---
_id: '12198'
abstract:
- lang: eng
text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes
DNA demethylation before fertilization, but the targeting preferences, mechanism,
and biological significance of this process remain unclear. Here, we show that
active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for
all of the demethylation in the central cell and preferentially targets small,
AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative
cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation
of similar sequences, and lack of DEMETER in vegetative cells causes reduced small
RNA–directed DNA methylation of transposons in sperm. Our results demonstrate
that demethylation in companion cells reinforces transposon methylation in plant
gametes and likely contributes to stable silencing of transposable elements across
generations.
acknowledgement: We thank S. Harmer for assistance with the analysis of histone modifications,
the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative
cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the
DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415)
to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young
Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian
Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral
Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship
from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas
Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).
article_processing_charge: No
article_type: original
author:
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Adriana
full_name: Machlicova, Adriana
last_name: Machlicova
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Denisse
full_name: Rojas, Denisse
last_name: Rojas
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
- first_name: Daniel
full_name: Zilberman, Daniel
last_name: Zilberman
citation:
ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion
cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364.
doi:10.1126/science.1224839
apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues,
J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1224839
chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie
Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in
Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science.
American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100.
American Association for the Advancement of Science, pp. 1360–1364, 2012.
ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A,
Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman
D. 2012. Active DNA demethylation in plant companion cells reinforces transposon
methylation in gametes. Science. 337(6100), 1360–1364.
mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells
Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100,
American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.
short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues,
A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H.
Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
date_created: 2023-01-16T09:21:24Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2023-10-16T09:27:26Z
day: '14'
department:
- _id: XiFe
doi: 10.1126/science.1224839
external_id:
pmid:
- '22984074'
intvolume: ' 337'
issue: '6100'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/
month: '09'
oa: 1
oa_version: Published Version
page: 1360-1364
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active DNA demethylation in plant companion cells reinforces transposon methylation
in gametes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 337
year: '2012'
...
---
_id: '6588'
abstract:
- lang: eng
text: First we note that the best polynomial approximation to vertical bar x vertical
bar on the set, which consists of an interval on the positive half-axis and a
point on the negative half-axis, can be given by means of the classical Chebyshev
polynomials. Then we explore the cases when a solution of the related problem
on two intervals can be given in elementary functions.
acknowledgement: "This work is supported by the Austrian Science Fund (FWF), Project
P22025-N18.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. Elementary solutions of the Bernstein problem on two intervals.
Journal of Mathematical Physics, Analysis, Geometry. 2012;8(1):63-78.
apa: Pausinger, F. (2012). Elementary solutions of the Bernstein problem on two
intervals. Journal of Mathematical Physics, Analysis, Geometry. B. Verkin
Institute for Low Temperature Physics and Engineering.
chicago: Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two
Intervals.” Journal of Mathematical Physics, Analysis, Geometry. B. Verkin
Institute for Low Temperature Physics and Engineering, 2012.
ieee: F. Pausinger, “Elementary solutions of the Bernstein problem on two intervals,”
Journal of Mathematical Physics, Analysis, Geometry, vol. 8, no. 1. B.
Verkin Institute for Low Temperature Physics and Engineering, pp. 63–78, 2012.
ista: Pausinger F. 2012. Elementary solutions of the Bernstein problem on two intervals.
Journal of Mathematical Physics, Analysis, Geometry. 8(1), 63–78.
mla: Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.”
Journal of Mathematical Physics, Analysis, Geometry, vol. 8, no. 1, B.
