rigorously described,
due mostly to their inherent complexity. The most promising strategy of modern
biophysics is thus to identify minimal biological systems showing self-organized
emergent behavior. One of the best-understood examples of protein self-organization,
which has recently been successfully reconstituted in vitro, is represented by
the oscillations of the Min proteins in Escherichia coli. In this review, we summarize
the current understanding of the mechanism of Min protein self-organization in
vivo and in vitro. We discuss the potential of the Min oscillations to sense the
geometry of the cell and suggest that spontaneous protein waves could be a general
means of intracellular organization. We hypothesize that cooperative membrane
binding and unbinding, e.g., as an energy-dependent switch, may act as an important
regulatory mechanism for protein oscillations and pattern formation in the cell.
author:
- first_name: Martin
full_name: Martin Loose
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Petra
full_name: 'Schwille, Petra '
last_name: Schwille
citation:
ama: 'Loose M, Kruse K, Schwille P. Protein self-organization: Lessons from the
min system. Annual Review of Biophysics. 2011;40(1):315-336. doi:10.1146/annurev-biophys-042910-155332'
apa: 'Loose, M., Kruse, K., & Schwille, P. (2011). Protein self-organization:
Lessons from the min system. Annual Review of Biophysics. Annual Reviews.
https://doi.org/10.1146/annurev-biophys-042910-155332'
chicago: 'Loose, Martin, Karsten Kruse, and Petra Schwille. “Protein Self-Organization:
Lessons from the Min System.” Annual Review of Biophysics. Annual Reviews,
2011. https://doi.org/10.1146/annurev-biophys-042910-155332.'
ieee: 'M. Loose, K. Kruse, and P. Schwille, “Protein self-organization: Lessons
from the min system,” Annual Review of Biophysics, vol. 40, no. 1. Annual
Reviews, pp. 315–336, 2011.'
ista: 'Loose M, Kruse K, Schwille P. 2011. Protein self-organization: Lessons from
the min system. Annual Review of Biophysics. 40(1), 315–336.'
mla: 'Loose, Martin, et al. “Protein Self-Organization: Lessons from the Min System.”
Annual Review of Biophysics, vol. 40, no. 1, Annual Reviews, 2011, pp.
315–36, doi:10.1146/annurev-biophys-042910-155332.'
short: M. Loose, K. Kruse, P. Schwille, Annual Review of Biophysics 40 (2011) 315–336.
date_created: 2018-12-11T11:55:04Z
date_published: 2011-06-09T00:00:00Z
date_updated: 2021-01-12T06:54:31Z
day: '09'
doi: 10.1146/annurev-biophys-042910-155332
extern: 1
intvolume: ' 40'
issue: '1'
month: '06'
page: 315 - 336
publication: Annual Review of Biophysics
publication_status: published
publisher: Annual Reviews
publist_id: '5097'
quality_controlled: 0
status: public
title: 'Protein self-organization: Lessons from the min system'
type: journal_article
volume: 40
year: '2011'
...
---
_id: '14305'
abstract:
- lang: eng
text: Understanding the mechanism of protein folding requires a detailed knowledge
of the structural properties of the barriers separating unfolded from native conformations.
The S-peptide from ribonuclease S forms its α-helical structure only upon binding
to the folded S-protein. We characterized the transition state for this binding-induced
folding reaction at high resolution by determining the effect of site-specific
backbone thioxylation and side-chain modifications on the kinetics and thermodynamics
of the reaction, which allows us to monitor formation of backbone hydrogen bonds
and side-chain interactions in the transition state. The experiments reveal that
α-helical structure in the S-peptide is absent in the transition state of binding.
Recognition between the unfolded S-peptide and the S-protein is mediated by loosely
packed hydrophobic side-chain interactions in two well defined regions on the
S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing
hydrophobic residues at positions outside the recognition region can drastically
slow down association.
article_processing_charge: No
article_type: original
author:
- first_name: Annett
full_name: Bachmann, Annett
last_name: Bachmann
- first_name: Dirk
full_name: Wildemann, Dirk
last_name: Wildemann
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Gunter
full_name: Fischer, Gunter
last_name: Fischer
- first_name: Thomas
full_name: Kiefhaber, Thomas
last_name: Kiefhaber
citation:
ama: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone
and side-chain interactions in the transition state of a coupled protein folding
and binding reaction. PNAS. 2011;108(10):3952-3957. doi:10.1073/pnas.1012668108
apa: Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., & Kiefhaber,
T. (2011). Mapping backbone and side-chain interactions in the transition state
of a coupled protein folding and binding reaction. PNAS. Proceedings of
the National Academy of Sciences. https://doi.org/10.1073/pnas.1012668108
chicago: Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer,
and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition
State of a Coupled Protein Folding and Binding Reaction.” PNAS. Proceedings
of the National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1012668108.
