---
_id: '11910'
abstract:
- lang: eng
text: "We state a new sampling lemma and use it to improve the running time of dynamic
graph algorithms.\r\n\r\nFor the dynamic connectivity problem the previously best
randomized algorithm takes expected time O(log3 n) per update, amortized over
Ω(m) updates. Using the new sampling lemma, we improve its running time to O(log2
n). There exists a lower bound in the cell probe model for the time per operation
of Ω(log n/ log log n) for this problem.\r\n\r\nSimilarly improved running times
are achieved for 2-edge connectivity, k-weight minimum spanning tree, and bipartiteness."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Mikkel
full_name: Thorup, Mikkel
last_name: Thorup
citation:
ama: 'Henzinger MH, Thorup M. Improved sampling with applications to dynamic graph
algorithms. In: 23rd International Colloquium on Automata, Languages, and Programming.
Vol 1099. Springer Nature; 1996:290-299. doi:10.1007/3-540-61440-0_136'
apa: 'Henzinger, M. H., & Thorup, M. (1996). Improved sampling with applications
to dynamic graph algorithms. In 23rd International Colloquium on Automata,
Languages, and Programming (Vol. 1099, pp. 290–299). Paderborn, Germany: Springer
Nature. https://doi.org/10.1007/3-540-61440-0_136'
chicago: Henzinger, Monika H, and Mikkel Thorup. “Improved Sampling with Applications
to Dynamic Graph Algorithms.” In 23rd International Colloquium on Automata,
Languages, and Programming, 1099:290–99. Springer Nature, 1996. https://doi.org/10.1007/3-540-61440-0_136.
ieee: M. H. Henzinger and M. Thorup, “Improved sampling with applications to dynamic
graph algorithms,” in 23rd International Colloquium on Automata, Languages,
and Programming, Paderborn, Germany, 1996, vol. 1099, pp. 290–299.
ista: 'Henzinger MH, Thorup M. 1996. Improved sampling with applications to dynamic
graph algorithms. 23rd International Colloquium on Automata, Languages, and Programming.
ICALP: International Colloquium on Automata, Languages, and Programming, LNCS,
vol. 1099, 290–299.'
mla: Henzinger, Monika H., and Mikkel Thorup. “Improved Sampling with Applications
to Dynamic Graph Algorithms.” 23rd International Colloquium on Automata, Languages,
and Programming, vol. 1099, Springer Nature, 1996, pp. 290–99, doi:10.1007/3-540-61440-0_136.
short: M.H. Henzinger, M. Thorup, in:, 23rd International Colloquium on Automata,
Languages, and Programming, Springer Nature, 1996, pp. 290–299.
conference:
end_date: 1996-07-12
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 1996-07-08
date_created: 2022-08-18T06:42:24Z
date_published: 1996-07-01T00:00:00Z
date_updated: 2023-02-14T07:57:14Z
day: '01'
doi: 10.1007/3-540-61440-0_136
extern: '1'
intvolume: ' 1099'
language:
- iso: eng
month: '07'
oa_version: None
page: 290-299
publication: 23rd International Colloquium on Automata, Languages, and Programming
publication_identifier:
eisbn:
- '9783540685807'
eissn:
- 1611-3349
isbn:
- '9783540614401'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved sampling with applications to dynamic graph algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1099
year: '1996'
...
