---
_id: '3909'
abstract:
- lang: eng
text: Social insect colonies have evolved collective immune defences against parasites.
These ‘social immune systems’ result from the cooperation of the individual group
members to combat the increased risk of disease transmission that arises from
sociality and group living. In this review we illustrate the pathways that parasites
can take to infect a social insect colony and use these pathways as a framework
to predict colony defence mechanisms and present the existing evidence. We find
that the collective defences can be both prophylactic and activated on demand
and consist of behavioural, physiological and organisational adaptations of the
colony that prevent parasite entrance, establishment and spread. We discuss the
regulation of collective immunity, which requires complex integration of information
about both the parasites and the internal status of the insect colony. Our review
concludes with an examination of the evolution of social immunity, which is based
on the consequences of selection at both the individual and the colony level.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
- first_name: Paul
full_name: Schmid Hempel, Paul
last_name: Schmid Hempel
citation:
ama: Cremer S, Armitage S, Schmid Hempel P. Social immunity. Current Biology.
2007;17(16):R693-R702. doi:10.1016/j.cub.2007.06.008
apa: Cremer, S., Armitage, S., & Schmid Hempel, P. (2007). Social immunity.
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2007.06.008
chicago: Cremer, Sylvia, Sophie Armitage, and Paul Schmid Hempel. “Social Immunity.”
Current Biology. Cell Press, 2007. https://doi.org/10.1016/j.cub.2007.06.008.
ieee: S. Cremer, S. Armitage, and P. Schmid Hempel, “Social immunity,” Current
Biology, vol. 17, no. 16. Cell Press, pp. R693–R702, 2007.
ista: Cremer S, Armitage S, Schmid Hempel P. 2007. Social immunity. Current Biology.
17(16), R693–R702.
mla: Cremer, Sylvia, et al. “Social Immunity.” Current Biology, vol. 17,
no. 16, Cell Press, 2007, pp. R693–702, doi:10.1016/j.cub.2007.06.008.
short: S. Cremer, S. Armitage, P. Schmid Hempel, Current Biology 17 (2007) R693–R702.
date_created: 2018-12-11T12:05:50Z
date_published: 2007-08-21T00:00:00Z
date_updated: 2021-01-12T07:53:07Z
day: '21'
doi: 10.1016/j.cub.2007.06.008
extern: '1'
intvolume: ' 17'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: R693 - R702
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2243'
status: public
title: Social immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '3910'
author:
- first_name: David
full_name: Hughes, David
last_name: Hughes
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Hughes D, Cremer S. Plasticity in anti-parasite behaviours and its suggested
role in invasion biology. Animal Behaviour. 2007;74(5):1593-1599. doi:10.1016/j.anbehav.2006.12.025
apa: Hughes, D., & Cremer, S. (2007). Plasticity in anti-parasite behaviours
and its suggested role in invasion biology. Animal Behaviour. Elsevier.
https://doi.org/10.1016/j.anbehav.2006.12.025
chicago: Hughes, David, and Sylvia Cremer. “Plasticity in Anti-Parasite Behaviours
and Its Suggested Role in Invasion Biology.” Animal Behaviour. Elsevier,
2007. https://doi.org/10.1016/j.anbehav.2006.12.025.
ieee: D. Hughes and S. Cremer, “Plasticity in anti-parasite behaviours and its suggested
role in invasion biology,” Animal Behaviour, vol. 74, no. 5. Elsevier,
pp. 1593–1599, 2007.
ista: Hughes D, Cremer S. 2007. Plasticity in anti-parasite behaviours and its suggested
role in invasion biology. Animal Behaviour. 74(5), 1593–1599.
mla: Hughes, David, and Sylvia Cremer. “Plasticity in Anti-Parasite Behaviours and
Its Suggested Role in Invasion Biology.” Animal Behaviour, vol. 74, no.
5, Elsevier, 2007, pp. 1593–99, doi:10.1016/j.anbehav.2006.12.025.
short: D. Hughes, S. Cremer, Animal Behaviour 74 (2007) 1593–1599.
date_created: 2018-12-11T12:05:50Z
date_published: 2007-11-01T00:00:00Z
date_updated: 2021-01-12T07:53:08Z
day: '01'
doi: 10.1016/j.anbehav.2006.12.025
extern: '1'
intvolume: ' 74'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 1593 - 1599
publication: Animal Behaviour
publication_status: published
publisher: Elsevier
publist_id: '2244'
status: public
title: Plasticity in anti-parasite behaviours and its suggested role in invasion biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2007'
...
---
_id: '3911'
abstract:
- lang: eng
text: Life in a social group increases the risk of disease transmission. To counteract
this threat, social insects have evolved manifold antiparasite defenses, ranging
from social exclusion of infected group members to intensive care. It is generally
assumed that individuals performing hygienic behaviors risk infecting themselves,
suggesting a high direct cost of helping. Our work instead indicates the opposite
for garden ants. Social contact with individual workers, which were experimentally
exposed to a fungal parasite, provided a clear survival benefit to nontreated,
naive group members upon later challenge with the same parasite. This first demonstration
of contact immunity in Social Hymenoptera and complementary results from other
animal groups and plants suggest its general importance in both antiparasite and
antiherbivore defense. In addition to this physiological prophylaxis of adult
ants, infection of the brood was prevented in our experiment by behavioral changes
of treated and naive workers. Parasite-treated ants stayed away from the brood
chamber, whereas their naive nestmates increased brood-care activities. Our findings
reveal a direct benefit for individuals to perform hygienic behaviors toward others,
and this might explain the widely observed maintenance of social cohesion under
parasite attack in insect societies.
author:
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Ugelvig LV, Cremer S. Social prophylaxis: group interaction promotes collective
immunity in ant colonies. Current Biology. 2007;17(22):1967-1971. doi:10.1016/j.cub.2007.10.029'
apa: 'Ugelvig, L. V., & Cremer, S. (2007). Social prophylaxis: group interaction
promotes collective immunity in ant colonies. Current Biology. Cell Press.
https://doi.org/10.1016/j.cub.2007.10.029'
chicago: 'Ugelvig, Line V, and Sylvia Cremer. “Social Prophylaxis: Group Interaction
Promotes Collective Immunity in Ant Colonies.” Current Biology. Cell Press,
2007. https://doi.org/10.1016/j.cub.2007.10.029.'
ieee: 'L. V. Ugelvig and S. Cremer, “Social prophylaxis: group interaction promotes
collective immunity in ant colonies,” Current Biology, vol. 17, no. 22.