Verkin Institute for Low Temperature Physics and Engineering, 2012, pp. 63–78.
short: F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012)
63–78.
date_created: 2019-06-27T08:16:56Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-10-16T09:41:31Z
day: '01'
department:
- _id: HeEd
external_id:
isi:
- '000301173600004'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://mi.mathnet.ru/eng/jmag525
month: '01'
oa: 1
oa_version: Published Version
page: 63-78
publication: Journal of Mathematical Physics, Analysis, Geometry
publication_identifier:
issn:
- 1812-9471
publication_status: published
publisher: B. Verkin Institute for Low Temperature Physics and Engineering
quality_controlled: '1'
scopus_import: '1'
status: public
title: Elementary solutions of the Bernstein problem on two intervals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '3123'
abstract:
- lang: eng
text: We introduce the idea of using an explicit triangle mesh to track the air/fluid
interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial
surface mesh is created, this mesh is carried forward in time using nearby particle
velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged
across time-steps; it is only modified locally for topology change events or for
the improvement of triangle quality. In order to ensure that the surface mesh
does not diverge from the underlying particle simulation, we periodically project
the mesh surface onto an implicit surface defined by the physics simulation. The
mesh surface gives us several advantages over previous SPH surface tracking techniques.
We demonstrate a new method for surface tension calculations that clearly outperforms
the state of the art in SPH surface tension for computer graphics. We also demonstrate
a method for tracking detailed surface information (like colors) that is less
susceptible to numerical diffusion than competing techniques. Finally, our temporally-coherent
surface mesh allows us to simulate high-resolution surface wave dynamics without
being limited by the particle resolution of the SPH simulation.
acknowledgement: This work was funded by NSF grant IIS-1017014 and CCF- 0917093.
alternative_title:
- Eurographics
article_processing_charge: No
author:
- first_name: Jihun
full_name: Yu, Jihun
last_name: Yu
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
- first_name: Chee
full_name: Yap, Chee
last_name: Yap
citation:
ama: 'Yu J, Wojtan C, Turk G, Yap C. Explicit mesh surfaces for particle based fluids.
In: Computer Graphics Forum. Vol 31. Wiley; 2012:815-824. doi:10.1111/j.1467-8659.2012.03062.x'
apa: 'Yu, J., Wojtan, C., Turk, G., & Yap, C. (2012). Explicit mesh surfaces
for particle based fluids. In Computer Graphics Forum (Vol. 31, pp. 815–824).
Cagliari, Sardinia, Italy: Wiley. https://doi.org/10.1111/j.1467-8659.2012.03062.x'
chicago: Yu, Jihun, Chris Wojtan, Greg Turk, and Chee Yap. “Explicit Mesh Surfaces
for Particle Based Fluids.” In Computer Graphics Forum, 31:815–24. Wiley,
2012. https://doi.org/10.1111/j.1467-8659.2012.03062.x.
ieee: J. Yu, C. Wojtan, G. Turk, and C. Yap, “Explicit mesh surfaces for particle
based fluids,” in Computer Graphics Forum, Cagliari, Sardinia, Italy, 2012,
vol. 31, no. 2, pp. 815–824.
ista: 'Yu J, Wojtan C, Turk G, Yap C. 2012. Explicit mesh surfaces for particle
based fluids. Computer Graphics Forum. EUROGRAPHICS: Conference on European Association
for Computer Graphics, Eurographics, vol. 31, 815–824.'
mla: Yu, Jihun, et al. “Explicit Mesh Surfaces for Particle Based Fluids.” Computer
Graphics Forum, vol. 31, no. 2, Wiley, 2012, pp. 815–24, doi:10.1111/j.1467-8659.2012.03062.x.
short: J. Yu, C. Wojtan, G. Turk, C. Yap, in:, Computer Graphics Forum, Wiley, 2012,
pp. 815–824.
conference:
end_date: 2012-05-18
location: Cagliari, Sardinia, Italy
name: 'EUROGRAPHICS: Conference on European Association for Computer Graphics'
start_date: 2012-05-13
date_created: 2018-12-11T12:01:31Z
date_published: 2012-05-01T00:00:00Z
date_updated: 2023-10-16T09:54:40Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/j.1467-8659.2012.03062.x
file:
- access_level: open_access
checksum: acb325dd1e31859bedd30e013f61d0b9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:39Z
date_updated: 2020-07-14T12:46:00Z
file_id: '5092'
file_name: IST-2016-601-v1+1_meshSPH.pdf
file_size: 5740527
relation: main_file
file_date_updated: 2020-07-14T12:46:00Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 815 - 824
publication: Computer Graphics Forum
publication_identifier:
eissn:
- 1467-8659
issn:
- 0167-7055
publication_status: published
publisher: Wiley
publist_id: '3576'
pubrep_id: '601'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Explicit mesh surfaces for particle based fluids
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2012'
...