---
_id: '11927'
abstract:
- lang: eng
text: "We are given a set 7 = {Tl , Tz, . . . , Tk} of rooted binary trees, each
Ti leaf-labeled by a subset L(x) c {1,2 )...) n}. IfT is a tree on {1,2, . . ,
n}, we let T]L denote the subtree of T induced by the nodes of L and all their
ancestors. The consensus tree problem asks whether there exists a tree T* such
that for every I, T’ IC(Ti) is homeomorphic to Ti. We present algorithms which
test if a given set of trees has a consensus tree and if so, construct one. The
deterministic algorithm takes time min{O(mn’/‘), O(m + n2 logn)}, where m = Ci
IZl and uses linear space. The randomized algorithm takes\r\ntime O(m log3 n)
and uses linear space. The previous best for this problem was an 1981 O(mn) algorithm
by Aho et al. Our faster deterministic algorithm uses a new efficient algorithm
for the following interesting dynamic graph problem: Given a graph G with n nodes
and m edges and a sequence of b batches of one or more edge deletions, then after
each batch, either find a new component that has just been created or determine
that there is no such component. For this\r\nproblem, we have a simple algorithm
with running time O(n2 log n + be min{ n2, m log n}), where be is the number of
batches which do not result in a new component. For our particular application,
bc 5 1. If all edges are deleted, then the best previously known deterministic
algorithm requires time O(mJ;ii) to solve this problem. computational evolutionary
biology. The first application is in the problem of inferring consensus of trees
when there can be disagreement[l6]. There have, been several models suggested
for this problem[2, 3, 4, 8, ?, 11, 17, 181, of which one is called the Local
Consensus Tree[l5]. The local consensus tree model presumes that the user provides
a local consensus rule which determines the form of the output tree on (perhaps)
each triple of leaves, and the objective is to determine whether a tree exists
which is consistent with each of the constraints. We will show that we can construct
the local consensus tree of k trees on n species in O(kn3) time, improving on
the O(lcn3 + n”) running time if we use the Aho et al algorithm. The second application
is a\r\nheuristic for constructing the maximum likelihood tree based upon combining
solutions to small subproblems.\r\nThis is a simple and yet potentially significantly
interesting approach to the evolutionary tree construction\r\nproblem. "
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Valerie
full_name: King, Valerie
last_name: King
- first_name: Tandy
full_name: Warnow, Tandy
last_name: Warnow
citation:
ama: 'Henzinger MH, King V, Warnow T. Constructing a tree from homeomorphic subtrees,
with applications to computational evolutionary biology. In: 7th Annual ACM-SIAM
Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics;
1996:333-340.'
apa: 'Henzinger, M. H., King, V., & Warnow, T. (1996). Constructing a tree from
homeomorphic subtrees, with applications to computational evolutionary biology.
In 7th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 333–340).
Atlanta, GA, United States: Society for Industrial and Applied Mathematics.'
chicago: Henzinger, Monika H, Valerie King, and Tandy Warnow. “Constructing a Tree
from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology.”
In 7th Annual ACM-SIAM Symposium on Discrete Algorithms, 333–40. Society
for Industrial and Applied Mathematics, 1996.
ieee: M. H. Henzinger, V. King, and T. Warnow, “Constructing a tree from homeomorphic
subtrees, with applications to computational evolutionary biology,” in 7th
Annual ACM-SIAM Symposium on Discrete Algorithms, Atlanta, GA, United States,
1996, pp. 333–340.
ista: 'Henzinger MH, King V, Warnow T. 1996. Constructing a tree from homeomorphic
subtrees, with applications to computational evolutionary biology. 7th Annual
ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms,
333–340.'
mla: Henzinger, Monika H., et al. “Constructing a Tree from Homeomorphic Subtrees,
with Applications to Computational Evolutionary Biology.” 7th Annual ACM-SIAM
Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics,
1996, pp. 333–40.
short: M.H. Henzinger, V. King, T. Warnow, in:, 7th Annual ACM-SIAM Symposium on
Discrete Algorithms, Society for Industrial and Applied Mathematics, 1996, pp.
333–340.
conference:
end_date: 1996-01-30
location: Atlanta, GA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 1996-01-28
date_created: 2022-08-19T06:57:47Z
date_published: 1996-01-28T00:00:00Z
date_updated: 2023-02-21T16:24:53Z
day: '28'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.5555/313852.314080
month: '01'
oa: 1
oa_version: Published Version
page: 333 -340
publication: 7th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '0898713668'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '11679'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Constructing a tree from homeomorphic subtrees, with applications to computational
evolutionary biology
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '1996'
...