ieee: A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber,
“Mapping backbone and side-chain interactions in the transition state of a coupled
protein folding and binding reaction,” PNAS, vol. 108, no. 10. Proceedings
of the National Academy of Sciences, pp. 3952–3957, 2011.
ista: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping
backbone and side-chain interactions in the transition state of a coupled protein
folding and binding reaction. PNAS. 108(10), 3952–3957.
mla: Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the
Transition State of a Coupled Protein Folding and Binding Reaction.” PNAS,
vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57,
doi:10.1073/pnas.1012668108.
short: A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS
108 (2011) 3952–3957.
date_created: 2023-09-06T12:54:36Z
date_published: 2011-01-12T00:00:00Z
date_updated: 2023-11-07T11:50:29Z
day: '12'
doi: 10.1073/pnas.1012668108
extern: '1'
external_id:
pmid:
- '21325613'
intvolume: ' 108'
issue: '10'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1012668108
month: '01'
oa: 1
oa_version: Published Version
page: 3952-3957
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mapping backbone and side-chain interactions in the transition state of a coupled
protein folding and binding reaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '1467'
abstract:
- lang: eng
text: We propose a general conjecture for the mixed Hodge polynomial of the generic
character varieties of representations of the fundamental group of a Riemann surface
of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures.
This conjecture generalizes the Cauchy identity for Macdonald polynomials and
is a common generalization of two formulas that we prove in this paper. The first
is a formula for the E-polynomial of these character varieties which we obtain
using the character table of GLn(Fq). We use this formula to compute the Euler
characteristic of character varieties. The second formula gives the Poincaré polynomial
of certain associated quiver varieties which we obtain using the character table
of gln(Fq). In the last main result we prove that the Poincaré polynomials of
the quiver varieties equal certain multiplicities in the tensor product of irreducible
characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody
algebras associated with comet-shaped, and typically wild, quivers and the representation
theory of GLn(Fq).
acknowledgement: |-
Hausel’s work was supported by National Science Foundation grants DMS-0305505 and DMS-0604775, by an Alfred Sloan Fellowship, and by a Royal Society University Research Fellowship. Letellier’s work supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01.
Rodriguez-Villegas’s work supported by National Science Foundation grant DMS-0200605, by an FRA from the University of Texas at Austin, by EPSRC grant EP/G027110/1, by visiting fellowships at All Souls and Wadham Colleges in Oxford, and by a Research Scholarship from the Clay Mathematical Institute.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Emmanuel
full_name: Letellier, Emmanuel
last_name: Letellier
- first_name: Fernando
full_name: Rodríguez Villegas, Fernando
last_name: Rodríguez Villegas
citation:
ama: Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on
character and quiver varieties. Duke Mathematical Journal. 2011;160(2):323-400.
doi:10.1215/00127094-1444258
apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2011). Arithmetic
harmonic analysis on character and quiver varieties. Duke Mathematical Journal.
Duke University Press. https://doi.org/10.1215/00127094-1444258
chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic
Harmonic Analysis on Character and Quiver Varieties.” Duke Mathematical Journal.
Duke University Press, 2011. https://doi.org/10.1215/00127094-1444258.
ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis
on character and quiver varieties,” Duke Mathematical Journal, vol. 160,
no. 2. Duke University Press, pp. 323–400, 2011.
ista: Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis
on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400.
mla: Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver
Varieties.” Duke Mathematical Journal, vol. 160, no. 2, Duke University
Press, 2011, pp. 323–400, doi:10.1215/00127094-1444258.
short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal
160 (2011) 323–400.
date_created: 2018-12-11T11:52:11Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:56Z
day: '01'
doi: 10.1215/00127094-1444258
extern: 1
intvolume: ' 160'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0810.2076
month: '01'
oa: 1
page: 323 - 400
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '5728'
quality_controlled: 0
status: public
title: Arithmetic harmonic analysis on character and quiver varieties
type: journal_article
volume: 160
year: '2011'
...
