---
_id: '8444'
abstract:
- lang: eng
text: Biophysical investigation of membrane proteins generally requires their extraction
from native sources using detergents, a step that can lead, possibly irreversibly,
to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent
widely utilized in NMR studies of membrane proteins, to distort their structure
has been the subject of much controversy. It has been recently proposed that the
binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward
cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment
in which to study membrane proteins. In this communication, we used all-atom molecular
dynamics simulations to investigate the specific binding of cardiolipins to yAAC3.
Our data demonstrate that the interaction interface observed in a native-like
environment differs markedly from that inferred from an NMR investigation in DPC,
implying that in this detergent, the protein structure is distorted. We further
investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with
thermal-shift assays. The loss of thermal transition observed in DPC confirms
that the protein is no longer properly folded in this environment.
article_processing_charge: No
article_type: original
author:
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Martin S.
full_name: King, Martin S.
last_name: King
- first_name: Edmund R.S.
full_name: Kunji, Edmund R.S.
last_name: Kunji
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
citation:
ama: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier
in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical
Journal. 2017;113(11):2311-2315. doi:10.1016/j.bpj.2017.09.019
apa: Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., & Chipot, C. (2017).
Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
non-native affinity. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2017.09.019
chicago: Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe
Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins
with Non-Native Affinity.” Biophysical Journal. Elsevier, 2017. https://doi.org/10.1016/j.bpj.2017.09.019.
ieee: F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial
ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,”
Biophysical Journal, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017.
ista: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP
carrier in dodecylphosphocholine binds cardiolipins with non-native affinity.
Biophysical Journal. 113(11), 2311–2315.
mla: Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine
Binds Cardiolipins with Non-Native Affinity.” Biophysical Journal, vol.
113, no. 11, Elsevier, 2017, pp. 2311–15, doi:10.1016/j.bpj.2017.09.019.
short: F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal
113 (2017) 2311–2315.
date_created: 2020-09-18T10:05:54Z
date_published: 2017-12-05T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '05'
doi: 10.1016/j.bpj.2017.09.019
extern: '1'
intvolume: ' 113'
issue: '11'
keyword:
- Biophysics
language:
- iso: eng
month: '12'
oa_version: None
page: 2311-2315
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
non-native affinity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2017'
...
---
_id: '8445'
abstract:
- lang: eng
text: Proteins perform their functions in solution but their structures are most
frequently studied inside crystals. Here we probe how the crystal packing alters
microsecond dynamics, using solid-state NMR measurements and multi-microsecond
MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance
relaxation dispersion (NERRD) experiments probe angular backbone motion, while
Bloch–McConnell relaxation dispersion data report on fluctuations of the local
electronic environment. These experiments and simulations reveal that the packing
of the protein can significantly alter the thermodynamics and kinetics of local
conformational exchange. Moreover, we report small-amplitude reorientational motion
of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds
time scale in one of the crystals, but not in others. An intriguing possibility
arises that overall motion is to some extent coupled to local dynamics. Our study
highlights the importance of considering the packing when analyzing dynamics of
crystalline proteins.
article_number: '145'
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Sergei A.
full_name: Izmailov, Sergei A.
last_name: Izmailov
- first_name: Olga N.
full_name: Rogacheva, Olga N.
last_name: Rogacheva
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Joyce
full_name: Woodhouse, Joyce
last_name: Woodhouse
- first_name: Anastasya
full_name: Shilova, Anastasya
last_name: Shilova
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Kurauskas V, Izmailov SA, Rogacheva ON, et al. Slow conformational exchange
and overall rocking motion in ubiquitin protein crystals. Nature Communications.
2017;8. doi:10.1038/s41467-017-00165-8
apa: Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse,
J., … Schanda, P. (2017). Slow conformational exchange and overall rocking motion
in ubiquitin protein crystals. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-00165-8
chicago: Kurauskas, Vilius, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel,
Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, et al. “Slow Conformational
Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” Nature
Communications. Springer Nature, 2017. https://doi.org/10.1038/s41467-017-00165-8.
ieee: V. Kurauskas et al., “Slow conformational exchange and overall rocking
motion in ubiquitin protein crystals,” Nature Communications, vol. 8. Springer
Nature, 2017.
ista: Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova
A, Xue Y, Yuwen T, Coquelle N, Colletier J-P, Skrynnikov NR, Schanda P. 2017.
Slow conformational exchange and overall rocking motion in ubiquitin protein crystals.
Nature Communications. 8, 145.
mla: Kurauskas, Vilius, et al. “Slow Conformational Exchange and Overall Rocking
Motion in Ubiquitin Protein Crystals.” Nature Communications, vol. 8, 145,
Springer Nature, 2017, doi:10.1038/s41467-017-00165-8.
short: V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse,
A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P.
Schanda, Nature Communications 8 (2017).
date_created: 2020-09-18T10:06:01Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2021-01-12T08:19:19Z
day: '27'
doi: 10.1038/s41467-017-00165-8
extern: '1'
intvolume: ' 8'
language:
- iso: eng
month: '07'
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Slow conformational exchange and overall rocking motion in ubiquitin protein
crystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8446'
abstract:
- lang: eng
text: Solid‐state NMR spectroscopy can provide insight into protein structure and
dynamics at the atomic level without inherent protein size limitations. However,
a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related
to spectral complexity and resonance overlap, which increase with molecular weight
and severely hamper the assignment process. Here the use of two sets of experiments
is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate
a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH),
or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be
extended to 5D). The experiments are based on efficient coherence transfers between
backbone atoms using INEPT transfers between carbons and cross‐polarization for
heteronuclear transfers. The utility of these experiments is exemplified with
application to assemblies of deuterated, fully amide‐protonated proteins from
approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies
from approximately 40 to 55 kHz. These experiments will also be applicable to
protonated proteins at higher MAS frequencies. The resonance assignment of a domain
within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is
compared to NMR assignments of the isolated domain in solution. This comparison
reveals contacts of this domain to the core of the polymeric tail tube assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Charles‐Adrien
full_name: Arnaud, Charles‐Adrien
last_name: Arnaud
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Maxime
full_name: Audin, Maxime
last_name: Audin
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Carsten
full_name: Krichel, Carsten
last_name: Krichel
- first_name: Jia‐Ying
full_name: Guan, Jia‐Ying
last_name: Guan
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
- first_name: Remco
full_name: Sprangers, Remco
last_name: Sprangers
- first_name: Cécile
full_name: Breyton, Cécile
last_name: Breyton
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Fraga H, Arnaud C, Gauto DF, et al. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D
correlation experiments for resonance assignment of large proteins. ChemPhysChem.