---
_id: '3462'
article_processing_charge: No
article_type: original
author:
- first_name: Thorsten
full_name: Melcher, Thorsten
last_name: Melcher
- first_name: Jörg
full_name: Geiger, Jörg
last_name: Geiger
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Hannah
full_name: Monyer, Hannah
last_name: Monyer
citation:
ama: Melcher T, Geiger J, Jonas PM, Monyer H. Analysis of molecular determinants
in native AMPA receptors. Neurochemistry International. 1996;28(2):141-144.
doi:10.1016/0197-0186(95)00077-1
apa: Melcher, T., Geiger, J., Jonas, P. M., & Monyer, H. (1996). Analysis of
molecular determinants in native AMPA receptors. Neurochemistry International.
Elsevier. https://doi.org/10.1016/0197-0186(95)00077-1
chicago: Melcher, Thorsten, Jörg Geiger, Peter M Jonas, and Hannah Monyer. “Analysis
of Molecular Determinants in Native AMPA Receptors.” Neurochemistry International.
Elsevier, 1996. https://doi.org/10.1016/0197-0186(95)00077-1.
ieee: T. Melcher, J. Geiger, P. M. Jonas, and H. Monyer, “Analysis of molecular
determinants in native AMPA receptors,” Neurochemistry International, vol.
28, no. 2. Elsevier, pp. 141–144, 1996.
ista: Melcher T, Geiger J, Jonas PM, Monyer H. 1996. Analysis of molecular determinants
in native AMPA receptors. Neurochemistry International. 28(2), 141–144.
mla: Melcher, Thorsten, et al. “Analysis of Molecular Determinants in Native AMPA
Receptors.” Neurochemistry International, vol. 28, no. 2, Elsevier, 1996,
pp. 141–44, doi:10.1016/0197-0186(95)00077-1.
short: T. Melcher, J. Geiger, P.M. Jonas, H. Monyer, Neurochemistry International
28 (1996) 141–144.
date_created: 2018-12-11T12:03:27Z
date_published: 1996-02-01T00:00:00Z
date_updated: 2022-08-11T09:42:29Z
day: '01'
doi: 10.1016/0197-0186(95)00077-1
extern: '1'
external_id:
pmid:
- '8719701 '
intvolume: ' 28'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 141 - 144
pmid: 1
publication: Neurochemistry International
publication_identifier:
issn:
- 0197-0186
publication_status: published
publisher: Elsevier
publist_id: '2925'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of molecular determinants in native AMPA receptors
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 28
year: '1996'
...
---
_id: '3553'
abstract:
- lang: eng
text: Virtual environments open up new opportunities and challenges for geometric
modeling systems. A general approach to geometric modeling suitable for the Cave
Automatic Virtual Environment is described. The approach is based on alpha complexes,
and some of its capabilities are demonstrated by applying it to the study of biomolecules.
acknowledgement: We thank Ernst Miicke and Michael Facello for their work on the Alpha
shape library, and Nataraj Akkiraju for his work on the surface triangulation library.
We thank NCSA for providing access to the CAVE.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
- first_name: Jiang
full_name: Quian, Jiang
last_name: Quian
citation:
ama: 'Edelsbrunner H, Fu P, Quian J. Geometric modeling in CAVE. In: Proceedings
of the ACM Symposium on Virtual Reality Software and Technology. ACM; 1996:35-41
and-193-194. doi:10.1145/3304181.3304190'
apa: 'Edelsbrunner, H., Fu, P., & Quian, J. (1996). Geometric modeling in CAVE.
In Proceedings of the ACM Symposium on Virtual Reality Software and Technology
(pp. 35-41 and-193–194). Hong Kong: ACM. https://doi.org/10.1145/3304181.3304190'
chicago: Edelsbrunner, Herbert, Ping Fu, and Jiang Quian. “Geometric Modeling in
CAVE.” In Proceedings of the ACM Symposium on Virtual Reality Software and
Technology, 35-41 and-193–94. ACM, 1996. https://doi.org/10.1145/3304181.3304190.
ieee: H. Edelsbrunner, P. Fu, and J. Quian, “Geometric modeling in CAVE,” in Proceedings
of the ACM Symposium on Virtual Reality Software and Technology, Hong Kong,
1996, pp. 35-41 and-193–194.