---
_id: '5387'
abstract:
- lang: eng
text: We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy
parity objectives. In system design, the parity objective is used to encode ω-regular
specifications, and the mean-payoff and energy objectives can be used to model
quantitative resource constraints. The energy condition re- quires that the resource
level never drops below 0, and the mean-payoff condi- tion requires that the limit-average
value of the resource consumption is within a threshold. While these two (energy
and mean-payoff) classical conditions are equivalent for two-player games, we
show that they differ for MDPs. We show that the problem of deciding whether a
state is almost-sure winning (i.e., winning with probability 1) in energy parity
MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable
in polynomial time, improving a recent PSPACE bound.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: Chatterjee K, Doyen L. Energy and Mean-Payoff Parity Markov Decision Processes.
IST Austria; 2011. doi:10.15479/AT:IST-2011-0001
apa: Chatterjee, K., & Doyen, L. (2011). Energy and mean-payoff parity Markov
decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2011-0001
chicago: Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity
Markov Decision Processes. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0001.
ieee: K. Chatterjee and L. Doyen, Energy and mean-payoff parity Markov decision
processes. IST Austria, 2011.
ista: Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision
processes, IST Austria, 20p.
mla: Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity
Markov Decision Processes. IST Austria, 2011, doi:10.15479/AT:IST-2011-0001.
short: K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes,
IST Austria, 2011.
date_created: 2018-12-12T11:39:02Z
date_published: 2011-02-16T00:00:00Z
date_updated: 2023-02-23T11:23:11Z
day: '16'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2011-0001
file:
- access_level: open_access
checksum: 824d6c70e6d3feb3e836b009e0b3cf73
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:52:57Z
date_updated: 2020-07-14T12:46:41Z
file_id: '5458'
file_name: IST-2011-0001_IST-2011-0001.pdf
file_size: 329976
relation: main_file
file_date_updated: 2020-07-14T12:46:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '23'
related_material:
record:
- id: '3345'
relation: later_version
status: public
status: public
title: Energy and mean-payoff parity Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '580'
author:
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
citation:
ama: 'Hosten O. Quantum physics: How to catch a wave. Nature. 2011;474(7350):170-171.
doi:10.1038/474170a'
apa: 'Hosten, O. (2011). Quantum physics: How to catch a wave. Nature. Nature
Publishing Group. https://doi.org/10.1038/474170a'
chicago: 'Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature. Nature
Publishing Group, 2011. https://doi.org/10.1038/474170a.'
ieee: 'O. Hosten, “Quantum physics: How to catch a wave,” Nature, vol. 474,
no. 7350. Nature Publishing Group, pp. 170–171, 2011.'
ista: 'Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350),
170–171.'
mla: 'Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature, vol.
474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:10.1038/474170a.'
short: O. Hosten, Nature 474 (2011) 170–171.
date_created: 2018-12-11T11:47:18Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T08:03:34Z
day: '08'
doi: 10.1038/474170a
extern: 1
intvolume: ' 474'
issue: '7350'
month: '06'
page: 170 - 171
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7224'
quality_controlled: 0
status: public
title: 'Quantum physics: How to catch a wave'
type: journal_article
volume: 474
year: '2011'
...
---
_id: '585'
abstract:
- lang: eng
text: |+
We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.
alternative_title:
- Optics InfoBase Conference Papers
author:
- first_name: David
full_name: Schmid, David
last_name: Schmid
- first_name: Shiraz
full_name: Hazrat, Shiraz
last_name: Hazrat
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Stephan
full_name: Quint, Stephan
last_name: Quint
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: 'Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards
achieving precise birefringent focusing. In: OSA; 2011. doi:10.1364/CLEO_AT.2011.JThB130'
apa: 'Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., & Kwiat,
P. (2011). Methods towards achieving precise birefringent focusing. Presented
at the QELS: Quantum Electronics and Laser Science, OSA. https://doi.org/10.1364/CLEO_AT.2011.JThB130'
chicago: Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan
Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.”
OSA, 2011. https://doi.org/10.1364/CLEO_AT.2011.JThB130.
ieee: 'D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods
towards achieving precise birefringent focusing,” presented at the QELS: Quantum
Electronics and Laser Science, 2011.'
ista: 'Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods
towards achieving precise birefringent focusing. QELS: Quantum Electronics and
Laser Science, Optics InfoBase Conference Papers, .'
mla: Schmid, David, et al. Methods towards Achieving Precise Birefringent Focusing.
OSA, 2011, doi:10.1364/CLEO_AT.2011.JThB130.
short: D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:,
OSA, 2011.
conference:
name: 'QELS: Quantum Electronics and Laser Science'
date_created: 2018-12-11T11:47:20Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:44Z
day: '01'
doi: 10.1364/CLEO_AT.2011.JThB130
extern: 1
month: '01'
publication_status: published
publisher: OSA
publist_id: '7220'
quality_controlled: 0
status: public
title: Methods towards achieving precise birefringent focusing
type: conference
year: '2011'
...