2017;18(19):2697-2703. doi:10.1002/cphc.201700572
apa: Fraga, H., Arnaud, C., Gauto, D. F., Audin, M., Kurauskas, V., Macek, P., …
Schanda, P. (2017). Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments
for resonance assignment of large proteins. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201700572
chicago: Fraga, Hugo, Charles‐Adrien Arnaud, Diego F. Gauto, Maxime Audin, Vilius
Kurauskas, Pavel Macek, Carsten Krichel, et al. “Solid‐state NMR H–N–(C)–H and
H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.”
ChemPhysChem. Wiley, 2017. https://doi.org/10.1002/cphc.201700572.
ieee: H. Fraga et al., “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation
experiments for resonance assignment of large proteins,” ChemPhysChem,
vol. 18, no. 19. Wiley, pp. 2697–2703, 2017.
ista: Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan
J, Boisbouvier J, Sprangers R, Breyton C, Schanda P. 2017. Solid‐state NMR H–N–(C)–H
and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins.
ChemPhysChem. 18(19), 2697–2703.
mla: Fraga, Hugo, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation
Experiments for Resonance Assignment of Large Proteins.” ChemPhysChem,
vol. 18, no. 19, Wiley, 2017, pp. 2697–703, doi:10.1002/cphc.201700572.
short: H. Fraga, C. Arnaud, D.F. Gauto, M. Audin, V. Kurauskas, P. Macek, C. Krichel,
J. Guan, J. Boisbouvier, R. Sprangers, C. Breyton, P. Schanda, ChemPhysChem 18
(2017) 2697–2703.
date_created: 2020-09-18T10:06:09Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2021-01-12T08:19:19Z
day: '09'
doi: 10.1002/cphc.201700572
extern: '1'
intvolume: ' 18'
issue: '19'
keyword:
- Physical and Theoretical Chemistry
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '08'
oa_version: None
page: 2697-2703
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
- 1439-7641
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance
assignment of large proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '8447'
abstract:
- lang: eng
text: 'Solid-state NMR spectroscopy can provide site-resolved information about
protein dynamics over many time scales. Here we combine protein deuteration, fast
magic-angle spinning (~45–60 kHz) and proton detection to study dynamics of ubiquitin
in microcrystals, and in particular a mutant in a region that undergoes microsecond
motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation
measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation
dispersion, to probe how the G53A mutation alters these dynamics. We report a
population-inversion of conformational states: the conformation that in the wild-type
protein is populated only sparsely becomes the predominant state. We furthermore
explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics.
We show that while quantitative interpretation of 1H relaxation remains beyond
reach under the experimental conditions, due to coherent contributions to decay,
one may extract qualitative information about flexibility.'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Petra
full_name: Rovó, Petra
last_name: Rovó
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Rasmus
full_name: Linser, Rasmus
last_name: Linser
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational
dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type
and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 2017;87(10):86-95.
doi:10.1016/j.ssnmr.2017.04.002'
apa: 'Gauto, D. F., Hessel, A., Rovó, P., Kurauskas, V., Linser, R., & Schanda,
P. (2017). Protein conformational dynamics studied by 15N and 1HR1ρ relaxation
dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State
Nuclear Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.ssnmr.2017.04.002'
chicago: 'Gauto, Diego F., Audrey Hessel, Petra Rovó, Vilius Kurauskas, Rasmus Linser,
and Paul Schanda. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation
Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” Solid State
Nuclear Magnetic Resonance. Elsevier, 2017. https://doi.org/10.1016/j.ssnmr.2017.04.002.'
ieee: 'D. F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, and P. Schanda,
“Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion:
Application to wild-type and G53A ubiquitin crystals,” Solid State Nuclear
Magnetic Resonance, vol. 87, no. 10. Elsevier, pp. 86–95, 2017.'
ista: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. 2017. Protein
conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application
to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance.
87(10), 86–95.'
mla: 'Gauto, Diego F., et al. “Protein Conformational Dynamics Studied by 15N and
1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.”
Solid State Nuclear Magnetic Resonance, vol. 87, no. 10, Elsevier, 2017,
pp. 86–95, doi:10.1016/j.ssnmr.2017.04.002.'
short: D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid
State Nuclear Magnetic Resonance 87 (2017) 86–95.
date_created: 2020-09-18T10:06:18Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '01'
doi: 10.1016/j.ssnmr.2017.04.002
extern: '1'
intvolume: ' 87'
issue: '10'
keyword:
- Nuclear and High Energy Physics
- Instrumentation
- General Chemistry
- Radiation
language:
- iso: eng
month: '10'
oa_version: None
page: 86-95
publication: Solid State Nuclear Magnetic Resonance
publication_identifier:
issn:
- 0926-2040
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion:
Application to wild-type and G53A ubiquitin crystals'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2017'
...
---
_id: '8448'
abstract:
- lang: eng
text: We present an improved fast mixing device based on the rapid mixing of two
solutions inside the NMR probe, as originally proposed by Hore and coworkers (J.
Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium
studies of molecular kinetics by multidimensional real-time NMR spectrsocopy.
The novelty of this device is that it allows removing the injector from the NMR
detection volume after mixing, and thus provides good magnetic field homogeneity
independently of the initial sample volume placed in the NMR probe. The apparatus
is simple to build, inexpensive, and can be used without any hardware modification
on any type of liquid-state NMR spectrometer. We demonstrate the performance of
our fast mixing device in terms of improved magnetic field homogeneity, and show
an application to the study of protein folding and the structural characterization
of transiently populated folding intermediates.
article_processing_charge: No
article_type: original
author:
- first_name: Rémi
full_name: Franco, Rémi
last_name: Franco
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for
real-time NMR applications. Journal of Magnetic Resonance. 2017;281(8):125-129.
doi:10.1016/j.jmr.2017.05.016
apa: Franco, R., Favier, A., Schanda, P., & Brutscher, B. (2017). Optimized
fast mixing device for real-time NMR applications. Journal of Magnetic Resonance.
