---
_id: '5410'
abstract:
- lang: eng
text: "Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only
in development of mathematical and logical skills, but also in emotional and social
development. In this paper, we address the problem of generating targeted starting
positions for such games. This can facilitate new approaches for bringing novice
players to mastery, and also leads to discovery of interesting game variants.
\r\nOur approach generates starting states of varying hardness levels for player
1 in a two-player board game, given rules of the board game, the desired number
of steps required for player 1 to win, and the expertise levels of the two players.
Our approach leverages symbolic methods and iterative simulation to efficiently
search the extremely large state space. We present experimental results that include
discovery of states of varying hardness levels for several simple grid-based board
games. Also, the presence of such states for standard game variants like Tic-Tac-Toe
on board size 4x4 opens up new games to be played that have not been played for
ages since the default start state is heavily biased. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Umair
full_name: Ahmed, Umair
last_name: Ahmed
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Sumit
full_name: Gulwani, Sumit
last_name: Gulwani
citation:
ama: Ahmed U, Chatterjee K, Gulwani S. Automatic Generation of Alternative Starting
Positions for Traditional Board Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-146-v1-1
apa: Ahmed, U., Chatterjee, K., & Gulwani, S. (2013). Automatic generation
of alternative starting positions for traditional board games. IST Austria.
https://doi.org/10.15479/AT:IST-2013-146-v1-1
chicago: Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. Automatic Generation
of Alternative Starting Positions for Traditional Board Games. IST Austria,
2013. https://doi.org/10.15479/AT:IST-2013-146-v1-1.
ieee: U. Ahmed, K. Chatterjee, and S. Gulwani, Automatic generation of alternative
starting positions for traditional board games. IST Austria, 2013.
ista: Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative
starting positions for traditional board games, IST Austria, 13p.
mla: Ahmed, Umair, et al. Automatic Generation of Alternative Starting Positions
for Traditional Board Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-146-v1-1.
short: U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative
Starting Positions for Traditional Board Games, IST Austria, 2013.
date_created: 2018-12-12T11:39:10Z
date_published: 2013-12-03T00:00:00Z
date_updated: 2025-05-19T11:10:16Z
day: '03'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-146-v1-1
file:
- access_level: open_access
checksum: 409f3aaaf1184e4057b89cbb449dac80
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:06Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5528'
file_name: IST-2013-146-v1+1_main.pdf
file_size: 818189
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '13'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '146'
related_material:
record:
- id: '1481'
relation: later_version
status: public
status: public
title: Automatic generation of alternative starting positions for traditional board
games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5747'
article_processing_charge: No
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- 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: 'Dragoi C, Gupta A, Henzinger TA. Automatic Linearizability Proofs of Concurrent
Objects with Cooperating Updates. In: Computer Aided Verification. Vol
8044. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013:174-190. doi:10.1007/978-3-642-39799-8_11'
apa: 'Dragoi, C., Gupta, A., & Henzinger, T. A. (2013). Automatic Linearizability
Proofs of Concurrent Objects with Cooperating Updates. In Computer Aided Verification
(Vol. 8044, pp. 174–190). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-39799-8_11'
chicago: 'Dragoi, Cezara, Ashutosh Gupta, and Thomas A Henzinger. “Automatic Linearizability
Proofs of Concurrent Objects with Cooperating Updates.” In Computer Aided Verification,
8044:174–90. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. https://doi.org/10.1007/978-3-642-39799-8_11.'
ieee: 'C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs
of Concurrent Objects with Cooperating Updates,” in Computer Aided Verification,
vol. 8044, Berlin, Heidelberg: Springer Berlin Heidelberg, 2013, pp. 174–190.'
ista: 'Dragoi C, Gupta A, Henzinger TA. 2013.Automatic Linearizability Proofs of
Concurrent Objects with Cooperating Updates. In: Computer Aided Verification.
vol. 8044, 174–190.'
mla: Dragoi, Cezara, et al. “Automatic Linearizability Proofs of Concurrent Objects
with Cooperating Updates.” Computer Aided Verification, vol. 8044, Springer
Berlin Heidelberg, 2013, pp. 174–90, doi:10.1007/978-3-642-39799-8_11.
short: C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer
Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190.
conference:
end_date: 2013-07-19
location: Saint Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-18T13:10:21Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2025-07-10T11:52:57Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-39799-8_11
ec_funded: 1
file:
- access_level: open_access
checksum: a901cc6b71db08b61c0d4c0cbacc6287
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:13:33Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5748'
file_name: 2013_CAV_Dragoi.pdf
file_size: 236480
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 8044'
language:
- iso: eng
month: '08'
oa: 1
oa_version: None
page: 174-190
place: Berlin, Heidelberg
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Computer Aided Verification
publication_identifier:
eisbn:
- '9783642397998'
eissn:
- 1611-3349
isbn:
- '9783642397981'
issn:
- 0302-9743
publication_status: published
publisher: Springer Berlin Heidelberg
pubrep_id: '195'
quality_controlled: '1'
scopus_import: '1'
series_title: CAV
status: public
title: Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '590'
abstract:
- lang: eng
text: We present two methods of creating two orthogonally-polarized focal points
at customizable relative locations. These schemes may be critical for enhancing
entanglement sources and other applications.
alternative_title:
- Optics InfoBase Conference Papers
author:
- first_name: David
full_name: Schmid, David
last_name: Schmid
- first_name: Ting
full_name: Huang, Ting-Yu
last_name: Huang
- first_name: Radhika
full_name: Dirks, Radhika
last_name: Dirks
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. Polarization dependent focusing.
In: OSA; 2013. doi:10.1364/QIM.2013.W6.23'
apa: 'Schmid, D., Huang, T., Dirks, R., Hosten, O., & Kwiat, P. (2013). Polarization
dependent focusing. Presented at the QIM: Quantum Information and Measurement,
OSA. https://doi.org/10.1364/QIM.2013.W6.23'
chicago: Schmid, David, Ting Huang, Radhika Dirks, Onur Hosten, and Paul Kwiat.
“Polarization Dependent Focusing.” OSA, 2013. https://doi.org/10.1364/QIM.2013.W6.23.
ieee: 'D. Schmid, T. Huang, R. Dirks, O. Hosten, and P. Kwiat, “Polarization dependent
focusing,” presented at the QIM: Quantum Information and Measurement, 2013.'
ista: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. 2013. Polarization dependent
focusing. QIM: Quantum Information and Measurement, Optics InfoBase Conference
Papers, .'
mla: Schmid, David, et al. Polarization Dependent Focusing. OSA, 2013, doi:10.1364/QIM.2013.W6.23.
short: D. Schmid, T. Huang, R. Dirks, O. Hosten, P. Kwiat, in:, OSA, 2013.
conference:
name: 'QIM: Quantum Information and Measurement'
date_created: 2018-12-11T11:47:22Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:05:10Z
day: '01'
doi: 10.1364/QIM.2013.W6.23
extern: 1
month: '01'
publication_status: published
publisher: OSA
publist_id: '7217'
quality_controlled: 0
status: public
title: Polarization dependent focusing
type: conference
year: '2013'
...