Cell Press, pp. 1967–1971, 2007.'
ista: 'Ugelvig LV, Cremer S. 2007. Social prophylaxis: group interaction promotes
collective immunity in ant colonies. Current Biology. 17(22), 1967–1971.'
mla: 'Ugelvig, Line V., and Sylvia Cremer. “Social Prophylaxis: Group Interaction
Promotes Collective Immunity in Ant Colonies.” Current Biology, vol. 17,
no. 22, Cell Press, 2007, pp. 1967–71, doi:10.1016/j.cub.2007.10.029.'
short: L.V. Ugelvig, S. Cremer, Current Biology 17 (2007) 1967–1971.
date_created: 2018-12-11T12:05:51Z
date_published: 2007-11-20T00:00:00Z
date_updated: 2021-01-12T07:53:08Z
day: '20'
doi: 10.1016/j.cub.2007.10.029
extern: '1'
intvolume: ' 17'
issue: '22'
language:
- iso: eng
month: '11'
oa_version: None
page: 1967 - 1971
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2245'
status: public
title: 'Social prophylaxis: group interaction promotes collective immunity in ant
colonies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '3937'
abstract:
- lang: eng
text: Lymphocyte motility in lymph nodes is regulated by chemokines, but the contribution
of integrins to this motility remains obscure. Here we examined lymphocyte migration
over CCR7-binding chemokines that 'decorate' lymph node stroma. In a shear-free
environment, surface-bound lymph node chemokines but not their soluble counterparts
promoted robust and sustained T lymphocyte motility. The chemokine CCL21 induced
compartmentalized clustering of the integrins LFA-1 and VLA-4 in motile lymphocytes,
but both integrins remained nonadhesive to ligands on lymphocytes, dendritic cells
and stroma. The application of shear stress to lymphocytes interacting with CCL21
and integrin ligands promoted robust integrin-mediated adhesion. Thus, lymph node
chemokines that promote motility and strongly activate lymphocyte integrins under
shear forces fail to stimulate stable integrin adhesiveness in extravascular shear-free
environments.
author:
- first_name: Eilon
full_name: Woolf, Eilon
last_name: Woolf
- first_name: Irina
full_name: Grigorova, Irina
last_name: Grigorova
- first_name: Adi
full_name: Sagiv, Adi
last_name: Sagiv
- first_name: Valentin
full_name: Grabovsky, Valentin
last_name: Grabovsky
- first_name: Sara
full_name: Feigelson, Sara W
last_name: Feigelson
- first_name: Ziv
full_name: Shulman, Ziv
last_name: Shulman
- first_name: Tanja
full_name: Hartmann, Tanja
last_name: Hartmann
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Jason
full_name: Cyster, Jason G
last_name: Cyster
- first_name: Ronen
full_name: Alon, Ronen
last_name: Alon
citation:
ama: Woolf E, Grigorova I, Sagiv A, et al. Lymph node chemokines promote sustained
T lymphocyte motility without triggering stable integrin adhesiveness in the absence
of shear forces. Nature Immunology. 2007;8(10):1076-1085. doi:10.1038/ni1499
apa: Woolf, E., Grigorova, I., Sagiv, A., Grabovsky, V., Feigelson, S., Shulman,
Z., … Alon, R. (2007). Lymph node chemokines promote sustained T lymphocyte motility
without triggering stable integrin adhesiveness in the absence of shear forces.
Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni1499
chicago: Woolf, Eilon, Irina Grigorova, Adi Sagiv, Valentin Grabovsky, Sara Feigelson,
Ziv Shulman, Tanja Hartmann, Michael K Sixt, Jason Cyster, and Ronen Alon. “Lymph
Node Chemokines Promote Sustained T Lymphocyte Motility without Triggering Stable
Integrin Adhesiveness in the Absence of Shear Forces.” Nature Immunology.
Nature Publishing Group, 2007. https://doi.org/10.1038/ni1499.
ieee: E. Woolf et al., “Lymph node chemokines promote sustained T lymphocyte
motility without triggering stable integrin adhesiveness in the absence of shear
forces,” Nature Immunology, vol. 8, no. 10. Nature Publishing Group, pp.
1076–1085, 2007.
ista: Woolf E, Grigorova I, Sagiv A, Grabovsky V, Feigelson S, Shulman Z, Hartmann
T, Sixt MK, Cyster J, Alon R. 2007. Lymph node chemokines promote sustained T
lymphocyte motility without triggering stable integrin adhesiveness in the absence
of shear forces. Nature Immunology. 8(10), 1076–1085.
mla: Woolf, Eilon, et al. “Lymph Node Chemokines Promote Sustained T Lymphocyte
Motility without Triggering Stable Integrin Adhesiveness in the Absence of Shear
Forces.” Nature Immunology, vol. 8, no. 10, Nature Publishing Group, 2007,
pp. 1076–85, doi:10.1038/ni1499.
short: E. Woolf, I. Grigorova, A. Sagiv, V. Grabovsky, S. Feigelson, Z. Shulman,
T. Hartmann, M.K. Sixt, J. Cyster, R. Alon, Nature Immunology 8 (2007) 1076–1085.
date_created: 2018-12-11T12:05:59Z
date_published: 2007-08-26T00:00:00Z
date_updated: 2021-01-12T07:53:19Z
day: '26'
doi: 10.1038/ni1499
extern: 1
intvolume: ' 8'
issue: '10'
month: '08'
page: 1076 - 1085
publication: Nature Immunology
publication_status: published
publisher: Nature Publishing Group
publist_id: '2189'
quality_controlled: 0
status: public
title: Lymph node chemokines promote sustained T lymphocyte motility without triggering
stable integrin adhesiveness in the absence of shear forces
type: journal_article
volume: 8
year: '2007'
...
---
_id: '3938'
abstract:
- lang: eng
text: RhoH is a small GTPase expressed only in the hematopoietic system. With the
use of mice with targeted disruption of the RhoH gene, we demonstrated that RhoH
is crucial for thymocyte maturation during DN3 to DN4 transition and during positive
selection. Furthermore, the differentiation and expansion of DN3 and DN4 thymocytes
in vitro were severely impaired. These defects corresponded to defective TCR signaling.
Although RhoH is not required for TCR-induced activation of ZAP70 and ZAP70-mediated
activation of p38, it is crucial for the tyrosine phosphorylation of LAT, PLCgamma1,
and Vav1 and for the activation of Erk and calcium influx. These data suggest
that RhoH is important for pre-TCR and TCR signaling because it allows the efficient
interaction of ZAP70 with the LAT signalosome, thus regulating thymocyte development.
author:
- first_name: Tatjana
full_name: Dorn, Tatjana
last_name: Dorn
- first_name: Ursula
full_name: Kuhn, Ursula
last_name: Kuhn
- first_name: Gerd
full_name: Bungartz, Gerd
last_name: Bungartz
- first_name: Sebastian
full_name: Stiller, Sebastian
last_name: Stiller
- first_name: Martina
full_name: Bauer, Martina
last_name: Bauer
- first_name: Joachim
full_name: Ellwart, Joachim
last_name: Ellwart
- first_name: Thorsten
full_name: Peters, Thorsten
last_name: Peters
- first_name: Karin
full_name: Scharffetter-Kochanek, Karin
last_name: Scharffetter Kochanek
- first_name: Monika
full_name: Semmrich, Monika
last_name: Semmrich
- first_name: Melanie
full_name: Laschinger, Melanie
last_name: Laschinger
- first_name: Bernhard
full_name: Holzmann, Bernhard
last_name: Holzmann
- first_name: Wolfgang
full_name: Klinkert, Wolfgang E
last_name: Klinkert
- first_name: Per
full_name: Straten, Per Thor
last_name: Straten
- first_name: Tania
full_name: Køllgaard, Tania
last_name: Køllgaard
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Cord
full_name: Brakebusch, Cord
last_name: Brakebusch
citation:
ama: Dorn T, Kuhn U, Bungartz G, et al. RhoH is important for positive thymocyte
selection and T-cell receptor signaling. Blood. 2007;109(6):2346-2355.
