---
_id: '8409'
abstract:
- lang: eng
text: The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer
that maintains the integrity of the bacterial cell. Due to its multi-gigadalton
size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex.
Solid-state NMR is an important technique to gain insight into its structure,
dynamics and interactions. Here, we explore the possibilities to study the PG
with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly
resolved spectra can be obtained, and show strategies to obtain site-specific
resonance assignments and distance information. We also explore the use of proton-proton
correlation experiments, thus opening the way for NMR studies of intact cell walls
without the need for isotope labeling.
article_processing_charge: No
article_type: original
author:
- first_name: Catherine
full_name: Bougault, Catherine
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Waldemar
full_name: Vollmer, Waldemar
last_name: Vollmer
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial
peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal
of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009
apa: Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019).
Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at
100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009
chicago: Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre,
and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected
NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology.
Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009.
ieee: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying
intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz
MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier,
pp. 66–72, 2019.
ista: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact
bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency.
Journal of Structural Biology. 206(1), 66–72.
mla: Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected
NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology,
vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009.
short: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of
Structural Biology 206 (2019) 66–72.
date_created: 2020-09-17T10:29:10Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:05Z
day: '01'
doi: 10.1016/j.jsb.2018.07.009
extern: '1'
external_id:
pmid:
- '30031884'
intvolume: ' 206'
issue: '1'
keyword:
- Structural Biology
language:
- iso: eng
month: '04'
oa_version: Submitted Version
page: 66-72
pmid: 1
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy
at 100 kHz MAS frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 206
year: '2019'
...
---
_id: '8407'
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Schanda P. Relaxing with liquids and solids – A perspective on biomolecular
dynamics. Journal of Magnetic Resonance. 2019;306:180-186. doi:10.1016/j.jmr.2019.07.025
apa: Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular
dynamics. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2019.07.025
chicago: Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular
Dynamics.” Journal of Magnetic Resonance. Elsevier, 2019. https://doi.org/10.1016/j.jmr.2019.07.025.
ieee: P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular
dynamics,” Journal of Magnetic Resonance, vol. 306. Elsevier, pp. 180–186,
2019.
ista: Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular
dynamics. Journal of Magnetic Resonance. 306, 180–186.
mla: Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular
Dynamics.” Journal of Magnetic Resonance, vol. 306, Elsevier, 2019, pp.
180–86, doi:10.1016/j.jmr.2019.07.025.
short: P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186.
date_created: 2020-09-17T10:28:47Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2021-01-12T08:19:04Z
day: '01'
doi: 10.1016/j.jmr.2019.07.025
extern: '1'
external_id:
pmid:
- '31350165'
intvolume: ' 306'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '09'
oa_version: Submitted Version
page: 180-186
pmid: 1
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Relaxing with liquids and solids – A perspective on biomolecular dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 306
year: '2019'
...
---
_id: '8410'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Eduard Y.
full_name: Chekmenev, Eduard Y.
last_name: Chekmenev
citation:
ama: Schanda P, Chekmenev EY. NMR for Biological Systems. ChemPhysChem. 2019;20(2):177-177.
doi:10.1002/cphc.201801100
apa: Schanda, P., & Chekmenev, E. Y. (2019). NMR for Biological Systems. ChemPhysChem.
Wiley. https://doi.org/10.1002/cphc.201801100
chicago: Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem.
Wiley, 2019. https://doi.org/10.1002/cphc.201801100.
ieee: P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” ChemPhysChem,
vol. 20, no. 2. Wiley, pp. 177–177, 2019.
ista: Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2),
177–177.
mla: Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem,
vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:10.1002/cphc.201801100.
short: P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177.
date_created: 2020-09-17T10:29:26Z
date_published: 2019-01-21T00:00:00Z
date_updated: 2021-01-12T08:19:05Z
day: '21'
doi: 10.1002/cphc.201801100
extern: '1'
external_id:
pmid:
- '30556633'
intvolume: ' 20'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/cphc.201801100
month: '01'
oa: 1
oa_version: Published Version
page: 177-177
pmid: 1
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: NMR for Biological Systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '8570'
abstract:
- lang: eng
text: 'This report presents the results of a friendly competition for formal verification
of continuous and hybrid systems with linear continuous dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been
applied to solve six different benchmark problems in the category for linear continuous
dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx,
and XSpeed. This report is a snapshot of the current landscape of tools and the
types of benchmarks they are particularly suited for. Due to the diversity of
problems, we are not ranking tools, yet the presented results provide one of the
most complete assessments of tools for the safety verification of continuous and
hybrid systems with linear continuous dynamics up to this date.'
article_processing_charge: No
author:
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Stefan
full_name: Schupp, Stefan
last_name: Schupp
citation:
ama: 'Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous
and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing.
Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w'
apa: 'Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp,
S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear
continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40).
Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w'
chicago: 'Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper,
Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report:
Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series
in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.'
ieee: 'M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid
systems with linear continuous dynamics,” in EPiC Series in Computing,
Montreal, Canada, 2019, vol. 61, pp. 14–40.'
ista: 'Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp
S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear
continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on
Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.'
mla: 'Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid
Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol.
61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.'
short: M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling,
S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.
conference:
end_date: 2019-04-15
location: Montreal, Canada
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2019-04-15
date_created: 2020-09-26T14:23:54Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2021-01-12T08:20:05Z
day: '25'
department:
- _id: ToHe
doi: 10.29007/bj1w
intvolume: ' 61'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://easychair.org/publications/open/1gbP
month: '05'
oa: 1
oa_version: Published Version
page: 14-40
publication: EPiC Series in Computing
publication_identifier:
eissn:
- '23987340'
publication_status: published
publisher: EasyChair
quality_controlled: '1'
status: public
title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous
dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '9016'
abstract:
- lang: eng
text: Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein
interaction (PPI) represents a potential approach for treating numerous cancers.
As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135)
is a strategy through which chemical probes might be elaborated to test this hypothesis.
In this work, variant H3118–135 peptides bearing pentenylglycine residues at the
i and i+4 positions were constrained by olefin metathesis. Biophysical analyses
revealed that promotion of a bioactive helical conformation depends on the position
at which the constraint is introduced, but that the potency of binding towards
ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation
occurs.
article_processing_charge: No
article_type: original
author:
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Silvia
full_name: Rodriguez‐Marin, Silvia
last_name: Rodriguez‐Marin
- first_name: Zsófia
full_name: Hegedüs, Zsófia
last_name: Hegedüs
- first_name: Marie E.
full_name: Perrin, Marie E.
last_name: Perrin
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
- first_name: Andrew J.
full_name: Wilson, Andrew J.
last_name: Wilson
citation:
ama: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ.
Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem.
2019;20(7):891-895. doi:10.1002/cbic.201800633
apa: Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein,
F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained
peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633
chicago: Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin,
Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained
Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633.
ieee: M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein,
and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,”
ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.
ista: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ.
2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem.
20(7), 891–895.
mla: Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained
Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633.
short: M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein,
A.J. Wilson, ChemBioChem 20 (2019) 891–895.
date_created: 2021-01-19T10:59:14Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-02-23T13:46:48Z
day: '01'
doi: 10.1002/cbic.201800633
extern: '1'
intvolume: ' 20'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1002/cbic.201800633'
month: '04'
oa: 1
oa_version: Published Version
page: 891-895
publication: ChemBioChem
publication_identifier:
issn:
- 1439-4227
- 1439-7633
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Recognition of ASF1 by using hydrocarbon‐constrained peptides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '9060'
abstract:
- lang: eng
text: Molecular motors are essential to the living, generating fluctuations that
boost transport and assist assembly. Active colloids, that consume energy to move,
hold similar potential for man-made materials controlled by forces generated from
within. Yet, their use as a powerhouse in materials science lacks. Here we show
a massive acceleration of the annealing of a monolayer of passive beads by moderate
addition of self-propelled microparticles. We rationalize our observations with
a model of collisions that drive active fluctuations and activate the annealing.
The experiment is quantitatively compared with Brownian dynamic simulations that
further unveil a dynamical transition in the mechanism of annealing. Active dopants
travel uniformly in the system or co-localize at the grain boundaries as a result
of the persistence of their motion. Our findings uncover the potential of internal
activity to control materials and lay the groundwork for the rise of materials
science beyond equilibrium.
article_number: '3380'
article_processing_charge: No
article_type: original
author:
- first_name: Sophie
full_name: Ramananarivo, Sophie
last_name: Ramananarivo
- first_name: Etienne
full_name: Ducrot, Etienne
last_name: Ducrot
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal
monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y
apa: Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled
annealing of colloidal monolayers. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-11362-y
chicago: Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled
Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature,
2019. https://doi.org/10.1038/s41467-019-11362-y.
ieee: S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing
of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer
Nature, 2019.
ista: Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing
of colloidal monolayers. Nature Communications. 10(1), 3380.
mla: Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.”
Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.
short: S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).
date_created: 2021-02-02T13:43:36Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-02-23T13:47:59Z
day: '29'
ddc:
- '530'
doi: 10.1038/s41467-019-11362-y
extern: '1'
external_id:
arxiv:
- '1909.07382'
pmid:
- '31358762'
file:
- access_level: open_access
checksum: 70c6e5d6fbea0932b0669505ab6633ec
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:47:21Z
date_updated: 2021-02-02T13:47:21Z
file_id: '9061'
file_name: 2019_NatureComm_Ramananarivo.pdf
file_size: 2820337
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:47:21Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Activity-controlled annealing of colloidal monolayers
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2019'
...
---
_id: '9460'
abstract:
- lang: eng
text: Epigenetic reprogramming is required for proper regulation of gene expression
in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for
seed viability, pollen function, and successful reproduction. The DEMETER (DME)
DNA glycosylase initiates localized DNA demethylation in vegetative and central
cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively.
In rice, the central cell genome displays local DNA hypomethylation, suggesting
that active DNA demethylation also occurs in rice; however, the enzyme responsible
for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING
1a (ROS1a) gene, which is related to DME and is essential for rice seed viability
and pollen function. Here, we report genome-wide analyses of DNA methylation in
wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative
cell genome is locally hypomethylated compared with sperm by a process that requires
ROS1a activity. We show that many ROS1a target sequences in the vegetative cell
are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates
the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation
is indirectly promoted by DNA demethylation in the vegetative cell. These results
reveal that DNA glycosylase-mediated DNA demethylation processes are conserved
in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally,
although global non-CG methylation levels of sperm and egg differ, the maternal
and paternal embryo genomes show similar non-CG methylation levels, suggesting
that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell
fusion.
article_processing_charge: No
article_type: original
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Akemi
full_name: Ono, Akemi
last_name: Ono
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative
cells promotes methylation in sperm. Proceedings of the National Academy of
Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116
apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T.,
& Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116
chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman,
Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative
Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.
ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm,” Proceedings of the National Academy of Sciences,
vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.
ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL.
2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation
in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.
mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells
Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences,
vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.
short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L.
Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.
date_created: 2021-06-04T12:38:20Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2021-12-14T07:52:30Z
day: '07'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1821435116
extern: '1'
external_id:
pmid:
- '31000601'
file:
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checksum: 5b0ae3779b8b21b5223bd2d3cceede3a
content_type: application/pdf
creator: asandaue
date_created: 2021-06-04T12:50:47Z
date_updated: 2021-06-04T12:50:47Z
file_id: '9461'
file_name: 2019_PNAS_Kim.pdf
file_size: 1142540
relation: main_file
success: 1
file_date_updated: 2021-06-04T12:50:47Z
has_accepted_license: '1'
intvolume: ' 116'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 9652-9657
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in
sperm
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 116
year: '2019'
...
---
_id: '9689'
abstract:
- lang: eng
text: A central goal of computational physics and chemistry is to predict material
properties by using first-principles methods based on the fundamental laws of
quantum mechanics. However, the high computational costs of these methods typically
prevent rigorous predictions of macroscopic quantities at finite temperatures,
such as heat capacity, density, and chemical potential. Here, we enable such predictions
by marrying advanced free-energy methods with data-driven machine-learning interatomic
potentials. We show that, for the ubiquitous and technologically essential system
of water, a first-principles thermodynamic description not only leads to excellent
agreement with experiments, but also reveals the crucial role of nuclear quantum
fluctuations in modulating the thermodynamic stabilities of different phases of
water.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Edgar A.
full_name: Engel, Edgar A.
last_name: Engel
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences.
2019;116(4):1110-1115. doi:10.1073/pnas.1815117116
apa: Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019).
Ab initio thermodynamics of liquid and solid water. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116
chicago: Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele
Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.
ieee: B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio
thermodynamics of liquid and solid water,” Proceedings of the National Academy
of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115,
2019.
ista: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4),
1110–1115.
mla: Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.”