---
_id: '591'
abstract:
- lang: eng
text: We present two methods for the precise independent focusing of orthogonal
linear polarizations of light at arbitrary relative locations. Our first scheme
uses a displaced lens in a polarization Sagnac interferometer to provide adjustable
longitudinal and lateral focal displacements via simple geometry; the second uses
uniaxial crystals to achieve the same effect in a compact collinear setup. We
develop the theoretical applications and limitations of our schemes, and provide
experimental confirmation of our calculations.
author:
- first_name: David
full_name: Schmid, David
last_name: Schmid
- first_name: Ting
full_name: Huang, Ting-Yu
last_name: Huang
- first_name: Shiraz
full_name: Hazrat, Shiraz
last_name: Hazrat
- first_name: Radhika
full_name: Dirks, Radhika
last_name: Dirks
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Stephan
full_name: Quint, Stephan
last_name: Quint
- first_name: Dickson
full_name: Thian, Dickson
last_name: Thian
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent
focusing. Optics Express. 2013;21(13):15538-15552. doi:10.1364/OE.21.015538
apa: Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat,
P. (2013). Adjustable and robust methods for polarization-dependent focusing.
Optics Express. Optical Society of America. https://doi.org/10.1364/OE.21.015538
chicago: Schmid, David, Ting Huang, Shiraz Hazrat, Radhika Dirks, Onur Hosten, Stephan
Quint, Dickson Thian, and Paul Kwiat. “Adjustable and Robust Methods for Polarization-Dependent
Focusing.” Optics Express. Optical Society of America, 2013. https://doi.org/10.1364/OE.21.015538.
ieee: D. Schmid et al., “Adjustable and robust methods for polarization-dependent
focusing,” Optics Express, vol. 21, no. 13. Optical Society of America,
pp. 15538–15552, 2013.
ista: Schmid D, Huang T, Hazrat S, Dirks R, Hosten O, Quint S, Thian D, Kwiat P.
2013. Adjustable and robust methods for polarization-dependent focusing. Optics
Express. 21(13), 15538–15552.
mla: Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent
Focusing.” Optics Express, vol. 21, no. 13, Optical Society of America,
2013, pp. 15538–52, doi:10.1364/OE.21.015538.
short: D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian,
P. Kwiat, Optics Express 21 (2013) 15538–15552.
date_created: 2018-12-11T11:47:22Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T08:05:12Z
day: '01'
doi: 10.1364/OE.21.015538
extern: 1
intvolume: ' 21'
issue: '13'
month: '07'
page: 15538 - 15552
publication: Optics Express
publication_status: published
publisher: Optical Society of America
publist_id: '7218'
quality_controlled: 0
status: public
title: Adjustable and robust methods for polarization-dependent focusing
type: journal_article
volume: 21
year: '2013'
...
---
OA_place: publisher
OA_type: free access
_id: '5920'
abstract:
- lang: eng
text: We study chains of lattice ideals that are invariant under a symmetric group
action. In our setting, the ambient rings for these ideals are polynomial rings
which are increasing in (Krull) dimension. Thus, these chains will fail to stabilize
in the traditional commutative algebra sense. However, we prove a theorem which
says that “up to the action of the group”, these chains locally stabilize. We
also give an algorithm, which we have implemented in software, for explicitly
constructing these stabilization generators for a family of Laurent toric ideals
involved in applications to algebraic statistics. We close with several open problems
and conjectures arising from our theoretical and computational investigations.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher J.
full_name: Hillar, Christopher J.
last_name: Hillar
- first_name: Abraham
full_name: Martin del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin del Campo Sanchez
citation:
ama: Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for
permutation invariant chains of Laurent lattice ideals. Journal of Symbolic
Computation. 2013;50:314-334. doi:10.1016/j.jsc.2012.06.006
apa: Hillar, C. J., & Martin del Campo Sanchez, A. (2013). Finiteness theorems
and algorithms for permutation invariant chains of Laurent lattice ideals. Journal
of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2012.06.006
chicago: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness
Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.”
Journal of Symbolic Computation. Elsevier, 2013. https://doi.org/10.1016/j.jsc.2012.06.006.
ieee: C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms
for permutation invariant chains of Laurent lattice ideals,” Journal of Symbolic
Computation, vol. 50. Elsevier, pp. 314–334, 2013.
ista: Hillar CJ, Martin del Campo Sanchez A. 2013. Finiteness theorems and algorithms
for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic
Computation. 50, 314–334.
mla: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems
and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal
of Symbolic Computation, vol. 50, Elsevier, 2013, pp. 314–34, doi:10.1016/j.jsc.2012.06.006.
short: C.J. Hillar, A. Martin del Campo Sanchez, Journal of Symbolic Computation
50 (2013) 314–334.
date_created: 2019-02-05T08:48:24Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2025-05-20T06:30:08Z
day: '01'
doi: 10.1016/j.jsc.2012.06.006
extern: '1'
intvolume: ' 50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jsc.2012.06.006
month: '03'
oa: 1
oa_version: Published Version
page: 314-334
publication: Journal of Symbolic Computation
publication_identifier:
issn:
- 0747-7171
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1016/j.jsc.2015.09.002
status: public
title: Finiteness theorems and algorithms for permutation invariant chains of Laurent
lattice ideals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2013'
...
---
_id: '595'
article_processing_charge: No
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: 'Bernecky C, Cramer P. Struggling to let go: A non-coding RNA directs its own
extension and destruction. EMBO Journal. 2013;32(6):771-772. doi:10.1038/emboj.2013.36'
apa: 'Bernecky, C., & Cramer, P. (2013). Struggling to let go: A non-coding
RNA directs its own extension and destruction. EMBO Journal. Wiley-Blackwell.
https://doi.org/10.1038/emboj.2013.36'
chicago: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding
RNA Directs Its Own Extension and Destruction.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2013.36.'
ieee: 'C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs
its own extension and destruction,” EMBO Journal, vol. 32, no. 6. Wiley-Blackwell,
pp. 771–772, 2013.'
ista: 'Bernecky C, Cramer P. 2013. Struggling to let go: A non-coding RNA directs
its own extension and destruction. EMBO Journal. 32(6), 771–772.'
mla: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding
RNA Directs Its Own Extension and Destruction.” EMBO Journal, vol. 32,
no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:10.1038/emboj.2013.36.'
short: C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772.
date_created: 2018-12-11T11:47:23Z
date_published: 2013-03-20T00:00:00Z
date_updated: 2021-01-12T08:05:20Z
day: '20'
doi: 10.1038/emboj.2013.36
extern: '1'
intvolume: ' 32'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/
month: '03'
oa: 1
oa_version: None
page: 771 - 772
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7207'
status: public
title: 'Struggling to let go: A non-coding RNA directs its own extension and destruction'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '6128'
abstract:
- lang: eng
text: Different interoceptive systems must be integrated to ensure that multiple
homeostatic insults evoke appropriate behavioral and physiological responses.
Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation
between systems that monitor temperature, O2 and CO2. CO2 is less aversive to
animals acclimated to 15°C than those grown at 22°C. This difference requires
the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes
distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective
in synaptic transmission can reprogram AFD CO2 responses according to temperature
experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely
sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different
Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further
contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing
neuron URX inhibits CO2 avoidance. This inhibition can be graded according to
O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient
to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred
partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance
involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked
Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to
modulate CO2 responsiveness. Our work highlights the integrated architecture of
homeostatic responses in C. elegans.
article_number: e1004011
author:
- first_name: Eiji
full_name: Kodama-Namba, Eiji
last_name: Kodama-Namba
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Andrew J.
full_name: Bretscher, Andrew J.
last_name: Bretscher
- first_name: Einav
full_name: Gross, Einav
last_name: Gross
- first_name: K. Emanuel
full_name: Busch, K. Emanuel
last_name: Busch
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. Cross-modulation
of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans.
PLoS Genetics. 2013;9(12). doi:10.1371/journal.pgen.1004011
apa: Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., &
de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature,
oxygen and carbon dioxide in C. elegans. PLoS Genetics. Public Library
of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004011
chicago: Kodama-Namba, Eiji, Lorenz A. Fenk, Andrew J. Bretscher, Einav Gross, K.
Emanuel Busch, and Mario de Bono. “Cross-Modulation of Homeostatic Responses to
Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics. Public
Library of Science (PLoS), 2013. https://doi.org/10.1371/journal.pgen.1004011.
ieee: E. Kodama-Namba, L. A. Fenk, A. J. Bretscher, E. Gross, K. E. Busch, and M.
de Bono, “Cross-modulation of homeostatic responses to temperature, oxygen and
carbon dioxide in C. elegans,” PLoS Genetics, vol. 9, no. 12. Public Library
of Science (PLoS), 2013.
ista: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. 2013.
Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide
in C. elegans. PLoS Genetics. 9(12), e1004011.
mla: Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature,
Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics, vol. 9, no. 12,
e1004011, Public Library of Science (PLoS), 2013, doi:10.1371/journal.pgen.1004011.
short: E. Kodama-Namba, L.A. Fenk, A.J. Bretscher, E. Gross, K.E. Busch, M. de Bono,
PLoS Genetics 9 (2013).
date_created: 2019-03-19T14:58:51Z
date_published: 2013-12-19T00:00:00Z
date_updated: 2021-01-12T08:06:15Z
day: '19'
ddc:
- '570'
doi: 10.1371/journal.pgen.1004011
extern: '1'
external_id:
pmid:
- '24385919'
file:
- access_level: open_access
checksum: 299b6321be79931c7c17c5db6e69c711
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T15:14:51Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6129'
file_name: 2013_PLOS_Kodama-Namba.PDF
file_size: 4499039
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science (PLoS)
quality_controlled: '1'
status: public
title: Cross-modulation of homeostatic responses to temperature, oxygen and carbon
dioxide in C. elegans
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: 9
year: '2013'
...
---
_id: '6132'
author:
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: W.R.
full_name: Schafer, W.R.
last_name: Schafer
- first_name: A.
full_name: Gottschalk, A.
last_name: Gottschalk
citation:
ama: 'de Bono M, Schafer WR, Gottschalk A. Optogenetic actuation, inhibition, modulation
and readout for neuronal networks generating behavior in the nematode Caenorhabditis
elegans. In: Hegemann P, Sigrist S, eds. Optogenetics. Walter de Gruyter;
2013:61-78.'
apa: de Bono, M., Schafer, W. R., & Gottschalk, A. (2013). Optogenetic actuation,
inhibition, modulation and readout for neuronal networks generating behavior in
the nematode Caenorhabditis elegans. In P. Hegemann & S. Sigrist (Eds.), Optogenetics
(pp. 61–78). Walter de Gruyter.
chicago: Bono, Mario de, W.R. Schafer, and A. Gottschalk. “Optogenetic Actuation,
Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in
the Nematode Caenorhabditis Elegans.” In Optogenetics, edited by Peter
Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013.
ieee: M. de Bono, W. R. Schafer, and A. Gottschalk, “Optogenetic actuation, inhibition,
modulation and readout for neuronal networks generating behavior in the nematode
Caenorhabditis elegans,” in Optogenetics, P. Hegemann and S. Sigrist, Eds.
Walter de Gruyter, 2013, pp. 61–78.
ista: 'de Bono M, Schafer WR, Gottschalk A. 2013.Optogenetic actuation, inhibition,
modulation and readout for neuronal networks generating behavior in the nematode
Caenorhabditis elegans. In: Optogenetics. , 61–78.'
mla: de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout
for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.”
Optogenetics, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter,
2013, pp. 61–78.
short: M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.),
Optogenetics, Walter de Gruyter, 2013, pp. 61–78.
date_created: 2019-03-20T13:54:05Z
date_published: 2013-08-28T00:00:00Z
date_updated: 2021-01-12T08:06:16Z
day: '28'
editor:
- first_name: Peter
full_name: Hegemann, Peter
last_name: Hegemann
- first_name: Stephan
full_name: Sigrist, Stephan
last_name: Sigrist
extern: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 61-78
publication: Optogenetics
publication_identifier:
isbn:
- 9783110270723; 9783110270716
publication_status: published
publisher: Walter de Gruyter
quality_controlled: '1'
status: public
title: Optogenetic actuation, inhibition, modulation and readout for neuronal networks
generating behavior in the nematode Caenorhabditis elegans
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '6133'
abstract:
- lang: eng
text: cGMP signaling is widespread in the nervous system. However, it has proved
difficult to visualize and genetically probe endogenously evoked cGMP dynamics
in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect
a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We
show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical
O2-binding soluble guanylate cyclase and that is sustained until oxygen levels
fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends
on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing
negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback
loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of
cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2)
and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation
following a rise in O2, apparently by keeping in check gating of cGMP channels
and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous
imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels
while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible
when the same neuron in an individual animal is stimulated repeatedly, suggesting
that cGMP transduction has high intrinsic reliability. However, responses vary
substantially across individuals, despite animals being genetically identical
and similarly reared. This variability may reflect stochastic differences in expression
of cGMP signaling components. Our work provides in vivo insights into the architecture
of neuronal cGMP signaling.
author:
- first_name: A.
full_name: Couto, A.
last_name: Couto
- first_name: S.
full_name: Oda, S.
last_name: Oda
- first_name: V. O.
full_name: Nikolaev, V. O.
last_name: Nikolaev
- first_name: Z.
full_name: Soltesz, Z.
last_name: Soltesz
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. In vivo genetic dissection
of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings
of the National Academy of Sciences. 2013;110(35):E3301-E3310. doi:10.1073/pnas.1217428110
apa: Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., & de Bono, M. (2013).