doi:10.1182/blood-2006-04-019034
apa: Dorn, T., Kuhn, U., Bungartz, G., Stiller, S., Bauer, M., Ellwart, J., … Brakebusch,
C. (2007). RhoH is important for positive thymocyte selection and T-cell receptor
signaling. Blood. American Society of Hematology. https://doi.org/10.1182/blood-2006-04-019034
chicago: Dorn, Tatjana, Ursula Kuhn, Gerd Bungartz, Sebastian Stiller, Martina Bauer,
Joachim Ellwart, Thorsten Peters, et al. “RhoH Is Important for Positive Thymocyte
Selection and T-Cell Receptor Signaling.” Blood. American Society of Hematology,
2007. https://doi.org/10.1182/blood-2006-04-019034.
ieee: T. Dorn et al., “RhoH is important for positive thymocyte selection
and T-cell receptor signaling,” Blood, vol. 109, no. 6. American Society
of Hematology, pp. 2346–2355, 2007.
ista: Dorn T, Kuhn U, Bungartz G, Stiller S, Bauer M, Ellwart J, Peters T, Scharffetter
Kochanek K, Semmrich M, Laschinger M, Holzmann B, Klinkert W, Straten P, Køllgaard
T, Sixt MK, Brakebusch C. 2007. RhoH is important for positive thymocyte selection
and T-cell receptor signaling. Blood. 109(6), 2346–2355.
mla: Dorn, Tatjana, et al. “RhoH Is Important for Positive Thymocyte Selection and
T-Cell Receptor Signaling.” Blood, vol. 109, no. 6, American Society of
Hematology, 2007, pp. 2346–55, doi:10.1182/blood-2006-04-019034.
short: T. Dorn, U. Kuhn, G. Bungartz, S. Stiller, M. Bauer, J. Ellwart, T. Peters,
K. Scharffetter Kochanek, M. Semmrich, M. Laschinger, B. Holzmann, W. Klinkert,
P. Straten, T. Køllgaard, M.K. Sixt, C. Brakebusch, Blood 109 (2007) 2346–2355.
date_created: 2018-12-11T12:05:59Z
date_published: 2007-03-15T00:00:00Z
date_updated: 2021-01-12T07:53:19Z
day: '15'
doi: 10.1182/blood-2006-04-019034
extern: 1
intvolume: ' 109'
issue: '6'
month: '03'
page: 2346 - 2355
publication: Blood
publication_status: published
publisher: American Society of Hematology
publist_id: '2190'
quality_controlled: 0
status: public
title: RhoH is important for positive thymocyte selection and T-cell receptor signaling
type: journal_article
volume: 109
year: '2007'
...
---
_id: '3972'
abstract:
- lang: eng
text: 'The persistence diagram of a real-valued function on a topological space
is a multiset of points in the extended plane. We prove that under mild assumptions
on the function, the persistence diagram is stable: small changes in the function
imply only small changes in the diagram. We apply this result to estimating the
homology of sets in a metric space and to comparing and classifying geometric
shapes.'
author:
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: Cohen Steiner D, Edelsbrunner H, Harer J. Stability of persistence diagrams.
Discrete & Computational Geometry. 2007;37(1):103-120. doi:10.1007/s00454-006-1276-5
apa: Cohen Steiner, D., Edelsbrunner, H., & Harer, J. (2007). Stability of persistence
diagrams. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1276-5
chicago: Cohen Steiner, David, Herbert Edelsbrunner, and John Harer. “Stability
of Persistence Diagrams.” Discrete & Computational Geometry. Springer,
2007. https://doi.org/10.1007/s00454-006-1276-5.
ieee: D. Cohen Steiner, H. Edelsbrunner, and J. Harer, “Stability of persistence
diagrams,” Discrete & Computational Geometry, vol. 37, no. 1. Springer,
pp. 103–120, 2007.
ista: Cohen Steiner D, Edelsbrunner H, Harer J. 2007. Stability of persistence diagrams.
Discrete & Computational Geometry. 37(1), 103–120.
mla: Cohen Steiner, David, et al. “Stability of Persistence Diagrams.” Discrete
& Computational Geometry, vol. 37, no. 1, Springer, 2007, pp. 103–20,
doi:10.1007/s00454-006-1276-5.
short: D. Cohen Steiner, H. Edelsbrunner, J. Harer, Discrete & Computational
Geometry 37 (2007) 103–120.
date_created: 2018-12-11T12:06:12Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:34Z
day: '01'
doi: 10.1007/s00454-006-1276-5
extern: 1
intvolume: ' 37'
issue: '1'
month: '01'
page: 103 - 120
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2153'
quality_controlled: 0
status: public
title: Stability of persistence diagrams
type: journal_article
volume: 37
year: '2007'
...
---
_id: '3973'
abstract:
- lang: eng
text: In this paper we bound the difference between the total mean curvatures of
two closed surfaces in R-3 in terms of their total absolute curvatures and the
Frechet distance between the volumes they enclose. The proof relies on a combination
of methods from algebraic topology and integral geometry. We also bound the difference
between the lengths of two curves using the same methods.
author:
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Cohen Steiner D, Edelsbrunner H. Inequalities for the curvature of curves and
surfaces. Foundations of Computational Mathematics. 2007;7(4):391-404.
doi:10.1007/s10208-005-0200-3
apa: Cohen Steiner, D., & Edelsbrunner, H. (2007). Inequalities for the curvature
of curves and surfaces. Foundations of Computational Mathematics. Springer.
https://doi.org/10.1007/s10208-005-0200-3
chicago: Cohen Steiner, David, and Herbert Edelsbrunner. “Inequalities for the Curvature
of Curves and Surfaces.” Foundations of Computational Mathematics. Springer,
2007. https://doi.org/10.1007/s10208-005-0200-3.
ieee: D. Cohen Steiner and H. Edelsbrunner, “Inequalities for the curvature of curves
and surfaces,” Foundations of Computational Mathematics, vol. 7, no. 4.
Springer, pp. 391–404, 2007.
ista: Cohen Steiner D, Edelsbrunner H. 2007. Inequalities for the curvature of curves
and surfaces. Foundations of Computational Mathematics. 7(4), 391–404.
mla: Cohen Steiner, David, and Herbert Edelsbrunner. “Inequalities for the Curvature
of Curves and Surfaces.” Foundations of Computational Mathematics, vol.
7, no. 4, Springer, 2007, pp. 391–404, doi:10.1007/s10208-005-0200-3.
short: D. Cohen Steiner, H. Edelsbrunner, Foundations of Computational Mathematics
7 (2007) 391–404.
date_created: 2018-12-11T12:06:12Z
date_published: 2007-11-01T00:00:00Z
date_updated: 2021-01-12T07:53:34Z
day: '01'
doi: 10.1007/s10208-005-0200-3
extern: 1
intvolume: ' 7'
issue: '4'
month: '11'
page: 391 - 404
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '2154'
quality_controlled: 0
status: public
title: Inequalities for the curvature of curves and surfaces
type: journal_article
volume: 7
year: '2007'
...
---
_id: '3975'
abstract:
- lang: eng
text: We study the reconstruction of a stratified space from a possibly noisy point
sample. Specifically, we use the vineyard of the distance function restricted
to a I-parameter family of neighborhoods of a point to assess the local homology
of the stratified space at that point. We prove the correctness of this assessment
under the assumption of a sufficiently dense sample. We also give an algorithm
that constructs the vineyard and makes the local assessment in time at most cubic
in the size of the Delaunay triangulation of the point sample.
author:
- first_name: Paul
full_name: Paul Bendich
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
citation:
ama: 'Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. Inferring
local homology from sampled stratified spaces. In: IEEE; 2007:536-546. doi:10.1109/FOCS.2007.33'
apa: 'Bendich, P., Cohen Steiner, D., Edelsbrunner, H., Harer, J., & Morozov,
D. (2007). Inferring local homology from sampled stratified spaces (pp. 536–546).
Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2007.33'
chicago: Bendich, Paul, David Cohen Steiner, Herbert Edelsbrunner, John Harer, and
Dmitriy Morozov. “Inferring Local Homology from Sampled Stratified Spaces,” 536–46.