---
_id: '3244'
abstract:
- lang: eng
text: "Bibliothekare haben die Aufgabe, sich mit neuen Medienformen auseinanderzusetzen.\r\n"
article_processing_charge: No
article_type: letter_note
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek und
Information. 2012;64(4):284.
apa: Danowski, P. (2012). Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek
und Information. Fachzeitschrift des BIB – Berufsverband Information Bibliothek.
chicago: Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” BuB - Forum
Bibliothek und Information. Fachzeitschrift des BIB – Berufsverband Information
Bibliothek, 2012.
ieee: P. Danowski, “Die Zeit des Abwartens ist vorbei!,” BuB - Forum Bibliothek
und Information, vol. 64, no. 4. Fachzeitschrift des BIB – Berufsverband Information
Bibliothek, p. 284, 2012.
ista: Danowski P. 2012. Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek
und Information. 64(4), 284.
mla: Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” BuB - Forum Bibliothek
und Information, vol. 64, no. 4, Fachzeitschrift des BIB – Berufsverband Information
Bibliothek, 2012, p. 284.
short: P. Danowski, BuB - Forum Bibliothek und Information 64 (2012) 284.
date_created: 2018-12-11T12:02:13Z
date_published: 2012-04-15T00:00:00Z
date_updated: 2023-10-16T10:19:14Z
day: '15'
department:
- _id: E-Lib
intvolume: ' 64'
issue: '4'
language:
- iso: ger
main_file_link:
- open_access: '1'
url: https://www.b-u-b.de/fileadmin/archiv/imports/pdf_files/2012/bub_2012_04_284.pdf
month: '04'
oa: 1
oa_version: Published Version
page: '284'
popular_science: '1'
publication: BuB - Forum Bibliothek und Information
publication_identifier:
issn:
- 1869 -1137
publication_status: published
publisher: Fachzeitschrift des BIB – Berufsverband Information Bibliothek
publist_id: '3432'
status: public
title: Die Zeit des Abwartens ist vorbei!
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2012'
...
---
_id: '3243'
abstract:
- lang: eng
text: 'Wie wandelt sich das Berufsbild in Wissenschaftlichen Bibliotheken? Patrick
Danowski gibt seine Einschätzung ab. '
article_processing_charge: No
article_type: letter_note
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. Zwischen Technologie und Information. Büchereiperspektiven.
2012;2012(1):11.
apa: Danowski, P. (2012). Zwischen Technologie und Information. Büchereiperspektiven.
Büchereiverband Österreichs.
chicago: Danowski, Patrick. “Zwischen Technologie und Information.” Büchereiperspektiven.
Büchereiverband Österreichs, 2012.
ieee: P. Danowski, “Zwischen Technologie und Information,” Büchereiperspektiven,
vol. 2012, no. 1. Büchereiverband Österreichs, p. 11, 2012.
ista: Danowski P. 2012. Zwischen Technologie und Information. Büchereiperspektiven.
2012(1), 11.
mla: Danowski, Patrick. “Zwischen Technologie und Information.” Büchereiperspektiven,
vol. 2012, no. 1, Büchereiverband Österreichs, 2012, p. 11.
short: P. Danowski, Büchereiperspektiven 2012 (2012) 11.
date_created: 2018-12-11T12:02:13Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2023-10-16T10:40:18Z
day: '01'
department:
- _id: E-Lib
intvolume: ' 2012'
issue: '1'
language:
- iso: ger
main_file_link:
- open_access: '1'
url: https://www.bvoe.at/sites/default/files/2022-07/BP_1_12.pdf
month: '03'
oa: 1
oa_version: Published Version
page: '11'
popular_science: '1'
publication: Büchereiperspektiven
publication_identifier:
issn:
- 1607-7172
publication_status: published
publisher: Büchereiverband Österreichs
publist_id: '3433'
status: public
title: Zwischen Technologie und Information
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2012
year: '2012'
...