In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans
gas sensor. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1217428110
chicago: Couto, A., S. Oda, V. O. Nikolaev, Z. Soltesz, and Mario de Bono. “In Vivo
Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas
Sensor.” Proceedings of the National Academy of Sciences. Proceedings of
the National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217428110.
ieee: A. Couto, S. Oda, V. O. Nikolaev, Z. Soltesz, and M. de Bono, “In vivo genetic
dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor,”
Proceedings of the National Academy of Sciences, vol. 110, no. 35. Proceedings
of the National Academy of Sciences, pp. E3301–E3310, 2013.
ista: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. 2013. In vivo genetic dissection
of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings
of the National Academy of Sciences. 110(35), E3301–E3310.
mla: Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in
a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of
Sciences, vol. 110, no. 35, Proceedings of the National Academy of Sciences,
2013, pp. E3301–10, doi:10.1073/pnas.1217428110.
short: A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the
National Academy of Sciences 110 (2013) E3301–E3310.
date_created: 2019-03-20T14:05:06Z
date_published: 2013-08-27T00:00:00Z
date_updated: 2021-01-12T08:06:16Z
day: '27'
ddc:
- '570'
doi: 10.1073/pnas.1217428110
extern: '1'
external_id:
pmid:
- '23940325'
file:
- access_level: open_access
checksum: 3ee28a694f74a49f0d098970ae391a91
content_type: application/pdf
creator: kschuh
date_created: 2019-03-20T14:07:53Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6134'
file_name: 2013_PNAS_Couto.pdf
file_size: 2198763
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '35'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: E3301-E3310
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans
gas sensor
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '6135'
abstract:
- lang: eng
text: Many organisms have stress response pathways, components of which share homology
with players in complex human disease pathways. Research on stress response in
the nematode worm Caenorhabditis elegans has provided detailed insights into the
genetic and molecular mechanisms underlying complex human diseases. In this review
we focus on four different types of environmental stress responses – heat shock,
oxidative stress, hypoxia, and osmotic stress – and on how these can be used to
study the genetics of complex human diseases. All four types of responses involve
the genetic machineries that underlie a number of complex human diseases such
as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's.
We highlight the types of stress response experiments required to detect the genes
and pathways underlying human disease and suggest that studying stress biology
in worms can be translated to understanding human disease and provide potential
targets for drug discovery.
author:
- first_name: Miriam
full_name: Rodriguez, Miriam
last_name: Rodriguez
- first_name: L. Basten
full_name: Snoek, L. Basten
last_name: Snoek
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Jan E.
full_name: Kammenga, Jan E.
last_name: Kammenga
citation:
ama: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. Worms under stress: C. elegans
stress response and its relevance to complex human disease and aging. Trends
in Genetics. 2013;29(6):367-374. doi:10.1016/j.tig.2013.01.010'
apa: 'Rodriguez, M., Snoek, L. B., de Bono, M., & Kammenga, J. E. (2013). Worms
under stress: C. elegans stress response and its relevance to complex human disease
and aging. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2013.01.010'
chicago: 'Rodriguez, Miriam, L. Basten Snoek, Mario de Bono, and Jan E. Kammenga.
“Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human
Disease and Aging.” Trends in Genetics. Elsevier, 2013. https://doi.org/10.1016/j.tig.2013.01.010.'
ieee: 'M. Rodriguez, L. B. Snoek, M. de Bono, and J. E. Kammenga, “Worms under stress:
C. elegans stress response and its relevance to complex human disease and aging,”
Trends in Genetics, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.'
ista: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. 2013. Worms under stress:
C. elegans stress response and its relevance to complex human disease and aging.
Trends in Genetics. 29(6), 367–374.'
mla: 'Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response
and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics,
vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:10.1016/j.tig.2013.01.010.'
short: M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29
(2013) 367–374.
date_created: 2019-03-20T14:17:42Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T08:06:17Z
day: '01'
doi: 10.1016/j.tig.2013.01.010
extern: '1'
intvolume: ' 29'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 367-374
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9525
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Worms under stress: C. elegans stress response and its relevance to complex
human disease and aging'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2013'
...
---
_id: '6370'
abstract:
- lang: eng
text: 'The molecular and supramolecular origins of the superior nonlinear optical
(NLO) properties observed in the organic phenolic triene material, OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile),
are presented. The molecular charge-transfer distribution is topographically mapped,
demonstrating that a uniformly delocalized passive electronic medium facilitates
the charge-transfer between the phenolic electron donor and the cyano electron
acceptors which lie at opposite ends of the molecule. Its ability to act as a
“push–pull” π-conjugated molecule is quantified, relative to similar materials,
by supporting empirical calculations; these include bond-length alternation and
harmonic-oscillator stabilization energy (HOSE) tests. Such tests, together with
frontier molecular orbital considerations, reveal that OH1 can exist readily in
its aromatic (neutral) or quinoidal (charge-separated) state, thereby overcoming
the “nonlinearity-thermal stability trade-off”. The HOSE calculation also reveals
a correlation between the quinoidal resonance contribution to the overall structure
of OH1 and the UV–vis absorption peak wavelength in the wider family of configurationally
locked polyene framework materials. Solid-state tensorial coefficients of the
molecular dipole, polarizability, and the first hyperpolarizability for OH1 are
derived from the first-, second-, and third-order electronic moments of the experimental
charge-density distribution. The overall solid-state molecular dipole moment is
compared with those from gas-phase calculations, revealing that crystal field
effects are very significant in OH1. The solid-state hyperpolarizability derived
from this charge-density study affords good agreement with gas-phase calculations
as well as optical measurements based on hyper-Rayleigh scattering (HRS) and electric-field-induced
second harmonic (EFISH) generation. This lends support to the further use of charge-density
studies to calculate solid-state hyperpolarizability coefficients in other organic
NLO materials. Finally, this charge-density study is also employed to provide
an advanced classification of hydrogen bonds in OH1, which requires more stringent
criteria than those from conventional structure analysis. As a result, only the
strongest OH···NC interaction is so classified as a true hydrogen bond. Indeed,
it is this electrostatic interaction that influences the molecular charge transfer:
the other four, weaker, nonbonded contacts nonetheless affect the crystal packing.