...
---
_id: '586'
abstract:
- lang: eng
text: We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a
high-finesse optical cavity. We observe robust continuous wave lasing in the atypical
regime where single atoms can considerably affect the cavity field. Consequently,
we discover unusual lasing threshold behavior in the system causing jumps in lasing
power, and propose a model to explain the effect. We also measure the intermode
laser linewidth, and observe values as low as 80Hz. The tunable gain properties
of this laser suggest multiple directions for future research.
author:
- first_name: Geert
full_name: Vrijsen, Geert
last_name: Vrijsen
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Jongmin
full_name: Lee, Jongmin
last_name: Lee
- first_name: Simon
full_name: Bernon, Simon
last_name: Bernon
- first_name: Mark
full_name: Kasevich, Mark A
last_name: Kasevich
citation:
ama: Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold
atom gain medium in a high-finesse optical cavity. Physical Review Letters.
2011;107(6). doi:10.1103/PhysRevLett.107.063904
apa: Vrijsen, G., Hosten, O., Lee, J., Bernon, S., & Kasevich, M. (2011). Raman
lasing with a cold atom gain medium in a high-finesse optical cavity. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.063904
chicago: Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich.
“Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.”
Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.063904.
ieee: G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with
a cold atom gain medium in a high-finesse optical cavity,” Physical Review
Letters, vol. 107, no. 6. American Physical Society, 2011.
ista: Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with
a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters.
107(6).
mla: Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse
Optical Cavity.” Physical Review Letters, vol. 107, no. 6, American Physical
Society, 2011, doi:10.1103/PhysRevLett.107.063904.
short: G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters
107 (2011).
date_created: 2018-12-11T11:47:20Z
date_published: 2011-08-04T00:00:00Z
date_updated: 2021-01-12T08:05:05Z
day: '04'
doi: 10.1103/PhysRevLett.107.063904
extern: 1
intvolume: ' 107'
issue: '6'
month: '08'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7223'
quality_controlled: 0
status: public
title: Raman lasing with a cold atom gain medium in a high-finesse optical cavity
type: journal_article
volume: 107
year: '2011'
...
---
_id: '597'
abstract:
- lang: eng
text: The macromolecular assembly required to initiate transcription of protein-coding
genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein
complexes and is approximately 3.5 MDa in size. At the heart of this assembly
is the Mediator complex, which helps regulate PIC activity and interacts with
the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol
II interface is not well-characterized, whereas attempts to structurally define
the Mediator-pol II interaction in yeast have relied on incomplete assemblies
of Mediator and/or pol II and have yielded inconsistent interpretations. We have
assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified
components and have characterized its structural organization using cryo-electron
microscopy and single-particle reconstruction techniques. The orientation of pol
II within this assembly was determined by crystal structure docking and further
validated with projection matching experiments, allowing the structural organization
of the entire human PIC to be envisioned. Significantly, pol II orientation within
the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined
the location of other PIC components relative to pol II itself. Pol II surfaces
required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II
cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered
along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding
additional factors; and no major structural re-organization is necessary to accommodate
the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol
II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural
basis for Mediator-dependent control of PIC assembly and function. Finally, parallel
structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF
plays a key role in stabilizing pol II orientation within the assembly.
article_processing_charge: No
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patricia
full_name: Grob, Patricia
last_name: Grob
- first_name: Christopher
full_name: Ebmeier, Christopher
last_name: Ebmeier
- first_name: Eva
full_name: Nogales, Eva
last_name: Nogales
- first_name: Dylan
full_name: Taatjes, Dylan
last_name: Taatjes
citation:
ama: Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 2011;9(3).
doi:10.1371/journal.pbio.1000603
apa: Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., & Taatjes, D. (2011).
Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000603
chicago: Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and
Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF
Assembly.” PLoS Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pbio.1000603.
ieee: C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly,” PLoS Biology,
vol. 9, no. 3. Public Library of Science, 2011.
ista: Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).
mla: Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA
Polymerase II-TFIIF Assembly.” PLoS Biology, vol. 9, no. 3, Public Library
of Science, 2011, doi:10.1371/journal.pbio.1000603.
short: C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9
(2011).
date_created: 2018-12-11T11:47:24Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T08:05:25Z
day: '01'
doi: 10.1371/journal.pbio.1000603
extern: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '7209'
status: public
title: Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2011'
...