Elsevier. https://doi.org/10.1016/j.jmr.2017.05.016
chicago: Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized
Fast Mixing Device for Real-Time NMR Applications.” Journal of Magnetic Resonance.
Elsevier, 2017. https://doi.org/10.1016/j.jmr.2017.05.016.
ieee: R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing
device for real-time NMR applications,” Journal of Magnetic Resonance,
vol. 281, no. 8. Elsevier, pp. 125–129, 2017.
ista: Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device
for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129.
mla: Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.”
Journal of Magnetic Resonance, vol. 281, no. 8, Elsevier, 2017, pp. 125–29,
doi:10.1016/j.jmr.2017.05.016.
short: R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance
281 (2017) 125–129.
date_created: 2020-09-18T10:06:27Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '01'
doi: 10.1016/j.jmr.2017.05.016
extern: '1'
intvolume: ' 281'
issue: '8'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '08'
oa_version: None
page: 125-129
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimized fast mixing device for real-time NMR applications
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2017'
...
---
_id: '8449'
abstract:
- lang: eng
text: Ensuring the correct folding of RNA molecules in the cell is of major importance
for a large variety of biological functions. Therefore, chaperone proteins that
assist RNA in adopting their functionally active states are abundant in all living
organisms. An important feature of RNA chaperone proteins is that they do not
require an external energy source to perform their activity, and that they interact
transiently and non-specifically with their RNA targets. So far, little is known
about the mechanistic details of the RNA chaperone activity of these proteins.
Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that
have been reported to bind single-stranded RNA and DNA. Here, we have used advanced
NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting
activity of CspA, the major cold shock protein of Escherichia coli, upon binding
to different RNA hairpins. Real-time NMR provides detailed information on the
folding kinetics and folding pathways. Finally, comparison of wild-type CspA with
single-point mutants and small peptides yields insights into the complementary
roles of aromatic and positively charged amino-acid side chains for the RNA chaperone
activity of the protein.
article_processing_charge: No
article_type: original
author:
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Tomáš
full_name: Sára, Tomáš
last_name: Sára
- first_name: Michael
full_name: Juen, Michael
last_name: Juen
- first_name: Christoph
full_name: Wunderlich, Christoph
last_name: Wunderlich
- first_name: Lionel
full_name: Imbert, Lionel
last_name: Imbert
- first_name: Zsofia
full_name: Solyom, Zsofia
last_name: Solyom
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Christoph
full_name: Kreutz, Christoph
last_name: Kreutz
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Rennella E, Sára T, Juen M, et al. RNA binding and chaperone activity of the
E.coli cold-shock protein CspA. Nucleic Acids Research. 2017;45(7):4255-4268.
doi:10.1093/nar/gkx044
apa: Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L., Solyom, Z., …
Brutscher, B. (2017). RNA binding and chaperone activity of the E.coli cold-shock
protein CspA. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkx044
chicago: Rennella, Enrico, Tomáš Sára, Michael Juen, Christoph Wunderlich, Lionel
Imbert, Zsofia Solyom, Adrien Favier, et al. “RNA Binding and Chaperone Activity
of the E.Coli Cold-Shock Protein CspA.” Nucleic Acids Research. Oxford
University Press, 2017. https://doi.org/10.1093/nar/gkx044.
ieee: E. Rennella et al., “RNA binding and chaperone activity of the E.coli
cold-shock protein CspA,” Nucleic Acids Research, vol. 45, no. 7. Oxford
University Press, pp. 4255–4268, 2017.
ista: Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala
I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. 2017. RNA binding
and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research.
45(7), 4255–4268.
mla: Rennella, Enrico, et al. “RNA Binding and Chaperone Activity of the E.Coli
Cold-Shock Protein CspA.” Nucleic Acids Research, vol. 45, no. 7, Oxford
University Press, 2017, pp. 4255–68, doi:10.1093/nar/gkx044.
short: E. Rennella, T. Sára, M. Juen, C. Wunderlich, L. Imbert, Z. Solyom, A. Favier,
I. Ayala, K. Weinhäupl, P. Schanda, R. Konrat, C. Kreutz, B. Brutscher, Nucleic
Acids Research 45 (2017) 4255–4268.
date_created: 2020-09-18T10:06:34Z
date_published: 2017-04-20T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '20'
doi: 10.1093/nar/gkx044
extern: '1'
intvolume: ' 45'
issue: '7'
language:
- iso: eng
month: '04'
oa_version: None
page: 4255-4268
publication: Nucleic Acids Research
publication_identifier:
issn:
- 0305-1048
- 1362-4962
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: RNA binding and chaperone activity of the E.coli cold-shock protein CspA
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2017'
...
---
_id: '8450'
abstract:
- lang: eng
text: Methyl groups are very useful probes of structure, dynamics, and interactions
in protein NMR spectroscopy. In particular, methyl-directed experiments provide
high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking
environment. In this chapter, we discuss the approach for labeling methyl groups
in E. coli-based protein expression, as exemplified with the mitochondrial carrier
GGC.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Remy
full_name: Sounier, Remy
last_name: Sounier
citation:
ama: 'Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies
for NMR studies of membrane proteins. In: Membrane Protein Structure and Function
Characterization. Vol 1635. Springer Nature; 2017:109-123. doi:10.1007/978-1-4939-7151-0_6'
apa: Kurauskas, V., Schanda, P., & Sounier, R. (2017). Methyl-specific isotope
labeling strategies for NMR studies of membrane proteins. In Membrane protein
structure and function characterization (Vol. 1635, pp. 109–123). Springer
Nature. https://doi.org/10.1007/978-1-4939-7151-0_6
chicago: Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope
Labeling Strategies for NMR Studies of Membrane Proteins.” In Membrane Protein
Structure and Function Characterization, 1635:109–23. Springer Nature, 2017.
https://doi.org/10.1007/978-1-4939-7151-0_6.