Overall, the establishment of these structure–property relationships lays a blueprint
for designing further, more NLO efficient, materials in this industrially leading
organic family of compounds.'
author:
- first_name: Tze-Chia
full_name: Lin, Tze-Chia
last_name: Lin
- first_name: Jacqueline M.
full_name: Cole, Jacqueline M.
last_name: Cole
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Alison J.
full_name: Edwards, Alison J.
last_name: Edwards
- first_name: Ross O.
full_name: Piltz, Ross O.
last_name: Piltz
- first_name: Javier
full_name: Pérez-Moreno, Javier
last_name: Pérez-Moreno
- first_name: Ji-Youn
full_name: Seo, Ji-Youn
last_name: Seo
- first_name: Seung-Chul
full_name: Lee, Seung-Chul
last_name: Lee
- first_name: Koen
full_name: Clays, Koen
last_name: Clays
- first_name: O-Pil
full_name: Kwon, O-Pil
last_name: Kwon
citation:
ama: 'Lin T-C, Cole JM, Higginbotham AP, et al. Molecular origins of the high-performance
nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density
distributions, hydrogen bonding, and ab initio calculations. The Journal of
Physical Chemistry C. 2013;117(18):9416-9430. doi:10.1021/jp400648q'
apa: 'Lin, T.-C., Cole, J. M., Higginbotham, A. P., Edwards, A. J., Piltz, R. O.,
Pérez-Moreno, J., … Kwon, O.-P. (2013). Molecular origins of the high-performance
nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density
distributions, hydrogen bonding, and ab initio calculations. The Journal of
Physical Chemistry C. American Chemical Society (ACS). https://doi.org/10.1021/jp400648q'
chicago: 'Lin, Tze-Chia, Jacqueline M. Cole, Andrew P Higginbotham, Alison J. Edwards,
Ross O. Piltz, Javier Pérez-Moreno, Ji-Youn Seo, Seung-Chul Lee, Koen Clays, and
O-Pil Kwon. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility
in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding,
and Ab Initio Calculations.” The Journal of Physical Chemistry C. American
Chemical Society (ACS), 2013. https://doi.org/10.1021/jp400648q.'
ieee: 'T.-C. Lin et al., “Molecular origins of the high-performance nonlinear
optical susceptibility in a phenolic polyene chromophore: Electron density distributions,
hydrogen bonding, and ab initio calculations,” The Journal of Physical Chemistry
C, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013.'
ista: 'Lin T-C, Cole JM, Higginbotham AP, Edwards AJ, Piltz RO, Pérez-Moreno J,
Seo J-Y, Lee S-C, Clays K, Kwon O-P. 2013. Molecular origins of the high-performance
nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density
distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical
Chemistry C. 117(18), 9416–9430.'
mla: 'Lin, Tze-Chia, et al. “Molecular Origins of the High-Performance Nonlinear
Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions,
Hydrogen Bonding, and Ab Initio Calculations.” The Journal of Physical Chemistry
C, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:10.1021/jp400648q.'
short: T.-C. Lin, J.M. Cole, A.P. Higginbotham, A.J. Edwards, R.O. Piltz, J. Pérez-Moreno,
J.-Y. Seo, S.-C. Lee, K. Clays, O.-P. Kwon, The Journal of Physical Chemistry
C 117 (2013) 9416–9430.
date_created: 2019-05-03T09:40:31Z
date_published: 2013-05-09T00:00:00Z
date_updated: 2021-01-12T08:07:17Z
day: '09'
doi: 10.1021/jp400648q
extern: '1'
intvolume: ' 117'
issue: '18'
language:
- iso: eng
month: '05'
oa_version: None
page: 9416-9430
publication: The Journal of Physical Chemistry C
publication_identifier:
issn:
- 1932-7447
- 1932-7455
publication_status: published
publisher: American Chemical Society (ACS)
quality_controlled: '1'
status: public
title: 'Molecular origins of the high-performance nonlinear optical susceptibility
in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding,
and ab initio calculations'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2013'
...
---
_id: '1978'
abstract:
- lang: eng
text: Complex I is the first and largest enzyme of the respiratory chain and has
a central role in cellular energy production through the coupling of NADH:ubiquinone
electron transfer to proton translocation. It is also implicated in many common
human neurodegenerative diseases. Here, we report the first crystal structure
of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution.
The structure of the 536-kDa complex comprises 16 different subunits, with a total
of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit
Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like
subunits. Small subunits nearby form a linked second half-channel, which completes
the fourth proton-translocation pathway (present in addition to the channels in
three antiporter-like subunits). The quinone-binding site is unusually long, narrow
and enclosed. The quinone headgroup binds at the deep end of this chamber, near
iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel
by a 'funnel' of charged residues. The link continues over the entire membrane
domain as a flexible central axis of charged and polar residues, and probably
has a leading role in the propagation of conformational changes, aided by coupling
elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction
chamber enables the redox energy to drive concerted long-range conformational
changes in the four antiporter-like domains, resulting in translocation of four
protons per cycle.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Rozbeh
full_name: 'Baradaran, Rozbeh '
last_name: Baradaran
- first_name: John
full_name: Berrisford, John M
last_name: Berrisford
- first_name: Gurdeep
full_name: Minhas, Gurdeep S
last_name: Minhas
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire
respiratory complex i. Nature. 2013;494(7438):443-448. doi:10.1038/nature11871
apa: Baradaran, R., Berrisford, J., Minhas, G., & Sazanov, L. A. (2013). Crystal
structure of the entire respiratory complex i. Nature. Nature Publishing
Group. https://doi.org/10.1038/nature11871
chicago: Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov.
“Crystal Structure of the Entire Respiratory Complex I.” Nature. Nature
Publishing Group, 2013. https://doi.org/10.1038/nature11871.
ieee: R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure
of the entire respiratory complex i,” Nature, vol. 494, no. 7438. Nature
Publishing Group, pp. 443–448, 2013.
ista: Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of
the entire respiratory complex i. Nature. 494(7438), 443–448.
mla: Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex
I.” Nature, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48,
doi:10.1038/nature11871.
short: R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448.
date_created: 2018-12-11T11:55:01Z
date_published: 2013-02-28T00:00:00Z
date_updated: 2021-01-12T06:54:28Z
day: '28'
doi: 10.1038/nature11871
extern: 1
intvolume: ' 494'
issue: '7438'
month: '02'
page: 443 - 448
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5107'
quality_controlled: 0
status: public
title: Crystal structure of the entire respiratory complex i
type: journal_article
volume: 494
year: '2013'
...
---
_id: '1988'
abstract:
- lang: eng
text: The rod-shaped bacterium Escherichia coli selects the cell center as site
of division with the help of the proteins MinC, MinD, and MinE. This protein system
collectively oscillates between the two cell poles by alternately binding to the
membrane in one of the two cell halves. This dynamic behavior, which emerges from
the interaction of the ATPase MinD and its activator MinE on the cell membrane,
has become a paradigm for protein self-organization. Recently, it has been found
that not only the binding of MinD to the membrane, but also interactions of MinE
with the membrane contribute to Min-protein self-organization. Here, we show that
by accounting for this finding in a computational model, we can comprehensively
describe all observed Min-protein patterns in vivo and in vitro. Furthermore,
by varying the system's geometry, our computations predict patterns that have
not yet been reported. We confirm these predictions experimentally.
author:
- first_name: Mike
full_name: 'Bonny, Mike '
last_name: Bonny
- first_name: Elisabeth
full_name: Fischer-Friedrich, Elisabeth
last_name: Fischer Friedrich
- first_name: Martin
full_name: Martin Loose
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Petra
full_name: 'Schwille, Petra '
last_name: Schwille
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
citation:
ama: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding
of MinE allows for a comprehensive description of Min-protein pattern formation.
PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003347
apa: Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., & Kruse, K.
(2013). Membrane binding of MinE allows for a comprehensive description of Min-protein
pattern formation. PLoS Computational Biology. Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1003347
chicago: Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille,
and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description
of Min-Protein Pattern Formation.” PLoS Computational Biology. Public Library
of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003347.
ieee: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane
binding of MinE allows for a comprehensive description of Min-protein pattern
formation,” PLoS Computational Biology, vol. 9, no. 12. Public Library
of Science, 2013.
ista: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane
binding of MinE allows for a comprehensive description of Min-protein pattern
formation. PLoS Computational Biology. 9(12).
mla: Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description
of Min-Protein Pattern Formation.” PLoS Computational Biology, vol. 9,
no. 12, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003347.
short: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational
Biology 9 (2013).
date_created: 2018-12-11T11:55:04Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T06:54:32Z
day: '01'
doi: 10.1371/journal.pcbi.1003347
extern: 1
intvolume: ' 9'
issue: '12'
month: '12'
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5095'
quality_controlled: 0
status: public
title: Membrane binding of MinE allows for a comprehensive description of Min-protein
pattern formation
type: journal_article
volume: 9
year: '2013'
...
---
_id: '1991'
abstract:
- lang: eng
text: Although transitions of sex-determination mechanisms are frequent in species
with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to
represent a terminal evolutionary stage owing to chromosome-specific adaptations
such as dosage compensation or an accumulation of sex-specific mutations. Here
we show that an autosome of Drosophila, the dot chromosome, was ancestrally a
differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae),
flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes
located on the dot chromosome of Drosophila are X-linked in outgroup species,
whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition
to early drosophilid evolution by sequencing the genome of other Drosophilidae.
Our results reveal several puzzling aspects of Drosophila dot chromosome biology
to be possible remnants of its former life as a sex chromosome, such as its minor
feminizing role in sex determination or its targeting by a chromosome-specific
regulatory mechanism. We also show that patterns of biased gene expression of
the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble
that of the current X chromosome. Thus, although sex chromosomes are not necessarily
evolutionary end points and can revert back to an autosomal inheritance, the highly
specialized genome architecture of this former X chromosome suggests that severe
fitness costs must be overcome for such a turnover to occur.
acknowledgement: Funded by National Institutes of Health grants (R01GM076007 and R01GM093182)
and a Packard Fellowship to D.B.
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome
in Drosophila. Nature. 2013;499(7458):332-335. doi:10.1038/nature12235
apa: Vicoso, B., & Bachtrog, D. (2013). Reversal of an ancient sex chromosome
to an autosome in Drosophila. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12235
chicago: Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome
to an Autosome in Drosophila.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12235.
ieee: B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome
in Drosophila,” Nature, vol. 499, no. 7458. Nature Publishing Group, pp.
332–335, 2013.
ista: Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome
in Drosophila. Nature. 499(7458), 332–335.
mla: Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome
to an Autosome in Drosophila.” Nature, vol. 499, no. 7458, Nature Publishing
Group, 2013, pp. 332–35, doi:10.1038/nature12235.
short: B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335.
date_created: 2018-12-11T11:55:05Z
date_published: 2013-07-18T00:00:00Z
date_updated: 2021-01-12T06:54:33Z
day: '18'
doi: 10.1038/nature12235
extern: 1
intvolume: ' 499'
issue: '7458'
month: '07'
page: 332 - 335
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5092'
quality_controlled: 0
status: public
title: Reversal of an ancient sex chromosome to an autosome in Drosophila
type: journal_article
volume: 499
year: '2013'
...
---
OA_place: repository
OA_type: green
_id: '19995'
abstract:
- lang: eng
text: Markov decision processes (MDPs) and simple stochastic games (SSGs) provide
a rich mathematical framework to study many important problems related to probabilistic
systems. MDPs and SSGs with finite-horizon objectives, where the goal is to maximize
the probability to reach a target state in a given finite time, is a classical
and well-studied problem. In this work we consider the strategy complexity of
finite-horizon MDPs and SSGs. We show that for all ε > 0, the natural class of
counter-based strategies require at most log log/(1/ε) + n + 1 memory states,
and memory of size Omega(log log(1/ε) + n) is required, for ε-optimality, where
n is the number of states of the MDP (resp. SSG). Thus our bounds are asymptotically
optimal. We then study the periodic property of optimal strategies, and show a
sub-exponential lower bound on the period for optimal strategies.
acknowledgement: 'Work of the second author supported by the Sino-Danish Center for
the Theory of Interactive Computation, funded by the Danish National Research Foundation
and the National Science Foundation of China (under the grant 61061130540). The
second author acknowledge support from the Center for research in the Foundations
of Electronic Markets (CFEM), supported by the Danish Strategic Research Council.
The first author was supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23
(RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. Strategy complexity of finite-horizon Markov
decision processes and simple stochastic games. In: Mathematical and Engineering
Methods in Computer Science. Vol 7721. Springer Nature; 2013:106-117. doi:10.1007/978-3-642-36046-6_11'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2013). Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games. In Mathematical and
Engineering Methods in Computer Science (Vol. 7721, pp. 106–117). Znojmo,
Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-642-36046-6_11'
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of
Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” In Mathematical
and Engineering Methods in Computer Science, 7721:106–17. Springer Nature,
2013. https://doi.org/10.1007/978-3-642-36046-6_11.
ieee: K. Chatterjee and R. Ibsen-Jensen, “Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games,” in Mathematical and
Engineering Methods in Computer Science, Znojmo, Czech Republic, 2013, vol.
7721, pp. 106–117.
ista: 'Chatterjee K, Ibsen-Jensen R. 2013. Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games. Mathematical and Engineering
Methods in Computer Science. MEMICS: Mathematical and Engineering Methods in Computer
Science, LNCS, vol. 7721, 106–117.'