IEEE, 2007. https://doi.org/10.1109/FOCS.2007.33.
ieee: 'P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, and D. Morozov,
“Inferring local homology from sampled stratified spaces,” presented at the FOCS:
Foundations of Computer Science, 2007, pp. 536–546.'
ista: 'Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. 2007. Inferring
local homology from sampled stratified spaces. FOCS: Foundations of Computer Science,
536–546.'
mla: Bendich, Paul, et al. Inferring Local Homology from Sampled Stratified Spaces.
IEEE, 2007, pp. 536–46, doi:10.1109/FOCS.2007.33.
short: P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, D. Morozov, in:,
IEEE, 2007, pp. 536–546.
conference:
name: 'FOCS: Foundations of Computer Science'
date_created: 2018-12-11T12:06:13Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:35Z
day: '01'
doi: 10.1109/FOCS.2007.33
extern: 1
month: '01'
page: 536 - 546
publication_status: published
publisher: IEEE
publist_id: '2150'
quality_controlled: 0
status: public
title: Inferring local homology from sampled stratified spaces
type: conference
year: '2007'
...
---
_id: '3976'
abstract:
- lang: eng
text: Herein, we study the interfaces of a set of 146 transient protein-protein
interfaces in order to better understand the principles of their interactions.
We define and generate the protein interface using tools from computational geometry
and topology and then apply statistical analysis to its residue composition. In
addition to counting individual occurrences, we evaluate pairing preferences,
both across and as neighbors on one side of an interface. Likelihood correction
emphasizes novel and unexpected pairs, such as the His-Cys pair found in most
complexes of serine proteases with their diverse inhibitors and the Met-Met neighbor
pair found in unrelated protein interfaces. We also present a visualization of
the protein interface that allows for facile identification of residue-residue
contacts and other biochemical properties.
author:
- first_name: Jeffrey
full_name: Headd, Jeffrey J
last_name: Headd
- first_name: Y E Andrew
full_name: Ban, Y E Andrew
last_name: Ban
- first_name: Paul
full_name: Brown, Paul
last_name: Brown
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Madhuwanti
full_name: Vaidya, Madhuwanti
last_name: Vaidya
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: 'Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. Protein-protein
interfaces: Properties, preferences, and projections. Journal of Proteome Research.
2007;6(7):2576-2586. doi:10.1021/pr070018+'
apa: 'Headd, J., Ban, Y. E. A., Brown, P., Edelsbrunner, H., Vaidya, M., & Rudolph,
J. (2007). Protein-protein interfaces: Properties, preferences, and projections.
Journal of Proteome Research. American Chemical Society. https://doi.org/10.1021/pr070018+'
chicago: 'Headd, Jeffrey, Y E Andrew Ban, Paul Brown, Herbert Edelsbrunner, Madhuwanti
Vaidya, and Johannes Rudolph. “Protein-Protein Interfaces: Properties, Preferences,
and Projections.” Journal of Proteome Research. American Chemical Society,
2007. https://doi.org/10.1021/pr070018+.'
ieee: 'J. Headd, Y. E. A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, and J. Rudolph,
“Protein-protein interfaces: Properties, preferences, and projections,” Journal
of Proteome Research, vol. 6, no. 7. American Chemical Society, pp. 2576–2586,
2007.'
ista: 'Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. 2007. Protein-protein
interfaces: Properties, preferences, and projections. Journal of Proteome Research.
6(7), 2576–2586.'
mla: 'Headd, Jeffrey, et al. “Protein-Protein Interfaces: Properties, Preferences,
and Projections.” Journal of Proteome Research, vol. 6, no. 7, American
Chemical Society, 2007, pp. 2576–86, doi:10.1021/pr070018+.'
short: J. Headd, Y.E.A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, J. Rudolph, Journal
of Proteome Research 6 (2007) 2576–2586.
date_created: 2018-12-11T12:06:13Z
date_published: 2007-06-02T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '02'
doi: 10.1021/pr070018+
extern: 1
intvolume: ' 6'
issue: '7'
month: '06'
page: 2576 - 2586
publication: Journal of Proteome Research
publication_status: published
publisher: American Chemical Society
publist_id: '2151'
quality_controlled: 0
status: public
title: 'Protein-protein interfaces: Properties, preferences, and projections'
type: journal_article
volume: 6
year: '2007'
...
---
_id: '3977'
abstract:
- lang: eng
text: Using inclusion-exclusion, we can write the indicator function of a union
of finitely many balls as an alternating sum of indicator functions of common
intersections of balls. We exhibit abstract simplicial complexes that correspond
to minimal inclusion-exclusion formulas. They include the dual complex, as defined
in [3], and are characterized by the independence of their simplices and by geometric
realizations with the same underlying space as the dual complex.
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Attali D, Edelsbrunner H. Inclusion-exclusion formulas from independent complexes.
Discrete & Computational Geometry. 2007;37(1):59-77. doi:10.1007/s00454-006-1274-7
apa: Attali, D., & Edelsbrunner, H. (2007). Inclusion-exclusion formulas from
independent complexes. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-006-1274-7
chicago: Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas
from Independent Complexes.” Discrete & Computational Geometry. Springer,
2007. https://doi.org/10.1007/s00454-006-1274-7.
ieee: D. Attali and H. Edelsbrunner, “Inclusion-exclusion formulas from independent
complexes,” Discrete & Computational Geometry, vol. 37, no. 1. Springer,
pp. 59–77, 2007.
ista: Attali D, Edelsbrunner H. 2007. Inclusion-exclusion formulas from independent
complexes. Discrete & Computational Geometry. 37(1), 59–77.
mla: Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas
from Independent Complexes.” Discrete & Computational Geometry, vol.
37, no. 1, Springer, 2007, pp. 59–77, doi:10.1007/s00454-006-1274-7.
short: D. Attali, H. Edelsbrunner, Discrete & Computational Geometry 37 (2007)
59–77.
date_created: 2018-12-11T12:06:14Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '01'
doi: 10.1007/s00454-006-1274-7
extern: 1
intvolume: ' 37'
issue: '1'
month: '01'
page: 59 - 77
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2152'
quality_controlled: 0
status: public
title: Inclusion-exclusion formulas from independent complexes
type: journal_article
volume: 37
year: '2007'
...
---
_id: '3981'
abstract:
- lang: eng
text: Building on the work of Martinetz, Schulten and de Silva, Carlsson, we introduce
a 2-parameter family of witness complexes and algorithms for constructing them.
This family can be used to determine the gross topology of point cloud data in
R-d or other metric spaces. The 2-parameter family is sensitive to differences
in sampling density and thus amenable to detecting patterns within the data set.
It also lends itself to theoretical analysis. For example, we can prove that in
the limit, when the witnesses cover the entire domain, witness complexes in the
family that share the first, scale parameter have the same homotopy type.
acknowledgement: Research by the authors is partially supported by DARPA under grant
HR0011-05-1-0007, by CNRS under grant PICS-3416 and by IST Program of the EU under
Contract IST-2002-506766.
alternative_title:
- LNCS
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
citation:
ama: 'Attali D, Edelsbrunner H, Harer J, Mileyko Y. Alpha-beta witness complexes.