ieee: V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling
strategies for NMR studies of membrane proteins,” in Membrane protein structure
and function characterization, vol. 1635, Springer Nature, 2017, pp. 109–123.
ista: 'Kurauskas V, Schanda P, Sounier R. 2017.Methyl-specific isotope labeling
strategies for NMR studies of membrane proteins. In: Membrane protein structure
and function characterization. Methods in Molecular Biology, vol. 1635, 109–123.'
mla: Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for
NMR Studies of Membrane Proteins.” Membrane Protein Structure and Function
Characterization, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:10.1007/978-1-4939-7151-0_6.
short: V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and
Function Characterization, Springer Nature, 2017, pp. 109–123.
date_created: 2020-09-18T10:06:44Z
date_published: 2017-07-29T00:00:00Z
date_updated: 2022-08-26T09:14:20Z
day: '29'
doi: 10.1007/978-1-4939-7151-0_6
extern: '1'
intvolume: ' 1635'
language:
- iso: eng
month: '07'
oa_version: None
page: 109-123
publication: Membrane protein structure and function characterization
publication_identifier:
isbn:
- '9781493971497'
- '9781493971510'
issn:
- 1064-3745
- 1940-6029
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Methyl-specific isotope labeling strategies for NMR studies of membrane proteins
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1635
year: '2017'
...
---
_id: '8451'
abstract:
- lang: eng
text: The structure, dynamics, and function of membrane proteins are intimately
linked to the properties of the membrane environment in which the proteins are
embedded. For structural and biophysical characterization, membrane proteins generally
need to be extracted from the membrane and reconstituted in a suitable membrane‐mimicking
environment. Ensuring functional and structural integrity in these environments
is often a major concern. The styrene/maleic acid co‐polymer has recently been
shown to be able to extract lipid/membrane protein patches directly from native
membranes to form nanosize discoidal proteolipid particles, also referred to as
native nanodiscs. In this work, we show that high‐resolution solid‐state NMR spectra
can be obtained from an integral membrane protein in native nanodiscs, as exemplified
by the 2×34 kDa bacterial cation diffusion facilitator CzcD.
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Jonas M.
full_name: Dörr, Jonas M.
last_name: Dörr
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: J. Antoinette
full_name: Killian, J. Antoinette
last_name: Killian
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-detected solid-state
NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs.
Angewandte Chemie International Edition. 2017;56(9):2508-2512. doi:10.1002/anie.201610441
apa: Bersch, B., Dörr, J. M., Hessel, A., Killian, J. A., & Schanda, P. (2017).
Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein
in native nanodiscs. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201610441
chicago: Bersch, Beate, Jonas M. Dörr, Audrey Hessel, J. Antoinette Killian, and
Paul Schanda. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion
Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International Edition.
Wiley, 2017. https://doi.org/10.1002/anie.201610441.
ieee: B. Bersch, J. M. Dörr, A. Hessel, J. A. Killian, and P. Schanda, “Proton-detected
solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native
nanodiscs,” Angewandte Chemie International Edition, vol. 56, no. 9. Wiley,
pp. 2508–2512, 2017.
ista: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. 2017. Proton-detected
solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native
nanodiscs. Angewandte Chemie International Edition. 56(9), 2508–2512.
mla: Bersch, Beate, et al. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc
Diffusion Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International
Edition, vol. 56, no. 9, Wiley, 2017, pp. 2508–12, doi:10.1002/anie.201610441.
short: B. Bersch, J.M. Dörr, A. Hessel, J.A. Killian, P. Schanda, Angewandte Chemie
International Edition 56 (2017) 2508–2512.
date_created: 2020-09-18T10:06:50Z
date_published: 2017-01-27T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '27'
doi: 10.1002/anie.201610441
extern: '1'
intvolume: ' 56'
issue: '9'
language:
- iso: eng
month: '01'
oa_version: None
page: 2508-2512
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator
protein in native nanodiscs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2017'
...
---
_id: '169'
abstract:
- lang: eng
text: We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman
sums leads to an optimal covering exponent for S3.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Vinay
full_name: Kumaraswamy, Vinay
last_name: Kumaraswamy
- first_name: Rapael
full_name: Steiner, Rapael
last_name: Steiner
citation:
ama: Browning TD, Kumaraswamy V, Steiner R. Twisted Linnik implies optimal covering
exponent for S3. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx116
apa: Browning, T. D., Kumaraswamy, V., & Steiner, R. (2017). Twisted Linnik
implies optimal covering exponent for S3. International Mathematics Research
Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx116
chicago: Browning, Timothy D, Vinay Kumaraswamy, and Rapael Steiner. “Twisted Linnik
Implies Optimal Covering Exponent for S3.” International Mathematics Research
Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx116.
ieee: T. D. Browning, V. Kumaraswamy, and R. Steiner, “Twisted Linnik implies optimal
covering exponent for S3,” International Mathematics Research Notices.
Oxford University Press, 2017.
ista: Browning TD, Kumaraswamy V, Steiner R. 2017. Twisted Linnik implies optimal
covering exponent for S3. International Mathematics Research Notices.
mla: Browning, Timothy D., et al. “Twisted Linnik Implies Optimal Covering Exponent
for S3.” International Mathematics Research Notices, Oxford University
Press, 2017, doi:10.1093/imrn/rnx116.
short: T.D. Browning, V. Kumaraswamy, R. Steiner, International Mathematics Research
Notices (2017).
date_created: 2018-12-11T11:44:59Z
date_published: 2017-06-19T00:00:00Z
date_updated: 2021-01-12T06:52:32Z
day: '19'
doi: 10.1093/imrn/rnx116
extern: '1'
external_id:
arxiv:
- '1609.06097'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.06097
month: '06'
oa: 1
oa_version: None
publication: International Mathematics Research Notices
publication_status: published
publisher: Oxford University Press
publist_id: '7752'
quality_controlled: '1'
status: public
title: Twisted Linnik implies optimal covering exponent for S3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '172'
abstract:
- lang: eng
text: We study strong approximation for some algebraic varieties over ℚ which are
defined using norm forms. This allows us to confirm a special case of a conjecture
due to Harpaz and Wittenberg.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Damaris
full_name: Schindler, Damaris
last_name: Schindler
citation:
ama: Browning TD, Schindler D. Strong approximation and a conjecture of Harpaz and
Wittenberg. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx252
apa: Browning, T. D., & Schindler, D. (2017). Strong approximation and a conjecture
of Harpaz and Wittenberg. International Mathematics Research Notices. Oxford
University Press. https://doi.org/10.1093/imrn/rnx252
chicago: Browning, Timothy D, and Damaris Schindler. “Strong Approximation and a
Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices.
Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx252.
ieee: T. D. Browning and D. Schindler, “Strong approximation and a conjecture of
Harpaz and Wittenberg,” International Mathematics Research Notices. Oxford
University Press, 2017.
ista: Browning TD, Schindler D. 2017. Strong approximation and a conjecture of Harpaz
and Wittenberg. International Mathematics Research Notices.
mla: Browning, Timothy D., and Damaris Schindler. “Strong Approximation and a Conjecture
of Harpaz and Wittenberg.” International Mathematics Research Notices,
Oxford University Press, 2017, doi:10.1093/imrn/rnx252.
short: T.D. Browning, D. Schindler, International Mathematics Research Notices (2017).
date_created: 2018-12-11T11:45:00Z
date_published: 2017-10-30T00:00:00Z
date_updated: 2021-01-12T06:52:45Z
day: '30'
doi: 10.1093/imrn/rnx252
extern: '1'
external_id:
arxiv:
- '1509.07744'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.07744
month: '10'
oa: 1
oa_version: None
publication: International Mathematics Research Notices
publication_status: published
publisher: Oxford University Press
publist_id: '7749'
quality_controlled: '1'
status: public
title: Strong approximation and a conjecture of Harpaz and Wittenberg
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '2016'
abstract:
- lang: eng
text: The Ising model is one of the simplest and most famous models of interacting
systems. It was originally proposed to model ferromagnetic interactions in statistical
physics and is now widely used to model spatial processes in many areas such as
ecology, sociology, and genetics, usually without testing its goodness-of-fit.
Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model.
The theory of Markov bases has been developed in algebraic statistics for exact
goodness-of-fit testing using a Monte Carlo approach. However, this beautiful
theory has fallen short of its promise for applications, because finding a Markov
basis is usually computationally intractable. We develop a Monte Carlo method
for exact goodness-of-fit testing for the Ising model which avoids computing a
Markov basis and also leads to a better connectivity of the Markov chain and hence
to a faster convergence. We show how this method can be applied to analyze the
spatial organization of receptors on the cell membrane.
article_processing_charge: No
arxiv: 1
author:
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
last_name: Martin Del Campo Sanchez
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306.
doi:10.1111/sjos.12251
apa: Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017).
Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of
Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251
chicago: Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline
Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal
of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251.
ieee: A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit
testing for the Ising model,” Scandinavian Journal of Statistics, vol.
44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.
ista: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.
mla: Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for
the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell,
2017, pp. 285–306, doi:10.1111/sjos.12251.
short: A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian
Journal of Statistics 44 (2017) 285–306.
date_created: 2018-12-11T11:55:13Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-19T15:13:27Z
day: '01'
department:
- _id: GaTk
doi: 10.1111/sjos.12251
external_id:
arxiv:
- '1410.1242'
isi:
- '000400985000001'
intvolume: ' 44'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.1242
month: '06'
oa: 1
oa_version: Preprint
page: 285 - 306
publication: Scandinavian Journal of Statistics
publication_identifier:
issn:
- '03036898'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5060'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Exact goodness-of-fit testing for the Ising model
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 44
year: '2017'
...
---
_id: '202'
abstract:
- lang: eng
text: 'Restriction-modification (RM) represents the simplest and possibly the most
widespread mechanism of self/non-self discrimination in nature. In order to provide
bacteria with immunity against bacteriophages and other parasitic genetic elements,
RM systems rely on a balance between two enzymes: the restriction enzyme, which
cleaves non-self DNA at specific restriction sites, and the modification enzyme,
which tags the host’s DNA as self and thus protects it from cleavage. In this
thesis, I use population and single-cell level experiments in combination with
mathematical modeling to study different aspects of the interplay between RM systems,
bacteria and bacteriophages. First, I analyze how mutations in phage restriction
sites affect the probability of phage escape – an inherently stochastic process,
during which phages accidently get modified instead of restricted. Next, I use
single-cell experiments to show that RM systems can, with a low probability, attack
the genome of their bacterial host and that this primitive form of autoimmunity
leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally,
I investigate the nature of interactions between bacteria, RM systems and temperate
bacteriophages to find that, as a consequence of phage escape and its impact on
population dynamics, RM systems can promote acquisition of symbiotic bacteriophages,
rather than limit it. The results presented here uncover new fundamental biological
properties of RM systems and highlight their importance in the ecology and evolution
of bacteria, bacteriophages and their interactions.'
acknowledgement: "During my PhD studies, I received help from many people, all of
which unfortunately cannot be listed here. I thank them deeply and hope that I never
made them regret their kindness.\r\nI would like to express my deepest gratitude
to Călin Guet, who went far beyond his responsibilities as an advisor and was to
me also a great mentor and a friend. Călin never questioned my potential or lacked
compassion and I cannot thank him enough for cultivating in me an independent scientist.