---
_id: '6137'
abstract:
- lang: eng
text: Variation in food quality and abundance requires animals to decide whether
to stay on a poor food patch or leave in search of better food. An important question
in behavioral ecology asks when is it optimal for an animal to leave a food patch
it is depleting. Although optimal foraging is central to evolutionary success,
the neural and molecular mechanisms underlying it are poorly understood. Here
we investigate the neuronal basis for adaptive food-leaving behavior in response
to resource depletion in Caenorhabditis elegans, and identify several of the signaling
pathways involved. The ASE neurons, previously implicated in salt chemoattraction,
promote food-leaving behavior via a cGMP pathway as food becomes limited. High
ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX.
Ectopic activation of these neurons using channelrhodopsin is sufficient to induce
high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which
regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH
neurons, and in the RMG interneuron to repress food-leaving. Finally, we show
that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are
necessary for adaptive food-leaving behavior. We suggest that animals integrate
information about their nutritional state with ambient oxygen and gustatory stimuli
to formulate optimal foraging strategies.
author:
- first_name: K.
full_name: Milward, K.
last_name: Milward
- first_name: K. E.
full_name: Busch, K. E.
last_name: Busch
- first_name: R. J.
full_name: Murphy, R. J.
last_name: Murphy
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: B.
full_name: Olofsson, B.
last_name: Olofsson
citation:
ama: Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular
substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the
National Academy of Sciences. 2011;108(51):20672-20677. doi:10.1073/pnas.1106134109
apa: Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., & Olofsson, B. (2011).
Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1106134109
chicago: Milward, K., K. E. Busch, R. J. Murphy, Mario de Bono, and B. Olofsson.
“Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2011. https://doi.org/10.1073/pnas.1106134109.
ieee: K. Milward, K. E. Busch, R. J. Murphy, M. de Bono, and B. Olofsson, “Neuronal
and molecular substrates for optimal foraging in Caenorhabditis elegans,” Proceedings
of the National Academy of Sciences, vol. 108, no. 51. National Academy of
Sciences, pp. 20672–20677, 2011.
ista: Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. 2011. Neuronal and
molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings
of the National Academy of Sciences. 108(51), 20672–20677.
mla: Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging
in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences,
vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:10.1073/pnas.1106134109.
short: K. Milward, K.E. Busch, R.J. Murphy, M. de Bono, B. Olofsson, Proceedings
of the National Academy of Sciences 108 (2011) 20672–20677.
date_created: 2019-03-20T14:30:06Z
date_published: 2011-12-20T00:00:00Z
date_updated: 2021-01-12T08:06:18Z
day: '20'
doi: 10.1073/pnas.1106134109
extern: '1'
external_id:
pmid:
- '22135454'
intvolume: ' 108'
issue: '51'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/
month: '12'
oa: 1
oa_version: Submitted Version
page: 20672-20677
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '6138'
author:
- first_name: Andrew Jonathan
full_name: Bretscher, Andrew Jonathan
last_name: Bretscher
- first_name: Eiji
full_name: Kodama-Namba, Eiji
last_name: Kodama-Namba
- first_name: Karl Emanuel
full_name: Busch, Karl Emanuel
last_name: Busch
- first_name: Robin Joseph
full_name: Murphy, Robin Joseph
last_name: Murphy
- first_name: Zoltan
full_name: Soltesz, Zoltan
last_name: Soltesz
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Bretscher AJ, Kodama-Namba E, Busch KE, et al. Temperature, oxygen, and salt-sensing
neurons in C. elegans are carbon dioxide sensors that control avoidance behavior.
Neuron. 2011;69(6):1099-1113. doi:10.1016/j.neuron.2011.02.023
apa: Bretscher, A. J., Kodama-Namba, E., Busch, K. E., Murphy, R. J., Soltesz, Z.,
Laurent, P., & de Bono, M. (2011). Temperature, oxygen, and salt-sensing neurons
in C. elegans are carbon dioxide sensors that control avoidance behavior. Neuron.