Proceedings of the National Academy of Sciences, vol. 116, no. 4, National
Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.
short: B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of
the National Academy of Sciences 116 (2019) 1110–1115.
date_created: 2021-07-19T10:17:09Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-02-23T14:05:08Z
day: '22'
doi: 10.1073/pnas.1815117116
extern: '1'
external_id:
arxiv:
- '1811.08630'
pmid:
- '30610171'
intvolume: ' 116'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1815117116
month: '01'
oa: 1
oa_version: Published Version
page: 1110-1115
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ab initio thermodynamics of liquid and solid water
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 116
year: '2019'
...
---
_id: '6819'
abstract:
- lang: eng
text: Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations
have been shown to exert toxicity via various mechanisms. It has been asserted
that glyphosate substitutes for glycine in polypeptide chains leading to protein
misfolding and toxicity. However, as no direct evidence exists for glycine to
glyphosate substitution in proteins, including in mammalian organisms, we tested
this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer
cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts
from three treated and three untreated cell cultures were analysed as one TMT-6plex
labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities
for peptides bearing true glyphosate treatment induced-post translational modifications
as well as allowing an investigation of the total proteome.
article_number: '494'
article_processing_charge: No
author:
- first_name: Michael N.
full_name: Antoniou, Michael N.
last_name: Antoniou
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Robin
full_name: Mesnage, Robin
last_name: Mesnage
- first_name: Martina
full_name: Biserni, Martina
last_name: Biserni
- first_name: Francesco V.
full_name: Rao, Francesco V.
last_name: Rao
- first_name: Cristina Vazquez
full_name: Martin, Cristina Vazquez
last_name: Martin
citation:
ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate
does not substitute for glycine in proteins of actively dividing mammalian cells.
BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3
apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin,
C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3
chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco
V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine
in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes.
BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.
ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin,
“Glyphosate does not substitute for glycine in proteins of actively dividing mammalian
cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.
ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate
does not substitute for glycine in proteins of actively dividing mammalian cells.
BMC Research Notes. 12, 494.
mla: Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in
Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol.
12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.
short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin,
BMC Research Notes 12 (2019).
date_created: 2019-08-18T22:00:39Z
date_published: 2019-08-08T00:00:00Z
date_updated: 2023-02-23T14:08:14Z
day: '08'
ddc:
- '570'
department:
- _id: LifeSc
doi: 10.1186/s13104-019-4534-3
external_id:
pmid:
- '31395095'
file:
- access_level: open_access
checksum: 4a2bb7994b7f2c432bf44f5127ea3102
content_type: application/pdf
creator: dernst
date_created: 2019-08-23T11:10:35Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6829'
file_name: 2019_BMC_Antoniou.pdf
file_size: 1177482
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Research Notes
publication_identifier:
eissn:
- 1756-0500
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
related_material:
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relation: research_data
status: public
scopus_import: 1
status: public
title: Glyphosate does not substitute for glycine in proteins of actively dividing
mammalian cells
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: 12
year: '2019'
...
---
_id: '9784'
abstract:
- lang: eng
text: 'Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either
the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1
of seeding flasks and following 6-days of continuous culture. Note: no differences
in cell numbers were observed between negative control and glyphosate treated
cultures.'
article_processing_charge: No
author:
- first_name: Michael N.
full_name: Antoniou, Michael N.
last_name: Antoniou
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Robin
full_name: Mesnage, Robin
last_name: Mesnage
- first_name: Martina
full_name: Biserni, Martina
last_name: Biserni
- first_name: Francesco V.
full_name: Rao, Francesco V.
last_name: Rao
- first_name: Cristina Vazquez
full_name: Martin, Cristina Vazquez
last_name: Martin
citation:
ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of
Glyphosate does not substitute for glycine in proteins of actively dividing mammalian
cells. 2019. doi:10.6084/m9.figshare.9411761.v1
apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin,
C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins
of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1
chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco
V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute
for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature,
2019. https://doi.org/10.6084/m9.figshare.9411761.v1.
ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin,
“MOESM1 of Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells.” Springer Nature, 2019.
ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1
of Glyphosate does not substitute for glycine in proteins of actively dividing
mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.
mla: Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for
Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature,
2019, doi:10.6084/m9.figshare.9411761.v1.
short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin,
(2019).
date_created: 2021-08-06T08:14:05Z
date_published: 2019-08-09T00:00:00Z
date_updated: 2023-02-23T12:52:29Z
day: '09'
department:
- _id: LifeSc
doi: 10.6084/m9.figshare.9411761.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9411761.v1
month: '08'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6819'
relation: used_in_publication
status: public
status: public
title: MOESM1 of Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...