I was amazed by his ability to recognize the most fascinating scientific problems
in objects of study that others would find mundane. I hope I adopted at least a
fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his
support and especially for giving me the best possible example of how one can practice
excellent science with humor and style. Working with Bruce was a true privilege.\r\nI
thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the
Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI
thank all our lab members: Tobias Bergmiller for his guidance, especially in the
first years of my research, and for being a good friend throughout; Remy Chait for
staying in the lab at unreasonable hours and for the good laughs at bad jokes we
shared; Anna Staron for supportively listening to my whines whenever I had to run
a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for
keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek
for always being nice to me, no matter how much bench space I took from her.\r\nI
thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing
the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics
analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical
modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally,
I would like to thank my family and especially my wife Edita, who sacrificed a lot
so that I can pursue my goals and dreams.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
citation:
ama: Pleska M. Biology of restriction-modification systems at the single-cell and
population level. 2017. doi:10.15479/AT:ISTA:th_916
apa: Pleska, M. (2017). Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916
chicago: Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell
and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.
ieee: M. Pleska, “Biology of restriction-modification systems at the single-cell
and population level,” Institute of Science and Technology Austria, 2017.
ista: Pleska M. 2017. Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria.
mla: Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell
and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916.
short: M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell
and Population Level, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:45:10Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-15T12:04:56Z
day: '01'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:th_916
file:
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date_updated: 2020-07-14T12:45:24Z
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file_date_updated: 2020-07-14T12:45:24Z
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page: '126'
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7711'
pubrep_id: '916'
related_material:
record:
- id: '1243'
relation: part_of_dissertation
status: public
- id: '561'
relation: part_of_dissertation
status: public
- id: '457'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Biology of restriction-modification systems at the single-cell and population
level
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '662'
abstract:
- lang: eng
text: 'We report a direct-numerical-simulation study of the Taylor-Couette flow
in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian
rotating flow has been investigated for decades as a simplified model system to
study the origin of turbulence in accretion disks that is not fully understood.
The flow in this study is axially periodic and thus the experimental end-wall
effects on the stability of the flow are avoided. Using optimal linear perturbations
as initial conditions, our simulations find no sustained turbulence: the strong
initial perturbations distort the velocity profile and trigger turbulence that
eventually decays.'
article_number: '044107'
author:
- first_name: Liang
full_name: Shi, Liang
last_name: Shi
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Markus
full_name: Rampp, Markus
last_name: Rampp
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian
rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525
apa: Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence
in quasi Keplerian rotating flows. Physics of Fluids. American Institute
of Physics. https://doi.org/10.1063/1.4981525
chicago: Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence
in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute
of Physics, 2017. https://doi.org/10.1063/1.4981525.
ieee: L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi
Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American
Institute of Physics, 2017.
ista: Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian
rotating flows. Physics of Fluids. 29(4), 044107.
mla: Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.”
Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics,
2017, doi:10.1063/1.4981525.
short: L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:08:15Z
day: '01'
department:
- _id: BjHo
doi: 10.1063/1.4981525
intvolume: ' 29'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.01714
month: '04'
oa: 1
oa_version: Submitted Version
project:
- _id: 2511D90C-B435-11E9-9278-68D0E5697425
grant_number: SFB 963 TP A8
name: Astrophysical instability of currents and turbulences
publication: Physics of Fluids
publication_identifier:
issn:
- '10706631'
publication_status: published
publisher: American Institute of Physics
publist_id: '7072'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hydrodynamic turbulence in quasi Keplerian rotating flows
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2017'
...
---
_id: '663'
abstract:
- lang: eng
text: 'In this paper, we propose an approach to automatically compute invariant
clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for
an ordinary differential equation (ODE) is a multivariate polynomial invariant
g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete
invariants by assigning different values to u→ so that every trajectory of the
system can be overapproximated precisely by the intersection of a group of concrete
invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial
right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant
cluster can be obtained by first computing the remainder of the Lie derivative
of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations
obtained from the coefficients of the remainder. Based on invariant clusters and
sum-of-squares (SOS) programming, we present a new method for the safety verification
of hybrid systems. Experiments on nonlinear benchmark systems from biology and
control theory show that our approach is efficient. '
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Sergiy
full_name: Bogomolov, Sergiy
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Christian
full_name: Schilling, Christian
last_name: Schilling
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification
of nonlinear hybrid systems based on invariant clusters. In: Proceedings of
the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814'
apa: 'Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A.
(2017). Safety verification of nonlinear hybrid systems based on invariant clusters.
In Proceedings of the 20th International Conference on Hybrid Systems (pp.
163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814'
chicago: Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas
A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant
Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems,
163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814.
ieee: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety
verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings
of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United
States, 2017, pp. 163–172.
ista: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification
of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th
International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and
Control , 163–172.'
mla: Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on
Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid
Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814.
short: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings
of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.
conference:
end_date: 2017-04-20
location: Pittsburgh, PA, United States
name: 'HSCC: Hybrid Systems Computation and Control '
start_date: 2017-04-18
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:08:17Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3049797.3049814
file:
- access_level: open_access
checksum: b7667434cbf5b5f0ade3bea1dbe5bf63
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:20Z
date_updated: 2020-07-14T12:47:34Z
file_id: '4873'
file_name: IST-2017-817-v1+1_p163-kong.pdf
file_size: 1650530
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 163 - 172
publication: Proceedings of the 20th International Conference on Hybrid Systems
publication_identifier:
isbn:
- 978-145034590-3
publication_status: published
publisher: ACM
publist_id: '7067'
pubrep_id: '817'
quality_controlled: '1'
scopus_import: 1
status: public
title: Safety verification of nonlinear hybrid systems based on invariant clusters
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '664'
abstract:
- lang: eng
text: Immune cells communicate using cytokine signals, but the quantitative rules
of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et
al. (2017) suggest that the distribution of a cytokine within a lymphatic organ
is primarily governed by the local density of cells consuming it.
author:
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520.
doi:10.1016/j.immuni.2017.04.006
apa: Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity.
Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006
chicago: Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity.
Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006.
ieee: F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity,
vol. 46, no. 4. Cell Press, pp. 519–520, 2017.
ista: Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.
mla: Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity,
vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006.
short: F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-18T00:00:00Z
date_updated: 2024-03-25T23:30:05Z
day: '18'
department:
- _id: MiSi
doi: 10.1016/j.immuni.2017.04.006
intvolume: ' 46'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 519 - 520
publication: Immunity
publication_identifier:
issn:
- '10747613'
publication_status: published
publisher: Cell Press
publist_id: '7065'
quality_controlled: '1'
related_material:
record:
- id: '6947'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: The dynamic cytokine niche
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2017'
...