ista: 'Edelsbrunner H, Fu P, Quian J. 1996. Geometric modeling in CAVE. Proceedings
of the ACM Symposium on Virtual Reality Software and Technology. VRST: Symposium
on Virtual Reality Software and Technology, 35-41 and-193–194.'
mla: Edelsbrunner, Herbert, et al. “Geometric Modeling in CAVE.” Proceedings
of the ACM Symposium on Virtual Reality Software and Technology, ACM, 1996,
pp. 35-41 and-193–94, doi:10.1145/3304181.3304190.
short: H. Edelsbrunner, P. Fu, J. Quian, in:, Proceedings of the ACM Symposium on
Virtual Reality Software and Technology, ACM, 1996, pp. 35-41 and-193–194.
conference:
end_date: 1996-07-04
location: Hong Kong
name: 'VRST: Symposium on Virtual Reality Software and Technology'
start_date: 1996-07-01
date_created: 2018-12-11T12:03:56Z
date_published: 1996-07-01T00:00:00Z
date_updated: 2022-08-10T13:42:02Z
day: '01'
doi: 10.1145/3304181.3304190
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 35-41 and - 193-194
publication: Proceedings of the ACM Symposium on Virtual Reality Software and Technology
publication_identifier:
isbn:
- '9780897918251'
publication_status: published
publisher: ACM
publist_id: '2832'
quality_controlled: '1'
status: public
title: Geometric modeling in CAVE
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1996'
...
---
_id: '3634'
abstract:
- lang: eng
text: The evolutionary processes responsible for adaptation and speciation on islands
differ in several ways from those on the mainland. Most attention has been given
to the random genetic drift that arises when a population is founded from just
a few colonizing genomes. Theoretical obstacles to 'founder effect speciation'
are discussed, together with recent proposals for avoiding them. It is argued
that although certain kinds of epistasis can facilitate the evolution of strong
reproductive isolation, this favours divergence by selection as much as by random
drift.
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: James
full_name: Mallet, James
last_name: Mallet
citation:
ama: Barton NH, Mallet J. Natural selection and random genetic drift as causes of
evolution on islands. Philosophical Transactions of the Royal Society of London
Series B, Biological Sciences. 1996;351(1341):785-795. doi:10.1098/rstb.1996.0073
apa: Barton, N. H., & Mallet, J. (1996). Natural selection and random genetic
drift as causes of evolution on islands. Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society of London.
https://doi.org/10.1098/rstb.1996.0073
chicago: Barton, Nicholas H, and James Mallet. “Natural Selection and Random Genetic
Drift as Causes of Evolution on Islands.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society of London,
1996. https://doi.org/10.1098/rstb.1996.0073.
ieee: N. H. Barton and J. Mallet, “Natural selection and random genetic drift as
causes of evolution on islands,” Philosophical Transactions of the Royal Society
of London. Series B, Biological Sciences, vol. 351, no. 1341. Royal Society
of London, pp. 785–795, 1996.
ista: Barton NH, Mallet J. 1996. Natural selection and random genetic drift as causes
of evolution on islands. Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences. 351(1341), 785–795.
mla: Barton, Nicholas H., and James Mallet. “Natural Selection and Random Genetic
Drift as Causes of Evolution on Islands.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 351, no. 1341,
Royal Society of London, 1996, pp. 785–95, doi:10.1098/rstb.1996.0073.
short: N.H. Barton, J. Mallet, Philosophical Transactions of the Royal Society of
London. Series B, Biological Sciences 351 (1996) 785–795.
date_created: 2018-12-11T12:04:21Z
date_published: 1996-06-29T00:00:00Z
date_updated: 2022-08-10T12:57:10Z
day: '29'
doi: 10.1098/rstb.1996.0073
extern: '1'
external_id:
pmid:
- '8693020'
intvolume: ' 351'
issue: '1341'
language:
- iso: eng
month: '06'
oa_version: None
page: 785 - 795
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_identifier:
issn:
- 0962-8436
publication_status: published
publisher: Royal Society of London
publist_id: '2749'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural selection and random genetic drift as causes of evolution on islands
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 351
year: '1996'
...