In: Vol 4619. Springer; 2007:386-397. doi:10.1007/978-3-540-73951-7_34'
apa: 'Attali, D., Edelsbrunner, H., Harer, J., & Mileyko, Y. (2007). Alpha-beta
witness complexes (Vol. 4619, pp. 386–397). Presented at the WADS: International
Workshop on Algrithms and Data Structures, Springer. https://doi.org/10.1007/978-3-540-73951-7_34'
chicago: Attali, Dominique, Herbert Edelsbrunner, John Harer, and Yuriy Mileyko.
“Alpha-Beta Witness Complexes,” 4619:386–97. Springer, 2007. https://doi.org/10.1007/978-3-540-73951-7_34.
ieee: 'D. Attali, H. Edelsbrunner, J. Harer, and Y. Mileyko, “Alpha-beta witness
complexes,” presented at the WADS: International Workshop on Algrithms and Data
Structures, 2007, vol. 4619, pp. 386–397.'
ista: 'Attali D, Edelsbrunner H, Harer J, Mileyko Y. 2007. Alpha-beta witness complexes.
WADS: International Workshop on Algrithms and Data Structures, LNCS, vol. 4619,
386–397.'
mla: Attali, Dominique, et al. Alpha-Beta Witness Complexes. Vol. 4619, Springer,
2007, pp. 386–97, doi:10.1007/978-3-540-73951-7_34.
short: D. Attali, H. Edelsbrunner, J. Harer, Y. Mileyko, in:, Springer, 2007, pp.
386–397.
conference:
name: 'WADS: International Workshop on Algrithms and Data Structures'
date_created: 2018-12-11T12:06:15Z
date_published: 2007-08-21T00:00:00Z
date_updated: 2021-01-12T07:53:38Z
day: '21'
doi: 10.1007/978-3-540-73951-7_34
extern: 1
intvolume: ' 4619'
month: '08'
page: 386 - 397
publication_status: published
publisher: Springer
publist_id: '2149'
quality_controlled: 0
status: public
title: Alpha-beta witness complexes
type: conference
volume: 4619
year: '2007'
...
---
_id: '4152'
abstract:
- lang: eng
text: 'Gastrulation is a morphogenetic process that results in the formation of
the embryonic germ layers. Here we detail the major cell movements that occur
during zebrafish gastrulation: epiboly, internalization, and convergent extension.
Although gastrulation is known to be regulated by signaling pathways such as the
Wnt/planar cell polarity pathway, many questions remain about the underlying molecular
and cellular mechanisms. Key factors that may play a role in gastrulation cell
movements are cell adhesion and cytoskeletal rearrangement. In addition, some
of the driving force for gastrulation may derive from tissue interactions such
as those described between the enveloping layer and the yolk syncytial layer.
Future exploration of gastrulation mechanisms relies on the development of sensitive
and quantitative techniques to characterize embryonic germ-layer properties.'
author:
- first_name: Laurel
full_name: Rohde, Laurel
last_name: Rohde
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Rohde L, Heisenberg C-PJ. Zebrafish gastrulation: Cell movements, signals,
and mechanisms. International Review of Cytology - A Survey of Cell Biology.
2007;261:159-192. doi:10.1016/S0074-7696(07)61004-3'
apa: 'Rohde, L., & Heisenberg, C.-P. J. (2007). Zebrafish gastrulation: Cell
movements, signals, and mechanisms. International Review of Cytology - A Survey
of Cell Biology. Academic Press. https://doi.org/10.1016/S0074-7696(07)61004-3'
chicago: 'Rohde, Laurel, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation:
Cell Movements, Signals, and Mechanisms.” International Review of Cytology
- A Survey of Cell Biology. Academic Press, 2007. https://doi.org/10.1016/S0074-7696(07)61004-3.'
ieee: 'L. Rohde and C.-P. J. Heisenberg, “Zebrafish gastrulation: Cell movements,
signals, and mechanisms,” International Review of Cytology - A Survey of Cell
Biology, vol. 261. Academic Press, pp. 159–192, 2007.'
ista: 'Rohde L, Heisenberg C-PJ. 2007. Zebrafish gastrulation: Cell movements, signals,
and mechanisms. International Review of Cytology - A Survey of Cell Biology. 261,
159–192.'
mla: 'Rohde, Laurel, and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Cell
Movements, Signals, and Mechanisms.” International Review of Cytology - A Survey
of Cell Biology, vol. 261, Academic Press, 2007, pp. 159–92, doi:10.1016/S0074-7696(07)61004-3.'
short: L. Rohde, C.-P.J. Heisenberg, International Review of Cytology - A Survey
of Cell Biology 261 (2007) 159–192.
date_created: 2018-12-11T12:07:15Z
date_published: 2007-06-06T00:00:00Z
date_updated: 2021-01-12T07:54:53Z
day: '06'
doi: 10.1016/S0074-7696(07)61004-3
extern: '1'
intvolume: ' 261'
language:
- iso: eng
month: '06'
oa_version: None
page: 159 - 192
publication: International Review of Cytology - A Survey of Cell Biology
publication_status: published
publisher: Academic Press
publist_id: '1967'
status: public
title: 'Zebrafish gastrulation: Cell movements, signals, and mechanisms'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2007'
...
---
_id: '4182'
abstract:
- lang: eng
text: We are interested in the cellular and molecular mechanisms underlying tissue
morphogenesis during zebrafish gastrulation. Both differential cell adhesion and
contractility have been proposed to be key mechanisms by which tissues form and
rearrange in development. To obtain insight into the potential roles of differential
cell adhesion and contraction for germ layer morphogenesis during gastrulation,
we are analyzing cell adhesion and contraction of germ layer progenitor cells
using atomic force microscopy, primary tissue culture and transplantation assays.
I will present and discuss data about the differential adhesiveness and contractility
of germ layer progenitor cells in the context of germ layer formation during vertebrate
gastrulation.
acknowledgement: Abstract for the Annual Meeting of the German Societey for Cell Biology.
article_processing_charge: No
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Yohanna
full_name: Arboleda, Yohanna
last_name: Arboleda
- first_name: Daniel
full_name: Müller, Daniel
last_name: Müller
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. The role of cell adhesion and
contractility for germ layer morphogenesis during zebrafish gastrulation. European
Journal of Cell Biology. 2007;86(Supplement 1):39-39. doi:10.1016/j.ejcb.2007.02.002
apa: Krieg, M., Arboleda, Y., Müller, D., & Heisenberg, C.-P. J. (2007). The
role of cell adhesion and contractility for germ layer morphogenesis during zebrafish
gastrulation. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2007.02.002
chicago: Krieg, Michael, Yohanna Arboleda, Daniel Müller, and Carl-Philipp J Heisenberg.
“The Role of Cell Adhesion and Contractility for Germ Layer Morphogenesis during
Zebrafish Gastrulation.” European Journal of Cell Biology. Elsevier, 2007.
https://doi.org/10.1016/j.ejcb.2007.02.002.
ieee: M. Krieg, Y. Arboleda, D. Müller, and C.-P. J. Heisenberg, “The role of cell
adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation,”
European Journal of Cell Biology, vol. 86, no. Supplement 1. Elsevier,
pp. 39–39, 2007.
ista: Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. 2007. The role of cell adhesion
and contractility for germ layer morphogenesis during zebrafish gastrulation.