Elsevier BV. https://doi.org/10.1016/j.neuron.2011.02.023
chicago: Bretscher, Andrew Jonathan, Eiji Kodama-Namba, Karl Emanuel Busch, Robin Joseph
Murphy, Zoltan Soltesz, Patrick Laurent, and Mario de Bono. “Temperature, Oxygen,
and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control
Avoidance Behavior.” Neuron. Elsevier BV, 2011. https://doi.org/10.1016/j.neuron.2011.02.023.
ieee: A. J. Bretscher et al., “Temperature, oxygen, and salt-sensing neurons
in C. elegans are carbon dioxide sensors that control avoidance behavior,” Neuron,
vol. 69, no. 6. Elsevier BV, pp. 1099–1113, 2011.
ista: Bretscher AJ, Kodama-Namba E, Busch KE, Murphy RJ, Soltesz Z, Laurent P, de
Bono M. 2011. Temperature, oxygen, and salt-sensing neurons in C. elegans are
carbon dioxide sensors that control avoidance behavior. Neuron. 69(6), 1099–1113.
mla: Bretscher, Andrew Jonathan, et al. “Temperature, Oxygen, and Salt-Sensing Neurons
in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” Neuron,
vol. 69, no. 6, Elsevier BV, 2011, pp. 1099–113, doi:10.1016/j.neuron.2011.02.023.
short: A.J. Bretscher, E. Kodama-Namba, K.E. Busch, R.J. Murphy, Z. Soltesz, P.
Laurent, M. de Bono, Neuron 69 (2011) 1099–1113.
date_created: 2019-03-20T15:01:41Z
date_published: 2011-03-24T00:00:00Z
date_updated: 2021-01-12T08:06:18Z
day: '24'
ddc:
- '570'
doi: 10.1016/j.neuron.2011.02.023
extern: '1'
external_id:
pmid:
- '21435556'
file:
- access_level: open_access
checksum: 547cffd123f4c508ae927c9244b8f92a
content_type: application/pdf
creator: kschuh
date_created: 2019-03-20T15:06:32Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6139'
file_name: 2011_Cell_Bretscher.pdf
file_size: 2448332
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 69'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1099-1113
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
status: public
title: Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide
sensors that control avoidance behavior
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2011'
...
---
_id: '6140'
abstract:
- lang: eng
text: 'Genome sequence comparisons have highlighted many novel gene families that
are conserved across animal phyla but whose biological function is unknown. Here,
we functionally characterize a member of one such family, the macoilins. Macoilins
are characterized by several highly conserved predicted transmembrane domains
towards the N-terminus and by coiled-coil regions C-terminally. They are found
throughout Eumetazoa but not in other organisms. Mutants for the single Caenorhabditis
elegans macoilin, maco-1, exhibit a constellation of behavioral phenotypes, including
defects in aggregation, O2 responses, and swimming. MACO-1 protein is expressed
broadly and specifically in the nervous system and localizes to the rough endoplasmic
reticulum; it is excluded from dendrites and axons. Apart from subtle synapse
defects, nervous system development appears wild-type in maco-1 mutants. However,
maco-1 animals are resistant to the cholinesterase inhibitor aldicarb and sensitive
to levamisole, suggesting pre-synaptic defects. Using in vivo imaging, we show
that macoilin is required to evoke Ca2+ transients, at least in some neurons:
in maco-1 mutants the O2-sensing neuron PQR is unable to generate a Ca2+ response
to a rise in O2. By genetically disrupting neurotransmission, we show that pre-synaptic
input is not necessary for PQR to respond to O2, indicating that the response
is mediated by cell-intrinsic sensory transduction and amplification. Disrupting
the sodium leak channels NCA-1/NCA-2, or the N-,P/Q,R-type voltage-gated Ca2+
channels, also fails to disrupt Ca2+ responses in the PQR cell body to O2 stimuli.
By contrast, mutations in egl-19, which encodes the only Caenorhabditis elegans
L-type voltage-gated Ca2+ channel α1 subunit, recapitulate the Ca2+ response defect
we see in maco-1 mutants, although we do not see defects in localization of EGL-19.
Together, our data suggest that macoilin acts in the ER to regulate assembly or
traffic of ion channels or ion channel regulators.'
article_number: e1001341
author:
- first_name: Fausto
full_name: Arellano-Carbajal, Fausto
last_name: Arellano-Carbajal
- first_name: Luis
full_name: Briseño-Roa, Luis
last_name: Briseño-Roa
- first_name: Africa
full_name: Couto, Africa
last_name: Couto
- first_name: Benny H. H.
full_name: Cheung, Benny H. H.
last_name: Cheung
- first_name: Michel
full_name: Labouesse, Michel
last_name: Labouesse
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono
M. Macoilin, a conserved nervous system–specific ER membrane protein that regulates
neuronal excitability. PLoS Genetics. 2011;7(3). doi:10.1371/journal.pgen.1001341
apa: Arellano-Carbajal, F., Briseño-Roa, L., Couto, A., Cheung, B. H. H., Labouesse,
M., & de Bono, M. (2011). Macoilin, a conserved nervous system–specific ER
membrane protein that regulates neuronal excitability. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1001341
chicago: Arellano-Carbajal, Fausto, Luis Briseño-Roa, Africa Couto, Benny H. H.