---
_id: '3635'
abstract:
- lang: eng
text: Experiments on Drosophila suggest that genetic recombination may result in
lowered fitness of progeny (a 'recombination load'). This has been interpreted
as evidence either for a direct effect of recombination on fitness, or for the
maintenance of linkage disequilibria by epistatic selection. Here we show that
such a recombination load is to be expected even if selection favours increased
genetic recombination. This is because of the fact that, although a modifier may
suffer an immediate loss of fitness if it increases recombination, it eventually
becomes associated with a higher additive genetic variance in fitness, which allows
a faster response to direction selection. This argument applies to mutation-selection
balance with synergistic epistasis, directional selection on quantitative traits,
and ectopic exchange among transposable elements. Further experiments are needed
to determine whether the selection against recombination due to the immediate
load is outweighed by the increased additive variance in fitness produced by recombination.
article_processing_charge: No
article_type: original
author:
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Charlesworth B, Barton NH. Recombination load associated with selection for
increased recombination. Genetical Research. 1996;67(1):27-41. doi:10.1017/S0016672300033450
apa: Charlesworth, B., & Barton, N. H. (1996). Recombination load associated
with selection for increased recombination. Genetical Research. Cambridge
University Press. https://doi.org/10.1017/S0016672300033450
chicago: Charlesworth, Brian, and Nicholas H Barton. “Recombination Load Associated
with Selection for Increased Recombination.” Genetical Research. Cambridge
University Press, 1996. https://doi.org/10.1017/S0016672300033450.
ieee: B. Charlesworth and N. H. Barton, “Recombination load associated with selection
for increased recombination,” Genetical Research, vol. 67, no. 1. Cambridge
University Press, pp. 27–41, 1996.
ista: Charlesworth B, Barton NH. 1996. Recombination load associated with selection
for increased recombination. Genetical Research. 67(1), 27–41.
mla: Charlesworth, Brian, and Nicholas H. Barton. “Recombination Load Associated
with Selection for Increased Recombination.” Genetical Research, vol. 67,
no. 1, Cambridge University Press, 1996, pp. 27–41, doi:10.1017/S0016672300033450.
short: B. Charlesworth, N.H. Barton, Genetical Research 67 (1996) 27–41.
date_created: 2018-12-11T12:04:21Z
date_published: 1996-02-01T00:00:00Z
date_updated: 2022-08-10T12:38:51Z
day: '01'
doi: 10.1017/S0016672300033450
extern: '1'
external_id:
pmid:
- '8919888 '
intvolume: ' 67'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 27 - 41
pmid: 1
publication: Genetical Research
publication_identifier:
issn:
- 0016-6723
publication_status: published
publisher: Cambridge University Press
publist_id: '2748'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recombination load associated with selection for increased recombination
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 67
year: '1996'
...
---
_id: '3756'
abstract:
- lang: eng
text: 'In many eukaryotic cells going through M-phase, a bipolar spindle is formed
by microtubules nucleated from centrosomes. These microtubules, in addition to
being `''captured” by kinetochores, may be stabilized by chromatin in two different
ways: short-range stabilization effects may affect microtubules in close contact
with the chromatin, while long-range stabilization effects may `''guide” microtubule
growth towards the chromatin (e.g., by introducing a diffusive gradient of an
enzymatic activity that affects microtubule assembly). Here, we use both meiotic
and mitotic extracts from Xenopus laevis eggs to study microtubule aster formation
and microtubule dynamics in the presence of chromatin. In `''low-speed” meiotic
extracts, in the presence of salmon sperm chromatin, we find that short-range
stabilization effects lead to a strong anisotropy of the microtubule asters. Analysis
of the dynamic parameters of microtubule growth shows that this anisotropy arises
from a decrease in the catastrophe frequency, an increase in the rescue frequency
and a decrease in the growth velocity. In this system we also find evidence for
long-range `''guidance” effects, which lead to a weak anisotropy of the asters.
Statistically relevant results on these long-range effects are obtained in `''high-speed”
mitotic extracts in the presence of artificially constructed chromatin stripes.