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon
Markov Decision Processes and Simple Stochastic Games.” Mathematical and Engineering
Methods in Computer Science, vol. 7721, Springer Nature, 2013, pp. 106–17,
doi:10.1007/978-3-642-36046-6_11.
short: K. Chatterjee, R. Ibsen-Jensen, in:, Mathematical and Engineering Methods
in Computer Science, Springer Nature, 2013, pp. 106–117.
conference:
end_date: 2012-10-28
location: Znojmo, Czech Republic
name: 'MEMICS: Mathematical and Engineering Methods in Computer Science'
start_date: 2012-10-25
corr_author: '1'
date_created: 2025-07-10T14:08:49Z
date_published: 2013-01-17T00:00:00Z
date_updated: 2025-09-23T09:24:13Z
day: '17'
department:
- _id: KrCh
doi: 10.1007/978-3-642-36046-6_11
ec_funded: 1
external_id:
arxiv:
- '1209.3617'
intvolume: ' 7721'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1209.3617
month: '01'
oa: 1
oa_version: Preprint
page: 106-117
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Mathematical and Engineering Methods in Computer Science
publication_identifier:
eisbn:
- '9783642360466'
eissn:
- 1611-3349
isbn:
- '9783642360442'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategy complexity of finite-horizon Markov decision processes and simple
stochastic games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7721
year: '2013'
...
---
_id: '2009'
abstract:
- lang: eng
text: Traditional statistical methods for confidentiality protection of statistical
databases do not scale well to deal with GWAS databases especially in terms of
guarantees regarding protection from linkage to external information. The more
recent concept of differential privacy, introduced by the cryptographic community,
is an approach which provides a rigorous definition of privacy with meaningful
privacy guarantees in the presence of arbitrary external information, although
the guarantees may come at a serious price in terms of data utility. Building
on such notions, we propose new methods to release aggregate GWAS data without
compromising an individual’s privacy. We present methods for releasing differentially
private minor allele frequencies, chi-square statistics and p-values. We compare
these approaches on simulated data and on a GWAS study of canine hair length involving
685 dogs. We also propose a privacy-preserving method for finding genome-wide
associations based on a differentially-private approach to penalized logistic
regression.
article_processing_charge: No
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Aleksandra
full_name: Slavkovic, Aleksandra
last_name: Slavkovic
- first_name: Stephen
full_name: Fienberg, Stephen
last_name: Fienberg
citation:
ama: Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide
association studies. Journal of Privacy and Confidentiality . 2013;5(1):137-166.
doi:10.29012/jpc.v5i1.629
apa: Uhler, C., Slavkovic, A., & Fienberg, S. (2013). Privacy-preserving data
sharing for genome-wide association studies. Journal of Privacy and Confidentiality
. Carnegie Mellon University. https://doi.org/10.29012/jpc.v5i1.629
chicago: Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving
Data Sharing for Genome-Wide Association Studies.” Journal of Privacy and Confidentiality
. Carnegie Mellon University, 2013. https://doi.org/10.29012/jpc.v5i1.629.
ieee: C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing
for genome-wide association studies,” Journal of Privacy and Confidentiality
, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.
ista: Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for
genome-wide association studies. Journal of Privacy and Confidentiality . 5(1),
137–166.
mla: Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association
Studies.” Journal of Privacy and Confidentiality , vol. 5, no. 1, Carnegie
Mellon University, 2013, pp. 137–66, doi:10.29012/jpc.v5i1.629.
short: C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality 5
(2013) 137–166.
date_created: 2018-12-11T11:55:11Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2026-06-18T18:20:21Z
day: '01'
ddc:
- '000'
department:
- _id: CaUh
doi: 10.29012/jpc.v5i1.629
intvolume: ' 5'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.cmu.edu/jpc/vol5/iss1/6
month: '08'
oa: 1
oa_version: Published Version
page: 137 - 166
publication: 'Journal of Privacy and Confidentiality '
publication_status: published
publisher: Carnegie Mellon University
publist_id: '5067'
quality_controlled: '1'
status: public
title: Privacy-preserving data sharing for genome-wide association studies
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2013'
...
---
_id: '2010'
abstract:
- lang: eng
text: Many algorithms for inferring causality rely heavily on the faithfulness assumption.
The main justification for imposing this assumption is that the set of unfaithful
distributions has Lebesgue measure zero, since it can be seen as a collection
of hypersurfaces in a hypercube. However, due to sampling error the faithfulness
condition alone is not sufficient for statistical estimation, and strong-faithfulness
has been proposed and assumed to achieve uniform or high-dimensional consistency.
In contrast to the plain faithfulness assumption, the set of distributions that
is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly
large as we show in this paper. We study the strong-faithfulness condition from
a geometric and combinatorial point of view and give upper and lower bounds on
the Lebesgue measure of strong-faithful distributions for various classes of directed
acyclic graphs. Our results imply fundamental limitations for the PC-algorithm
and potentially also for other algorithms based on partial correlation testing
in the Gaussian case.
article_processing_charge: No
arxiv: 1
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Garvesh
full_name: Raskutti, Garvesh
last_name: Raskutti
- first_name: Peter
full_name: Bühlmann, Peter
last_name: Bühlmann
- first_name: Bin
full_name: Yu, Bin
last_name: Yu
citation:
ama: Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption
in causal inference. The Annals of Statistics. 2013;41(2):436-463. doi:10.1214/12-AOS1080
apa: Uhler, C., Raskutti, G., Bühlmann, P., & Yu, B. (2013). Geometry of the
faithfulness assumption in causal inference. The Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/12-AOS1080
chicago: Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry
of the Faithfulness Assumption in Causal Inference.” The Annals of Statistics.
Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/12-AOS1080.
ieee: C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness
assumption in causal inference,” The Annals of Statistics, vol. 41, no.
2. Institute of Mathematical Statistics, pp. 436–463, 2013.
ista: Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness
assumption in causal inference. The Annals of Statistics. 41(2), 436–463.
mla: Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal
Inference.” The Annals of Statistics, vol. 41, no. 2, Institute of Mathematical
Statistics, 2013, pp. 436–63, doi:10.1214/12-AOS1080.
short: C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013)
436–463.
date_created: 2018-12-11T11:55:11Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2026-06-18T18:20:45Z
day: '01'
ddc:
- '500'
department:
- _id: CaUh
doi: 10.1214/12-AOS1080
external_id:
arxiv:
- '1207.0547'
isi:
- '000320488200002'
intvolume: ' 41'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.doi.org/10.1214/12-AOS1080
month: '04'
oa: 1
oa_version: Published Version
page: 436 - 463
publication: The Annals of Statistics
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5066'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of the faithfulness assumption in causal inference
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2013'
...
---
_id: '2074'
abstract:
- lang: eng
text: 'Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic
mutations on protosex chromosomes selects for a loss of recombination and sets
in motion the evolutionary processes generating heteromorphic sex chromosomes.
Recombination suppression and differentiation are generally viewed as the default
path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes,
such as those of ratite birds, has remained a mystery. Here, we analyze the genome
and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes
on the sex chromosome are shared between the Z and W. Surprisingly, however, levels
of gene expression are generally sex-biased for all sex-linked genes relative
to autosomes, including those in the pseudoautosomal region, and the male-bias
increases after gonad formation. This expression bias suggests that the emu sex
chromosomes have become masculinized, even in the absence of ZW differentiation.