European Journal of Cell Biology. 86(Supplement 1), 39–39.
mla: Krieg, Michael, et al. “The Role of Cell Adhesion and Contractility for Germ
Layer Morphogenesis during Zebrafish Gastrulation.” European Journal of Cell
Biology, vol. 86, no. Supplement 1, Elsevier, 2007, pp. 39–39, doi:10.1016/j.ejcb.2007.02.002.
short: M. Krieg, Y. Arboleda, D. Müller, C.-P.J. Heisenberg, European Journal of
Cell Biology 86 (2007) 39–39.
date_created: 2018-12-11T12:07:26Z
date_published: 2007-03-22T00:00:00Z
date_updated: 2021-01-12T07:55:07Z
day: '22'
doi: 10.1016/j.ejcb.2007.02.002
extern: '1'
intvolume: ' 86'
issue: Supplement 1
language:
- iso: eng
month: '03'
oa_version: None
page: 39 - 39
publication: European Journal of Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '1937'
status: public
title: The role of cell adhesion and contractility for germ layer morphogenesis during
zebrafish gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 86
year: '2007'
...
---
_id: '4205'
abstract:
- lang: eng
text: 'Background: Bone morphogenetic proteins (Bmps) are required for the specification
of ventrolateral cell fates during embryonic dorsoventral patterning and for proper
convergence and extension gastrulation movements, but the mechanisms underlying
the latter role remained elusive. Results: Via bead implantations, we show that
the Bmp gradient determines the direction of lateral mesodermal cell migration
during dorsal convergence in the zebrafish gastrula. This effect is independent
of its role during dorsoventral patterning and of noncanonical Wnt signaling.
However, it requires Bmp signal transduction through AIk8 and Smad5 to negatively
regulate Ca2+/Cadherin-dependent cell-cell adhesiveness. In vivo, converging mesodermal
cells form lamellipodia that attach to adjacent cells. Bmp signaling diminishes
the Cadherin-dependent stability of such contact points, thereby abrogating subsequent
cell displacement during lamellipodial retraction. Conclusions: We propose that
the ventral-to-dorsal Bmp gradient has an instructive role to establish a reverse
gradient of cell-cell adhesiveness, thereby defining different migratory zones
and directing lamellipodia-driven cell migrations during dorsal convergence in
lateral regions of the zebrafish gastrula.'
article_processing_charge: No
author:
- first_name: Sophia
full_name: Von Der Hardt, Sophia
last_name: Von Der Hardt
- first_name: Jeroen
full_name: Bakkers, Jeroen
last_name: Bakkers
- first_name: Adi
full_name: Inbal, Adi
last_name: Inbal
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Lilianna
full_name: Solnica Krezel, Lilianna
last_name: Solnica Krezel
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
citation:
ama: Von Der Hardt S, Bakkers J, Inbal A, et al. The Bmp gradient of the zebrafish
gastrula guides migrating lateral cells by regulating cell-cell adhesion. Current
Biology. 2007;17(6):475-487. doi:10.1016/j.cub.2007.02.013
apa: Von Der Hardt, S., Bakkers, J., Inbal, A., Carvalho, L., Solnica Krezel, L.,
Heisenberg, C.-P. J., & Hammerschmidt, M. (2007). The Bmp gradient of the
zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion.
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2007.02.013
chicago: Von Der Hardt, Sophia, Jeroen Bakkers, Adi Inbal, Lara Carvalho, Lilianna
Solnica Krezel, Carl-Philipp J Heisenberg, and Matthias Hammerschmidt. “The Bmp
Gradient of the Zebrafish Gastrula Guides Migrating Lateral Cells by Regulating
Cell-Cell Adhesion.” Current Biology. Cell Press, 2007. https://doi.org/10.1016/j.cub.2007.02.013.
ieee: S. Von Der Hardt et al., “The Bmp gradient of the zebrafish gastrula
guides migrating lateral cells by regulating cell-cell adhesion,” Current Biology,
vol. 17, no. 6. Cell Press, pp. 475–487, 2007.
ista: Von Der Hardt S, Bakkers J, Inbal A, Carvalho L, Solnica Krezel L, Heisenberg
C-PJ, Hammerschmidt M. 2007. The Bmp gradient of the zebrafish gastrula guides
migrating lateral cells by regulating cell-cell adhesion. Current Biology. 17(6),
475–487.
mla: Von Der Hardt, Sophia, et al. “The Bmp Gradient of the Zebrafish Gastrula Guides
Migrating Lateral Cells by Regulating Cell-Cell Adhesion.” Current Biology,
vol. 17, no. 6, Cell Press, 2007, pp. 475–87, doi:10.1016/j.cub.2007.02.013.
short: S. Von Der Hardt, J. Bakkers, A. Inbal, L. Carvalho, L. Solnica Krezel, C.-P.J.
Heisenberg, M. Hammerschmidt, Current Biology 17 (2007) 475–487.
date_created: 2018-12-11T12:07:34Z
date_published: 2007-03-20T00:00:00Z
date_updated: 2021-01-12T07:55:17Z
day: '20'
doi: 10.1016/j.cub.2007.02.013
extern: '1'
intvolume: ' 17'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 475 - 487
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '1910'
status: public
title: The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by
regulating cell-cell adhesion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '4225'
abstract:
- lang: eng
text: The discovery of the genetic code was one of the most important advances of
modern biology. But there is more to a DNA code than protein sequence; DNA carries
signals for splicing, localization, folding, and regulation that are often embedded
within the protein-coding sequence. In this issue, Itzkovitz and Alon show that
the specific 64-to-20 mapping found in the genetic code may have been optimized
for permitting protein-coding regions to carry this extra information and suggest
that this property may have evolved as a side benefit of selection to minimize
the negative effects of frameshift errors.
article_processing_charge: No
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Kalin
full_name: Vetsigian, Kalin
last_name: Vetsigian
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Bollenbach MT, Vetsigian K, Kishony R. Evolution and multilevel optimization
of the genetic code. Genome Research. 2007;17(4):401-404. doi:10.1101/gr.6144007
apa: Bollenbach, M. T., Vetsigian, K., & Kishony, R. (2007). Evolution and multilevel
optimization of the genetic code. Genome Research. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gr.6144007
chicago: Bollenbach, Mark Tobias, Kalin Vetsigian, and Roy Kishony. “Evolution and
Multilevel Optimization of the Genetic Code.” Genome Research. Cold Spring
Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.6144007.
ieee: M. T. Bollenbach, K. Vetsigian, and R. Kishony, “Evolution and multilevel
optimization of the genetic code,” Genome Research, vol. 17, no. 4. Cold
Spring Harbor Laboratory Press, pp. 401–404, 2007.
ista: Bollenbach MT, Vetsigian K, Kishony R. 2007. Evolution and multilevel optimization
of the genetic code. Genome Research. 17(4), 401–404.
mla: Bollenbach, Mark Tobias, et al. “Evolution and Multilevel Optimization of the
Genetic Code.” Genome Research, vol. 17, no. 4, Cold Spring Harbor Laboratory
Press, 2007, pp. 401–04, doi:10.1101/gr.6144007.
short: M.T. Bollenbach, K. Vetsigian, R. Kishony, Genome Research 17 (2007) 401–404.
date_created: 2018-12-11T12:07:42Z
date_published: 2007-03-09T00:00:00Z
date_updated: 2021-01-12T07:55:26Z
day: '09'
doi: 10.1101/gr.6144007
extern: '1'
intvolume: ' 17'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 401 - 404
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '1891'
status: public
title: Evolution and multilevel optimization of the genetic code
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '4226'
abstract:
- lang: eng
text: 'In the developing fly wing, secreted morphogens such as Decapentaplegic (Dpp)
and Wingless (Wg) form gradients of concentration providing positional information.