We find that aster anisotropy is biased in the direction of the chromatin and
that the catastrophe frequency is reduced in its vicinity. In this system we also
find a surprising dependence of the catastrophe and the rescue frequencies on
the length of microtubules nucleated from centrosomes: the catastrophe frequency
increases and the rescue frequency decreases with microtubule length.'
acknowledgement: "We would like to thank T. Holy and T. Mitchison for providing us
with centrosomes; M. Glotzer and T. Mitchison for giving us the plasmid for A90
cyclin B; J. Stock and members of his laboratory for help with biochemical preparations;
R. Zimmerman for help with the biotinylation of DNA; J. Shepard for help with the
patterning of surfaces; D. Tsui for use\r\nof his clean room facility, and D. Fygenson,
T. Holy, E. Karsenti, E. Kennedy, A. Levine, T. Mitchison, and G. Waters for valuable
discussions, constant encouragement and technical help. This work was partially
supported by the National Institutes of Health (Grant No. GM-50712) and the Human
Frontier Science Program."
article_processing_charge: No
article_type: original
author:
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
- first_name: M.
full_name: Felix, M.
last_name: Felix
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Stanislas
full_name: Leibler, Stanislas
last_name: Leibler
citation:
ama: 'Dogterom M, Felix M, Guet CC, Leibler S. Influence of M-phase chromatin on
the anisotropy of microtubule asters. Journal of Cell Biology. 1996;133(1):125-140.
doi:doi: 10.1083/jcb.133.1.125
'
apa: 'Dogterom, M., Felix, M., Guet, C. C., & Leibler, S. (1996). Influence
of M-phase chromatin on the anisotropy of microtubule asters. Journal of Cell
Biology. Rockefeller University Press. https://doi.org/doi: 10.1083/jcb.133.1.125 '
chicago: 'Dogterom, Marileen, M. Felix, Calin C Guet, and Stanislas Leibler. “Influence
of M-Phase Chromatin on the Anisotropy of Microtubule Asters.” Journal of Cell
Biology. Rockefeller University Press, 1996. https://doi.org/doi: 10.1083/jcb.133.1.125 .'
ieee: M. Dogterom, M. Felix, C. C. Guet, and S. Leibler, “Influence of M-phase chromatin
on the anisotropy of microtubule asters,” Journal of Cell Biology, vol.
133, no. 1. Rockefeller University Press, pp. 125–140, 1996.
ista: Dogterom M, Felix M, Guet CC, Leibler S. 1996. Influence of M-phase chromatin
on the anisotropy of microtubule asters. Journal of Cell Biology. 133(1), 125–140.
mla: 'Dogterom, Marileen, et al. “Influence of M-Phase Chromatin on the Anisotropy
of Microtubule Asters.” Journal of Cell Biology, vol. 133, no. 1, Rockefeller
University Press, 1996, pp. 125–40, doi:doi: 10.1083/jcb.133.1.125 .'
short: M. Dogterom, M. Felix, C.C. Guet, S. Leibler, Journal of Cell Biology 133
(1996) 125–140.
date_created: 2018-12-11T12:05:00Z
date_published: 1996-01-01T00:00:00Z
date_updated: 2022-08-09T14:20:13Z
day: '01'
doi: 'doi: 10.1083/jcb.133.1.125 '
extern: '1'
external_id:
pmid:
- '8601601'
intvolume: ' 133'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2120784/
month: '01'
oa: 1
oa_version: Published Version
page: 125 - 140
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
publist_id: '2473'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Influence of M-phase chromatin on the anisotropy of microtubule asters
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 133
year: '1996'
...