---
_id: '665'
abstract:
- lang: eng
text: The molecular mechanisms underlying phenotypic variation in isogenic bacterial
populations remain poorly understood.We report that AcrAB-TolC, the main multidrug
efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell
poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex
formation. Mother cells inheriting old poles are phenotypically distinct and display
increased drug efflux activity relative to daughters. Consequently, we find systematic
and long-lived growth differences between mother and daughter cells in the presence
of subinhibitory drug concentrations. A simple model for biased partitioning predicts
a population structure of long-lived and highly heterogeneous phenotypes. This
straightforward mechanism of generating sustained growth rate differences at subinhibitory
antibiotic concentrations has implications for understanding the emergence of
multidrug resistance in bacteria.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M
full_name: Andersson, Anna M
id: 2B8A40DA-F248-11E8-B48F-1D18A9856A87
last_name: Andersson
orcid: 0000-0003-2912-6769
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Enrique
full_name: Balleza, Enrique
last_name: Balleza
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug
efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science.
2017;356(6335):311-315. doi:10.1126/science.aaf4762
apa: Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild,
R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB
TolC underlies long lived phenotypic heterogeneity. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.aaf4762
chicago: Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza,
Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning
of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.
ieee: T. Bergmiller et al., “Biased partitioning of the multidrug efflux
pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science,
vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315,
2017.
ista: Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik
G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC
underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
mla: Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump
AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol.
356, no. 6335, American Association for the Advancement of Science, 2017, pp.
311–15, doi:10.1126/science.aaf4762.
short: T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild,
G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-21T00:00:00Z
date_updated: 2024-02-21T13:49:00Z
day: '21'
department:
- _id: CaGu
- _id: GaTk
- _id: Bio
doi: 10.1126/science.aaf4762
intvolume: ' 356'
issue: '6335'
language:
- iso: eng
month: '04'
oa_version: None
page: 311 - 315
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7064'
quality_controlled: '1'
related_material:
record:
- id: '5560'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long
lived phenotypic heterogeneity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 356
year: '2017'
...
---
_id: '666'
abstract:
- lang: eng
text: Antibiotics elicit drastic changes in microbial gene expression, including
the induction of stress response genes. While certain stress responses are known
to “cross-protect” bacteria from other stressors, it is unclear whether cellular
responses to antibiotics have a similar protective role. By measuring the genome-wide
transcriptional response dynamics of Escherichia coli to four antibiotics, we
found that trimethoprim induces a rapid acid stress response that protects bacteria
from subsequent exposure to acid. Combining microfluidics with time-lapse imaging
to monitor survival and acid stress response in single cells revealed that the
noisy expression of the acid resistance operon gadBC correlates with single-cell
survival. Cells with higher gadBC expression following trimethoprim maintain higher
intracellular pH and survive the acid stress longer. The seemingly random single-cell
survival under acid stress can therefore be predicted from gadBC expression and
rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap
for identifying the molecular mechanisms of single-cell cross-protection between
antibiotics and other stressors.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts
subsequent single cell survival in an acidic environment. Cell Systems.
2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001
apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to
antibiotic stress predicts subsequent single cell survival in an acidic environment.
Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001
chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response
to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.”
Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001.
ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic
stress predicts subsequent single cell survival in an acidic environment,” Cell
Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.
ista: Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress
predicts subsequent single cell survival in an acidic environment. Cell Systems.
4(4), 393–403.
mla: Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent
Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no.
4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.
short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-07T12:00:25Z
day: '26'
ddc:
- '576'
- '610'
department:
- _id: ToBo
- _id: GaTk
doi: 10.1016/j.cels.2017.03.001
ec_funded: 1
file:
- access_level: open_access
checksum: 04ff20011c3d9a601c514aa999a5fe1a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:54Z
date_updated: 2020-07-14T12:47:35Z
file_id: '5041'
file_name: IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf
file_size: 2438660
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 393 - 403
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Cell Systems
publication_identifier:
issn:
- '24054712'
publication_status: published
publisher: Cell Press
publist_id: '7061'
pubrep_id: '901'
quality_controlled: '1'
related_material:
record:
- id: '818'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Noisy response to antibiotic stress predicts subsequent single cell survival
in an acidic environment
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
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2017'
...
---
_id: '667'
abstract:
- lang: eng
text: Perinatal exposure to penicillin may result in longlasting gut and behavioral
changes.
article_number: '2786'
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Novarino G. The antisocial side of antibiotics. Science Translational Medicine.
2017;9(387). doi:10.1126/scitranslmed.aan2786
apa: Novarino, G. (2017). The antisocial side of antibiotics. Science Translational
Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786
chicago: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational
Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786.
ieee: G. Novarino, “The antisocial side of antibiotics,” Science Translational
Medicine, vol. 9, no. 387. American Association for the Advancement of Science,
2017.
ista: Novarino G. 2017. The antisocial side of antibiotics. Science Translational
Medicine. 9(387), 2786.
mla: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational
Medicine, vol. 9, no. 387, 2786, American Association for the Advancement
of Science, 2017, doi:10.1126/scitranslmed.aan2786.
short: G. Novarino, Science Translational Medicine 9 (2017).
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2021-01-12T08:08:30Z
day: '26'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aan2786
intvolume: ' 9'
issue: '387'
language:
- iso: eng
month: '04'
oa_version: None
publication: Science Translational Medicine
publication_identifier:
issn:
- '19466234'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7060'
quality_controlled: '1'
scopus_import: 1
status: public
title: The antisocial side of antibiotics
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '6679'
abstract:
- lang: eng
text: 'Polar codes represent one of the major recent breakthroughs in coding theory
and, because of their attractive features, they have been selected for the incoming
5G standard. As such, a lot of attention has been devoted to the development of
decoding algorithms with good error performance and efficient hardware implementation.
One of the leading candidates in this regard is represented by successive-cancellation
list (SCL) decoding. However, its hardware implementation requires a large amount
of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly
reduce the memory consumption [1]. In this paper, we examine the paradigm of PSCL
decoding from both theoretical and practical standpoints: (i) by changing the
construction of the code, we are able to improve the performance at no additional
computational, latency or memory cost, (ii) we present an optimal scheme to allocate
cyclic redundancy checks (CRCs), and (iii) we provide an upper bound on the list
size that allows MAP performance.'
arxiv: 1
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Ruediger
full_name: Urbanke, Ruediger
last_name: Urbanke
- first_name: Warren
full_name: Gross, Warren
last_name: Gross
citation:
ama: 'Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. Partitioned list decoding
of polar codes: Analysis and improvement of finite length performance. In: 2017
IEEE Global Communications Conference. IEEE; 2017:1-7. doi:10.1109/glocom.2017.8254940'
apa: 'Hashemi, S. A., Mondelli, M., Hassani, H., Urbanke, R., & Gross, W. (2017).