Dpp forms a longer-range gradient than Wg. To understand how the range is controlled,
we measured the four key kinetic parameters governing morphogen spreading: the
production rate, the effective diffusion coefficient, the degradation rate, and
the immobile fraction. The four parameters had different values for Dpp versus
Wg. In addition, Dynamin-dependent endocytosis was required for spreading of Dpp,
but not Wg. Thus, the cellular mechanisms of Dpp and Wingless spreading are different:
Dpp spreading requires endocytic, intracellular trafficking.'
author:
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: Yannis
full_name: Kalaidzidis, Yannis
last_name: Kalaidzidis
- first_name: Thomas
full_name: Bittig, Thomas
last_name: Bittig
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Marcos
full_name: Gonzalez-Gaitan, Marcos
last_name: Gonzalez Gaitan
citation:
ama: Kicheva A, Pantazis P, Bollenbach T, et al. Kinetics of morphogen gradient
formation. Science. 2007;315(5811):521-525. doi:10.1126/science.1135774
apa: Kicheva, A., Pantazis, P., Bollenbach, T., Kalaidzidis, Y., Bittig, T., Julicher,
F., & Gonzalez Gaitan, M. (2007). Kinetics of morphogen gradient formation.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1135774
chicago: Kicheva, Anna, Periklis Pantazis, Tobias Bollenbach, Yannis Kalaidzidis,
Thomas Bittig, Frank Julicher, and Marcos Gonzalez Gaitan. “Kinetics of Morphogen
Gradient Formation.” Science. American Association for the Advancement
of Science, 2007. https://doi.org/10.1126/science.1135774.
ieee: A. Kicheva et al., “Kinetics of morphogen gradient formation,” Science,
vol. 315, no. 5811. American Association for the Advancement of Science, pp. 521–525,
2007.
ista: Kicheva A, Pantazis P, Bollenbach T, Kalaidzidis Y, Bittig T, Julicher F,
Gonzalez Gaitan M. 2007. Kinetics of morphogen gradient formation. Science. 315(5811),
521–525.
mla: Kicheva, Anna, et al. “Kinetics of Morphogen Gradient Formation.” Science,
vol. 315, no. 5811, American Association for the Advancement of Science, 2007,
pp. 521–25, doi:10.1126/science.1135774.
short: A. Kicheva, P. Pantazis, T. Bollenbach, Y. Kalaidzidis, T. Bittig, F. Julicher,
M. Gonzalez Gaitan, Science 315 (2007) 521–525.
date_created: 2018-12-11T12:07:42Z
date_published: 2007-01-26T00:00:00Z
date_updated: 2021-01-12T07:55:26Z
day: '26'
doi: 10.1126/science.1135774
extern: 1
intvolume: ' 315'
issue: '5811'
month: '01'
page: 521 - 525
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '1892'
quality_controlled: 0
status: public
title: Kinetics of morphogen gradient formation
type: journal_article
volume: 315
year: '2007'
...
---
_id: '4233'
article_processing_charge: No
author:
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
citation:
ama: 'de Vladar H. Alternativas prebióticas para la síntesis de amino- ácidos y
otras moléculas relacionadas. In: Falcón N, Loyo De Sardi Y, eds. Consejo de Desarrollo
Cientifico y Tecnologico; 2007:91-109.'
apa: 'de Vladar, H. (2007). Alternativas prebióticas para la síntesis de amino-
ácidos y otras moléculas relacionadas. In N. Falcón & Y. Loyo De Sardi (Eds.)
(pp. 91–109). Presented at the Ab Initio: Orígenes Del Universo, La Vida, Y La
Inteligencia, Consejo de Desarrollo Cientifico y Tecnologico.'
chicago: Vladar, Harold de. “Alternativas Prebióticas Para La Síntesis de Amino-
Ácidos y Otras Moléculas Relacionadas.” edited by N. Falcón and Y. Loyo De Sardi,
91–109. Consejo de Desarrollo Cientifico y Tecnologico, 2007.
ieee: 'H. de Vladar, “Alternativas prebióticas para la síntesis de amino- ácidos
y otras moléculas relacionadas,” presented at the Ab Initio: Orígenes Del Universo,
La Vida, Y La Inteligencia, 2007, pp. 91–109.'
ista: 'de Vladar H. 2007. Alternativas prebióticas para la síntesis de amino- ácidos
y otras moléculas relacionadas. Ab Initio: Orígenes Del Universo, La Vida, Y La
Inteligencia, 91–109.'
mla: de Vladar, Harold. Alternativas Prebióticas Para La Síntesis de Amino- Ácidos
y Otras Moléculas Relacionadas. Edited by N. Falcón and Y. Loyo De Sardi,
Consejo de Desarrollo Cientifico y Tecnologico, 2007, pp. 91–109.
short: H. de Vladar, in:, N. Falcón, Y. Loyo De Sardi (Eds.), Consejo de Desarrollo
Cientifico y Tecnologico, 2007, pp. 91–109.
conference:
name: 'Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia'
date_created: 2018-12-11T12:07:45Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2025-07-01T13:09:25Z
day: '01'
editor:
- first_name: N.
full_name: Falcón, N.
last_name: Falcón
- first_name: Y.
full_name: Loyo De Sardi, Y.
last_name: Loyo De Sardi
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 91 - 109
publication_status: published
publisher: Consejo de Desarrollo Cientifico y Tecnologico
publist_id: '1880'
status: public
title: Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas
relacionadas
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2007'
...
---
_id: '4234'
abstract:
- lang: eng
text: We study a generalised model of population growth in which the state variable
is population growth rate instead of population size. Stochastic parametric perturbations,
modelling phenotypic variability, lead to a Langevin system with two sources of
multiplicative noise. The stationary probability distributions have two characteristic
power-law scales. Numerical simulations show that noise suppresses the explosion
of the growth rate which occurs in the deterministic counterpart. Instead, in
different parameter regimes populations will grow with "anomalous" stochastic
rates and (i) stabilise at "random carrying capacities", or (ii) go
extinct in random times. Using logistic fits to reconstruct the simulated data,
we find that even highly significant estimations do not recover or reflect information
about the deterministic part of the process. Therefore, the logistic interpretation
is not biologically meaningful. These results have implications for distinct model-aided
calculations in biological situations because these kinds of estimations could
lead to spurious conclusions. (c) 2006 Elsevier B.V. All rights reserved.
article_processing_charge: No
arxiv: 1
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: I.
full_name: Pen, I.
last_name: Pen
citation:
ama: de Vladar H, Pen I. Determinism, noise, and spurious estimations in a generalised
model of population growth. Physica A. 2007;373:477-485. doi:10.1016/j.physa.2006.06.025
apa: de Vladar, H., & Pen, I. (2007). Determinism, noise, and spurious estimations
in a generalised model of population growth. Physica A. Elsevier. https://doi.org/10.1016/j.physa.2006.06.025
chicago: Vladar, Harold de, and I. Pen. “Determinism, Noise, and Spurious Estimations
in a Generalised Model of Population Growth.” Physica A. Elsevier, 2007.