---
_id: '4024'
abstract:
- lang: eng
text: We have developed general modeling software for a Cave Automatic Virtual Environment
(CAVE); one of its applications is modeling 3D protein structures, generating
both outside-in and inside-out views of geometric models. An advantage of the
CAVE over other virtual environments is that multiple viewers can observe the
same scene at the same time and place. Our software is scalable-from high-end
virtual environments such as the CAVE, to mid-range immersive desktop systems,
down to low-end graphics workstations. In the current configuration, a parallel
Silicon Graphics Power Challenge supercomputer architecture performs the computationally
intensive construction of surface patches remotely, and sends the results through
the I-WAY (Information Wide Area Year) using VBNS (Very-high-Bandwidth Network
Systems) to the graphics machines that drive the CAVE and our graphics visualization
software, Valvis (Virtual ALpha shapes VISualizer).
article_processing_charge: No
article_type: original
author:
- first_name: Nataraj
full_name: Akkiraju, Nataraj
last_name: Akkiraju
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
- first_name: Jiang
full_name: Qian, Jiang
last_name: Qian
citation:
ama: Akkiraju N, Edelsbrunner H, Fu P, Qian J. Viewing geometric protein structures
from inside a CAVE. IEEE Computer Graphics and Applications. 1996;16(4):58-61.
doi:10.1109/38.511855
apa: Akkiraju, N., Edelsbrunner, H., Fu, P., & Qian, J. (1996). Viewing geometric
protein structures from inside a CAVE. IEEE Computer Graphics and Applications.
IEEE. https://doi.org/10.1109/38.511855
chicago: Akkiraju, Nataraj, Herbert Edelsbrunner, Ping Fu, and Jiang Qian. “Viewing
Geometric Protein Structures from inside a CAVE.” IEEE Computer Graphics and
Applications. IEEE, 1996. https://doi.org/10.1109/38.511855.
ieee: N. Akkiraju, H. Edelsbrunner, P. Fu, and J. Qian, “Viewing geometric protein
structures from inside a CAVE,” IEEE Computer Graphics and Applications,
vol. 16, no. 4. IEEE, pp. 58–61, 1996.
ista: Akkiraju N, Edelsbrunner H, Fu P, Qian J. 1996. Viewing geometric protein
structures from inside a CAVE. IEEE Computer Graphics and Applications. 16(4),
58–61.
mla: Akkiraju, Nataraj, et al. “Viewing Geometric Protein Structures from inside
a CAVE.” IEEE Computer Graphics and Applications, vol. 16, no. 4, IEEE,
1996, pp. 58–61, doi:10.1109/38.511855.
short: N. Akkiraju, H. Edelsbrunner, P. Fu, J. Qian, IEEE Computer Graphics and
Applications 16 (1996) 58–61.
date_created: 2018-12-11T12:06:30Z
date_published: 1996-07-01T00:00:00Z
date_updated: 2022-08-09T13:32:21Z
day: '01'
doi: 10.1109/38.511855
extern: '1'
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
page: 58 - 61
publication: IEEE Computer Graphics and Applications
publication_identifier:
issn:
- 0018-9162
publication_status: published
publisher: IEEE
publist_id: '2101'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Viewing geometric protein structures from inside a CAVE
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 16
year: '1996'
...
---
_id: '4025'
abstract:
- lang: eng
text: Questions of chemical reactivity can often be cast as questions of molecular
geometry. Common geometric models for proteins and other molecules are the space-filling
diagram, the solvent accessible surface and the molecular surface. In this paper
we present a new approach to triangulating the surface of a molecule under the
three models, which is fast, robust, and results in topologically correct triangulations.
Our computations are based on a simplicial complex dual to the molecule models.
All proposed algorithms are parallelizable.
acknowledgement: 'The research of both authors is partially supported by the Office
of Naval Research. Herbert Edelsbrunner is also supported through the Alan T. Waterman
award, grant CCR-9118874. '
article_processing_charge: No
article_type: original
author:
- first_name: Nataraj
full_name: Akkiraju, Nataraj
last_name: Akkiraju
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Akkiraju N, Edelsbrunner H. Triangulating the surface of a molecule. Discrete
Applied Mathematics. 1996;71(1-3):5-22. doi:10.1016/S0166-218X(96)00054-6
apa: Akkiraju, N., & Edelsbrunner, H. (1996). Triangulating the surface of a
molecule. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/S0166-218X(96)00054-6
chicago: Akkiraju, Nataraj, and Herbert Edelsbrunner. “Triangulating the Surface
of a Molecule.” Discrete Applied Mathematics. Elsevier, 1996. https://doi.org/10.1016/S0166-218X(96)00054-6.
ieee: N. Akkiraju and H. Edelsbrunner, “Triangulating the surface of a molecule,”
Discrete Applied Mathematics, vol. 71, no. 1–3. Elsevier, pp. 5–22, 1996.
ista: Akkiraju N, Edelsbrunner H. 1996. Triangulating the surface of a molecule.