Thus, birds may have taken different evolutionary solutions to minimize the deleterious
effects imposed by sexually antagonistic mutations: some lineages eliminate recombination
along the protosex chromosomes to physically restrict sexually antagonistic alleles
to one sex, whereas ratites evolved sex-biased expression to confine the product
of a sexually antagonistic allele to the sex it benefits. This difference in conflict
resolution may explain the preservation of recombining, homomorphic sex chromosomes
in other lineages and illustrates the importance of sexually antagonistic mutations
driving the evolution of sex chromosomes. '
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Vera
full_name: Kaiser, Vera B
last_name: Kaiser
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex
chromosomes in emus and its implication for sex chromosome evolution. PNAS.
2013;110(16):6453-6458. doi:10.1073/pnas.1217027110
apa: Vicoso, B., Kaiser, V., & Bachtrog, D. (2013). Sex biased gene expression
at homomorphic sex chromosomes in emus and its implication for sex chromosome
evolution. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1217027110
chicago: Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression
at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome
Evolution.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217027110.
ieee: B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic
sex chromosomes in emus and its implication for sex chromosome evolution,” PNAS,
vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.
ista: Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic
sex chromosomes in emus and its implication for sex chromosome evolution. PNAS.
110(16), 6453–6458.
mla: Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes
in Emus and Its Implication for Sex Chromosome Evolution.” PNAS, vol. 110,
no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:10.1073/pnas.1217027110.
short: B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458.
date_created: 2018-12-11T11:55:33Z
date_published: 2013-04-16T00:00:00Z
date_updated: 2021-01-12T06:55:08Z
day: '16'
doi: 10.1073/pnas.1217027110
extern: 1
intvolume: ' 110'
issue: '16'
month: '04'
page: 6453 - 6458
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '4964'
quality_controlled: 0
status: public
title: Sex biased gene expression at homomorphic sex chromosomes in emus and its implication
for sex chromosome evolution
type: journal_article
volume: 110
year: '2013'
...
---
_id: '2076'
abstract:
- lang: eng
text: |
Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.
acknowledgement: Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard
Fellowship to DB.
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Jr
full_name: Emerson, Jr J.
last_name: Emerson
- first_name: Yulia
full_name: Zektser, Yulia
last_name: Zektser
- first_name: Shivani
full_name: Mahajan, Shivani
last_name: Mahajan
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: 'Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome
genomics in snakes: Differentiation evolutionary strata and lack of global dosage
compensation. PLoS Biology. 2013;11(8). doi:10.1371/journal.pbio.1001643'
apa: 'Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., & Bachtrog, D. (2013).
Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata
and lack of global dosage compensation. PLoS Biology. Public Library of
Science. https://doi.org/10.1371/journal.pbio.1001643'
chicago: 'Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris
Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary
Strata and Lack of Global Dosage Compensation.” PLoS Biology. Public Library
of Science, 2013. https://doi.org/10.1371/journal.pbio.1001643.'
ieee: 'B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative
sex chromosome genomics in snakes: Differentiation evolutionary strata and lack
of global dosage compensation,” PLoS Biology, vol. 11, no. 8. Public Library
of Science, 2013.'
ista: 'Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative
sex chromosome genomics in snakes: Differentiation evolutionary strata and lack
of global dosage compensation. PLoS Biology. 11(8).'
mla: 'Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation
Evolutionary Strata and Lack of Global Dosage Compensation.” PLoS Biology,
vol. 11, no. 8, Public Library of Science, 2013, doi:10.1371/journal.pbio.1001643.'
short: B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology
11 (2013).
date_created: 2018-12-11T11:55:34Z
date_published: 2013-08-27T00:00:00Z
date_updated: 2021-01-12T06:55:09Z
day: '27'
doi: 10.1371/journal.pbio.1001643
extern: 1
intvolume: ' 11'
issue: '8'
month: '08'
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '4962'
quality_controlled: 0
status: public
title: 'Comparative sex chromosome genomics in snakes: Differentiation evolutionary
strata and lack of global dosage compensation'
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
volume: 11
year: '2013'
...
---
_id: '10384'
abstract:
- lang: eng
text: 'Recent studies aimed at investigating artificial analogs of bacterial colonies
have shown that low-density suspensions of self-propelled particles confined in
two dimensions can assemble into finite aggregates that merge and split, but have
a typical size that remains constant (living clusters). In this Letter, we address
the problem of the formation of living clusters and crystals of active particles
in three dimensions. We study two systems: self-propelled particles interacting
via a generic attractive potential and colloids that can move toward each other
as a result of active agents (e.g., by molecular motors). In both cases, fluidlike
“living” clusters form. We explain this general feature in terms of the balance
between active forces and regression to thermodynamic equilibrium. This balance
can be quantified in terms of a dimensionless number that allows us to collapse
the observed clustering behavior onto a universal curve. We also discuss how active
motion affects the kinetics of crystal formation.'
acknowledgement: This work was supported by the ERC Advanced Grant 227758, the National
Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3
of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge
T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support
from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941
ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support
from the Alexander von Humboldt Foundation.
article_number: '245702'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: B. M.
full_name: Mognetti, B. M.
last_name: Mognetti
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: S.
full_name: Angioletti-Uberti, S.
last_name: Angioletti-Uberti
- first_name: A.
full_name: Cacciuto, A.
last_name: Cacciuto
- first_name: C.
full_name: Valeriani, C.
last_name: Valeriani
- first_name: D.
full_name: Frenkel, D.
last_name: Frenkel
citation:
ama: Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel
D. Living clusters and crystals from low-density suspensions of active colloids.
Physical Review Letters. 2013;111(24). doi:10.1103/physrevlett.111.245702
apa: Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani,
C., & Frenkel, D. (2013). Living clusters and crystals from low-density suspensions
of active colloids. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.111.245702
chicago: Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of
Active Colloids.” Physical Review Letters. American Physical Society, 2013.
https://doi.org/10.1103/physrevlett.111.245702.
ieee: B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
and D. Frenkel, “Living clusters and crystals from low-density suspensions of
active colloids,” Physical Review Letters, vol. 111, no. 24. American Physical
Society, 2013.
ista: Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel
D. 2013. Living clusters and crystals from low-density suspensions of active colloids.
Physical Review Letters. 111(24), 245702.
mla: Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions
of Active Colloids.” Physical Review Letters, vol. 111, no. 24, 245702,
American Physical Society, 2013, doi:10.1103/physrevlett.111.245702.
short: B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
D. Frenkel, Physical Review Letters 111 (2013).
date_created: 2021-11-29T13:29:31Z
date_published: 2013-12-11T00:00:00Z
date_updated: 2021-11-29T14:05:19Z
day: '11'
doi: 10.1103/physrevlett.111.245702
extern: '1'
external_id:
arxiv:
- '1311.4681'
pmid:
- '24483677'
intvolume: ' 111'
issue: '24'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.4681
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Living clusters and crystals from low-density suspensions of active colloids
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2013'
...