Cheung, Michel Labouesse, and Mario de Bono. “Macoilin, a Conserved Nervous System–Specific
ER Membrane Protein That Regulates Neuronal Excitability.” PLoS Genetics.
Public Library of Science, 2011. https://doi.org/10.1371/journal.pgen.1001341.
ieee: F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B. H. H. Cheung, M. Labouesse,
and M. de Bono, “Macoilin, a conserved nervous system–specific ER membrane protein
that regulates neuronal excitability,” PLoS Genetics, vol. 7, no. 3. Public
Library of Science, 2011.
ista: Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono
M. 2011. Macoilin, a conserved nervous system–specific ER membrane protein that
regulates neuronal excitability. PLoS Genetics. 7(3), e1001341.
mla: Arellano-Carbajal, Fausto, et al. “Macoilin, a Conserved Nervous System–Specific
ER Membrane Protein That Regulates Neuronal Excitability.” PLoS Genetics,
vol. 7, no. 3, e1001341, Public Library of Science, 2011, doi:10.1371/journal.pgen.1001341.
short: F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B.H.H. Cheung, M. Labouesse,
M. de Bono, PLoS Genetics 7 (2011).
date_created: 2019-03-20T15:08:23Z
date_published: 2011-03-17T00:00:00Z
date_updated: 2021-01-12T08:06:19Z
day: '17'
ddc:
- '570'
doi: 10.1371/journal.pgen.1001341
extern: '1'
external_id:
pmid:
- '21437263'
file:
- access_level: open_access
checksum: c609b2ce616d7dafbb617ec5d022f1ea
content_type: application/pdf
creator: kschuh
date_created: 2019-03-20T15:18:11Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6141'
file_name: 2011_PLOS_Arellano-Carbajal.PDF
file_size: 5625063
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: Macoilin, a conserved nervous system–specific ER membrane protein that regulates
neuronal excitability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2011'
...
---
_id: '6298'
abstract:
- lang: eng
text: Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyalu-ronan (HA)-binding
protein that plays important roles ininflammation and ovulation. TSG-6-mediated
cross-linking ofHA has been proposed as a functional mechanism (e.g.for regu-lating
leukocyte adhesion), but direct evidence for cross-linkingis lacking, and we know
very little about its impact on HA ultra-structure. Here we used films of polymeric
and oligomeric HAchains, end-grafted to a solid support, and a combination ofsurface-sensitive
biophysical techniques to quantify the bindingof TSG-6 into HA films and to correlate
binding to morpholog-ical changes. We find that full-length TSG-6 binds with pro-nounced
positive cooperativity and demonstrate that it cancross-link HA at physiologically
relevant concentrations. Ourdata indicate that cooperative binding of full-length
TSG-6arises from HA-induced protein oligomerization and that theTSG-6 oligomers
act as cross-linkers. In contrast, the HA-bind-ing domain of TSG-6 (the Link module)
alone binds withoutpositive cooperativity and weaker than the full-length protein.Both
the Link module and full-length TSG-6 condensed andrigidified HA films, and the
degree of condensation scaled withthe affinity between the TSG-6 constructs and
HA. We proposethat condensation is the result of protein-mediated HA cross-linking.
Our findings firmly establish that TSG-6 is a potent HAcross-linking agent and
might hence have important implica-tions for the mechanistic understanding of
the biological func-tion of TSG-6 (e.g.in inflammation).
author:
- first_name: Natalia
full_name: Baranova, Natalia
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Erik
full_name: Nilebäck, Erik
last_name: Nilebäck
- first_name: F. Michael
full_name: Haller, F. Michael
last_name: Haller
- first_name: David C.
full_name: Briggs, David C.
last_name: Briggs
- first_name: Sofia
full_name: Svedhem, Sofia
last_name: Svedhem
- first_name: Anthony J.
full_name: Day, Anthony J.
last_name: Day
- first_name: Ralf P.
full_name: Richter, Ralf P.
last_name: Richter
citation:
ama: Baranova NS, Nilebäck E, Haller FM, et al. The inflammation-associated protein
TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal
of Biological Chemistry. 2011;286(29):25675-25686. doi:10.1074/jbc.m111.247395
apa: Baranova, N. S., Nilebäck, E., Haller, F. M., Briggs, D. C., Svedhem, S., Day,
A. J., & Richter, R. P. (2011). The inflammation-associated protein TSG-6
cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal of Biological
Chemistry. American Society for Biochemistry & Molecular Biology. https://doi.org/10.1074/jbc.m111.247395
chicago: Baranova, Natalia S., Erik Nilebäck, F. Michael Haller, David C. Briggs,
Sofia Svedhem, Anthony J. Day, and Ralf P. Richter. “The Inflammation-Associated
Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.”