Partitioned list decoding of polar codes: Analysis and improvement of finite length
performance. In 2017 IEEE Global Communications Conference (pp. 1–7). Singapore,
Singapore: IEEE. https://doi.org/10.1109/glocom.2017.8254940'
chicago: 'Hashemi, Seyyed Ali, Marco Mondelli, Hamed Hassani, Ruediger Urbanke,
and Warren Gross. “Partitioned List Decoding of Polar Codes: Analysis and Improvement
of Finite Length Performance.” In 2017 IEEE Global Communications Conference,
1–7. IEEE, 2017. https://doi.org/10.1109/glocom.2017.8254940.'
ieee: 'S. A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, and W. Gross, “Partitioned
list decoding of polar codes: Analysis and improvement of finite length performance,”
in 2017 IEEE Global Communications Conference, Singapore, Singapore, 2017,
pp. 1–7.'
ista: 'Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. 2017. Partitioned
list decoding of polar codes: Analysis and improvement of finite length performance.
2017 IEEE Global Communications Conference. GLOBECOM: Global Communications Conference,
1–7.'
mla: 'Hashemi, Seyyed Ali, et al. “Partitioned List Decoding of Polar Codes: Analysis
and Improvement of Finite Length Performance.” 2017 IEEE Global Communications
Conference, IEEE, 2017, pp. 1–7, doi:10.1109/glocom.2017.8254940.'
short: S.A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, W. Gross, in:, 2017 IEEE
Global Communications Conference, IEEE, 2017, pp. 1–7.
conference:
end_date: 2017-12-08
location: Singapore, Singapore
name: 'GLOBECOM: Global Communications Conference'
start_date: 2017-12-04
date_created: 2019-07-24T13:55:25Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:08:34Z
day: '01'
doi: 10.1109/glocom.2017.8254940
extern: '1'
external_id:
arxiv:
- '1705.05497'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.05497
month: '12'
oa: 1
oa_version: Preprint
page: 1-7
publication: 2017 IEEE Global Communications Conference
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'Partitioned list decoding of polar codes: Analysis and improvement of finite
length performance'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '668'
abstract:
- lang: eng
text: Macrophage filopodia, finger-like membrane protrusions, were first implicated
in phagocytosis more than 100 years ago, but little is still known about the involvement
of these actin-dependent structures in particle clearance. Using spinning disk
confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP
macrophages, we show that filopodia, or filopodia-like structures, support pathogen
clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial
(Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing
toward the cell body, the most common mode of capture; (ii) capturing via the
tip followed by retraction; (iii) combinations of surfing and retraction; or (iv)
sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces
cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and
filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii)
the rapid growth of new protrusions. To explore the role of filopodia-inducing
Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages
exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which
could be explained by the marked rounded-up morphology of these cells. Macrophages
lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility,
and phagocytic cup formation, but displayed markedly reduced filopodia formation.
In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage
filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia
or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial
spreading.
article_type: original
author:
- first_name: Markus
full_name: Horsthemke, Markus
last_name: Horsthemke
- first_name: Anne
full_name: Bachg, Anne
last_name: Bachg
- first_name: Katharina
full_name: Groll, Katharina
last_name: Groll
- first_name: Sven
full_name: Moyzio, Sven
last_name: Moyzio
- first_name: Barbara
full_name: Müther, Barbara
last_name: Müther
- first_name: Sandra
full_name: Hemkemeyer, Sandra
last_name: Hemkemeyer
- first_name: Roland
full_name: Wedlich Söldner, Roland
last_name: Wedlich Söldner
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Sebastian
full_name: Tacke, Sebastian
last_name: Tacke
- first_name: Martin
full_name: Bähler, Martin
last_name: Bähler
- first_name: Peter
full_name: Hanley, Peter
last_name: Hanley
citation:
ama: Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics
in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion.
Journal of Biological Chemistry. 2017;292(17):7258-7273. doi:10.1074/jbc.M116.766923
apa: Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S.,
… Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture
and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological
Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.766923
chicago: Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther,
Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial
Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10
Deletion.” Journal of Biological Chemistry. American Society for Biochemistry
and Molecular Biology, 2017. https://doi.org/10.1074/jbc.M116.766923.
ieee: M. Horsthemke et al., “Multiple roles of filopodial dynamics in particle
capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” Journal
of Biological Chemistry, vol. 292, no. 17. American Society for Biochemistry
and Molecular Biology, pp. 7258–7273, 2017.
ista: Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich
Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial
dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10
deletion. Journal of Biological Chemistry. 292(17), 7258–7273.
mla: Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle
Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal
of Biological Chemistry, vol. 292, no. 17, American Society for Biochemistry
and Molecular Biology, 2017, pp. 7258–73, doi:10.1074/jbc.M116.766923.
short: M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R.
Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological
Chemistry 292 (2017) 7258–7273.
date_created: 2018-12-11T11:47:49Z
date_published: 2017-04-28T00:00:00Z
date_updated: 2021-01-12T08:08:34Z
day: '28'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1074/jbc.M116.766923
file:
- access_level: open_access
checksum: d488162874326a4bb056065fa549dc4a
content_type: application/pdf
creator: dernst
date_created: 2019-10-24T15:25:42Z
date_updated: 2020-07-14T12:47:37Z
file_id: '6971'
file_name: 2017_JBC_Horsthemke.pdf
file_size: 5647880
relation: main_file
file_date_updated: 2020-07-14T12:47:37Z
has_accepted_license: '1'
intvolume: ' 292'
issue: '17'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 7258 - 7273
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- '00219258'
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '7059'
quality_controlled: '1'
scopus_import: 1
status: public
title: Multiple roles of filopodial dynamics in particle capture and phagocytosis
and phenotypes of Cdc42 and Myo10 deletion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 292
year: '2017'
...