https://doi.org/10.1016/j.physa.2006.06.025.
ieee: H. de Vladar and I. Pen, “Determinism, noise, and spurious estimations in
a generalised model of population growth,” Physica A, vol. 373. Elsevier,
pp. 477–485, 2007.
ista: de Vladar H, Pen I. 2007. Determinism, noise, and spurious estimations in
a generalised model of population growth. Physica A. 373, 477–485.
mla: de Vladar, Harold, and I. Pen. “Determinism, Noise, and Spurious Estimations
in a Generalised Model of Population Growth.” Physica A, vol. 373, Elsevier,
2007, pp. 477–85, doi:10.1016/j.physa.2006.06.025.
short: H. de Vladar, I. Pen, Physica A 373 (2007) 477–485.
date_created: 2018-12-11T12:07:45Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:30Z
day: '01'
doi: 10.1016/j.physa.2006.06.025
extern: '1'
external_id:
arxiv:
- abs/q-bio/0602018
intvolume: ' 373'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0602018
month: '01'
oa: 1
oa_version: Preprint
page: 477 - 485
publication: Physica A
publication_status: published
publisher: Elsevier
publist_id: '1881'
status: public
title: Determinism, noise, and spurious estimations in a generalised model of population
growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 373
year: '2007'
...
---
_id: '4246'
abstract:
- lang: eng
text: Gaia theory, which describes the life–environment system of the Earth as stable
and self-regulating, has remained at the fringes of mainstream biological science
owing to its historically inadequate definition and apparent incompatibility with
individual-level natural selection. The key issue is whether and why the biosphere
might tend towards stability and self-regulation. We review the various ways in
which these issues have been addressed by evolutionary and ecological theory,
and relate these to ‘Gaia theory’. We then ask how this theory extends the perspectives
offered by these disciplines, and how it might be tested by novel modelling approaches
and laboratory experiments using emergent technologies.
author:
- first_name: Andrew
full_name: Free, Andrew
last_name: Free
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Free A, Barton NH. Do evolution and ecology need the Gaia hypothesis? Trends
in Ecology and Evolution. 2007;22(11):611-619. doi:10.1016/j.tree.2007.07.007
apa: Free, A., & Barton, N. H. (2007). Do evolution and ecology need the Gaia
hypothesis? Trends in Ecology and Evolution. Cell Press. https://doi.org/10.1016/j.tree.2007.07.007
chicago: Free, Andrew, and Nicholas H Barton. “Do Evolution and Ecology Need the
Gaia Hypothesis?” Trends in Ecology and Evolution. Cell Press, 2007. https://doi.org/10.1016/j.tree.2007.07.007.
ieee: A. Free and N. H. Barton, “Do evolution and ecology need the Gaia hypothesis?,”
Trends in Ecology and Evolution, vol. 22, no. 11. Cell Press, pp. 611–619,
2007.
ista: Free A, Barton NH. 2007. Do evolution and ecology need the Gaia hypothesis?
Trends in Ecology and Evolution. 22(11), 611–619.
mla: Free, Andrew, and Nicholas H. Barton. “Do Evolution and Ecology Need the Gaia
Hypothesis?” Trends in Ecology and Evolution, vol. 22, no. 11, Cell Press,
2007, pp. 611–19, doi:10.1016/j.tree.2007.07.007.
short: A. Free, N.H. Barton, Trends in Ecology and Evolution 22 (2007) 611–619.
date_created: 2018-12-11T12:07:49Z
date_published: 2007-11-01T00:00:00Z
date_updated: 2021-01-12T07:55:35Z
day: '01'
doi: 10.1016/j.tree.2007.07.007
extern: 1
intvolume: ' 22'
issue: '11'
month: '11'
page: 611 - 619
publication: Trends in Ecology and Evolution
publication_status: published
publisher: Cell Press
publist_id: '1856'
quality_controlled: 0
status: public
title: Do evolution and ecology need the Gaia hypothesis?
type: journal_article
volume: 22
year: '2007'
...
---
_id: '4247'
abstract:
- lang: eng
text: Evolution at multiple gene positions is complicated. Direct selection on one
gene disturbs the evolutionary dynamics of associated genes. Recent years have
seen the development of a multilocus methodology for modeling evolution at arbitrary
numbers of gene positions with arbitrary dominance and epistatic relations, mode
of inheritance, genetic linkage, and recombination. We show that the approach
is conceptually analogous to social evolutionary methodology, which focuses on
selection acting on associated individuals. In doing so, we (1) make explicit
the links between the multilocus methodology and the foundations of social evolution
theory, namely, Price’s theorem and Hamilton’s rule; (2) relate the multilocus
approach to levels‐of‐selection and neighbor‐modulated‐fitness approaches in social
evolution; (3) highlight the equivalence between genetical hitchhiking and kin
selection; (4) demonstrate that the multilocus methodology allows for social evolutionary
analyses involving coevolution of multiple traits and genetical associations between
nonrelatives, including individuals of different species; (5) show that this methodology
helps solve problems of dynamic sufficiency in social evolution theory; (6) form
links between invasion criteria in multilocus systems and Hamilton’s rule of kin
selection; (7) illustrate the generality and exactness of Hamilton’s rule, which
has previously been described as an approximate, heuristic result.
author:
- first_name: Andy
full_name: Gardner, Andy
last_name: Gardner
- first_name: Stuart
full_name: West, Stuart A
last_name: West
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Gardner A, West S, Barton NH. The relation between multilocus population genetics
and social evolution theory. American Naturalist. 2007;169(2):207-226.
doi:10.1086/510602
apa: Gardner, A., West, S., & Barton, N. H. (2007). The relation between multilocus
population genetics and social evolution theory. American Naturalist. University
of Chicago Press. https://doi.org/10.1086/510602
chicago: Gardner, Andy, Stuart West, and Nicholas H Barton. “The Relation between
Multilocus Population Genetics and Social Evolution Theory.” American Naturalist.
University of Chicago Press, 2007. https://doi.org/10.1086/510602.
ieee: A. Gardner, S. West, and N. H. Barton, “The relation between multilocus population
genetics and social evolution theory,” American Naturalist, vol. 169, no.
2. University of Chicago Press, pp. 207–226, 2007.
ista: Gardner A, West S, Barton NH. 2007. The relation between multilocus population
genetics and social evolution theory. American Naturalist. 169(2), 207–226.
mla: Gardner, Andy, et al. “The Relation between Multilocus Population Genetics
and Social Evolution Theory.” American Naturalist, vol. 169, no. 2, University
of Chicago Press, 2007, pp. 207–26, doi:10.1086/510602.
short: A. Gardner, S. West, N.H. Barton, American Naturalist 169 (2007) 207–226.
date_created: 2018-12-11T12:07:50Z
date_published: 2007-02-01T00:00:00Z
date_updated: 2021-01-12T07:55:35Z
day: '01'
doi: 10.1086/510602
extern: 1
intvolume: ' 169'
issue: '2'
month: '02'
page: 207 - 226
publication: American Naturalist
publication_status: published
publisher: University of Chicago Press
publist_id: '1857'
quality_controlled: 0
status: public
title: The relation between multilocus population genetics and social evolution theory
type: journal_article
volume: 169
year: '2007'
...