Journal of Biological Chemistry. American Society for Biochemistry &
Molecular Biology, 2011. https://doi.org/10.1074/jbc.m111.247395.
ieee: N. S. Baranova et al., “The inflammation-associated protein TSG-6 cross-links
hyaluronan via hyaluronan-induced TSG-6 oligomers,” Journal of Biological Chemistry,
vol. 286, no. 29. American Society for Biochemistry & Molecular Biology, pp.
25675–25686, 2011.
ista: Baranova NS, Nilebäck E, Haller FM, Briggs DC, Svedhem S, Day AJ, Richter
RP. 2011. The inflammation-associated protein TSG-6 cross-links hyaluronan via
hyaluronan-induced TSG-6 oligomers. Journal of Biological Chemistry. 286(29),
25675–25686.
mla: Baranova, Natalia S., et al. “The Inflammation-Associated Protein TSG-6 Cross-Links
Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” Journal of Biological Chemistry,
vol. 286, no. 29, American Society for Biochemistry & Molecular Biology, 2011,
pp. 25675–86, doi:10.1074/jbc.m111.247395.
short: N.S. Baranova, E. Nilebäck, F.M. Haller, D.C. Briggs, S. Svedhem, A.J. Day,
R.P. Richter, Journal of Biological Chemistry 286 (2011) 25675–25686.
date_created: 2019-04-11T20:57:43Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T08:06:58Z
day: '22'
doi: 10.1074/jbc.m111.247395
extern: '1'
intvolume: ' 286'
issue: '29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.jbc.org/content/286/29/25675.full.pdf
month: '07'
oa: 1
oa_version: Published Version
page: 25675-25686
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
- 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced
TSG-6 oligomers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 286
year: '2011'
...
---
_id: '6496'
abstract:
- lang: eng
text: We report the switching behavior of the full bacterial flagellum system that
includes the filament and the motor in wild-type Escherichia coli cells. In sorting
the motor behavior by the clockwise bias, we find that the distributions of the
clockwise (CW) and counterclockwise (CCW) intervals are either exponential or
nonexponential with long tails. At low bias, CW intervals are exponentially distributed
and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and
CCW intervals are mainly exponentially distributed. A simple model suggests that
these two distinct switching behaviors are governed by the presence of signaling
noise within the chemotaxis network. Low noise yields exponentially distributed
intervals, whereas large noise yields nonexponential behavior with long tails.
These drastically different motor statistics may play a role in optimizing bacterial
behavior for a wide range of environmental conditions.
article_processing_charge: No
author:
- first_name: Heungwon
full_name: Park, Heungwon
last_name: Park
- first_name: Panos
full_name: Oikonomou, Panos
last_name: Oikonomou
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Philippe
full_name: Cluzel, Philippe
last_name: Cluzel
citation:
ama: Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior
of the bacterial flagellum. Biophysical Journal. 2011;101(10):2336-2340.
doi:10.1016/j.bpj.2011.09.040
apa: Park, H., Oikonomou, P., Guet, C. C., & Cluzel, P. (2011). Noise underlies
switching behavior of the bacterial flagellum. Biophysical Journal. Elsevier.
https://doi.org/10.1016/j.bpj.2011.09.040
chicago: Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise
Underlies Switching Behavior of the Bacterial Flagellum.” Biophysical Journal.
Elsevier, 2011. https://doi.org/10.1016/j.bpj.2011.09.040.
ieee: H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching
behavior of the bacterial flagellum,” Biophysical Journal, vol. 101, no.
10. Elsevier, pp. 2336–2340, 2011.
ista: Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior
of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.
mla: Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial
Flagellum.” Biophysical Journal, vol. 101, no. 10, Elsevier, 2011, pp.
2336–40, doi:10.1016/j.bpj.2011.09.040.
short: H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011)
2336–2340.
date_created: 2019-05-28T11:54:29Z
date_published: 2011-11-16T00:00:00Z
date_updated: 2021-04-16T11:54:49Z
day: '16'
department:
- _id: CaGu
doi: 10.1016/j.bpj.2011.09.040
external_id:
pmid:
- '22098731'
intvolume: ' 101'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/
month: '11'
oa: 1
oa_version: Published Version
page: 2336-2340
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Noise underlies switching behavior of the bacterial flagellum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2011'
...