Discrete Applied Mathematics. 71(1–3), 5–22.
mla: Akkiraju, Nataraj, and Herbert Edelsbrunner. “Triangulating the Surface of
a Molecule.” Discrete Applied Mathematics, vol. 71, no. 1–3, Elsevier,
1996, pp. 5–22, doi:10.1016/S0166-218X(96)00054-6.
short: N. Akkiraju, H. Edelsbrunner, Discrete Applied Mathematics 71 (1996) 5–22.
date_created: 2018-12-11T12:06:30Z
date_published: 1996-12-05T00:00:00Z
date_updated: 2022-08-09T14:06:12Z
day: '05'
doi: 10.1016/S0166-218X(96)00054-6
extern: '1'
intvolume: ' 71'
issue: 1-3
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/S0166218X96000546?via%3Dihub
month: '12'
oa: 1
oa_version: Published Version
page: 5 - 22
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166-218X
publication_status: published
publisher: Elsevier
publist_id: '2102'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Triangulating the surface of a molecule
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 71
year: '1996'
...
---
_id: '4026'
abstract:
- lang: eng
text: A set of n weighted points in general position in R(d) defines a unique regular
triangulation. This paper proves that if the points are added one by one, then
flipping in a topological order will succeed in constructing this triangulation.
If, in addition, the points are added in a random sequence and the history of
the flips is used for locating the next point, then the algorithm takes expected
time at most O(n log n + n(inverted left perpendicular d/2 inverted right perpendicular)).
Under the assumption that the points and weights are independently and identically
distributed, the expected running time is between proportional to and a factor
log n more than the expected size of the regular triangulation. The expectation
is over choosing the points and over independent coin-flips performed by the algorithm.
acknowledgement: National Science Foundation under Grant CCR-8921421, Alan T. Waterman
award, Grant CCR-9118874.
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Nimish
full_name: Shah, Nimish
last_name: Shah
citation:
ama: Edelsbrunner H, Shah N. Incremental topological flipping works for regular
triangulations. Algorithmica. 1996;15(3):223-241. doi:10.1007/BF01975867
apa: Edelsbrunner, H., & Shah, N. (1996). Incremental topological flipping works
for regular triangulations. Algorithmica. Springer. https://doi.org/10.1007/BF01975867
chicago: Edelsbrunner, Herbert, and Nimish Shah. “Incremental Topological Flipping
Works for Regular Triangulations.” Algorithmica. Springer, 1996. https://doi.org/10.1007/BF01975867.
ieee: H. Edelsbrunner and N. Shah, “Incremental topological flipping works for regular
triangulations,” Algorithmica, vol. 15, no. 3. Springer, pp. 223–241, 1996.
ista: Edelsbrunner H, Shah N. 1996. Incremental topological flipping works for regular
triangulations. Algorithmica. 15(3), 223–241.
mla: Edelsbrunner, Herbert, and Nimish Shah. “Incremental Topological Flipping Works
for Regular Triangulations.” Algorithmica, vol. 15, no. 3, Springer, 1996,
pp. 223–41, doi:10.1007/BF01975867.
short: H. Edelsbrunner, N. Shah, Algorithmica 15 (1996) 223–241.
date_created: 2018-12-11T12:06:31Z
date_published: 1996-03-01T00:00:00Z
date_updated: 2022-08-09T09:46:07Z
day: '01'
doi: 10.1007/BF01975867
extern: '1'
intvolume: ' 15'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 223 - 241
publication: Algorithmica
publication_identifier:
issn:
- 0178-4617
publication_status: published
publisher: Springer
publist_id: '2099'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incremental topological flipping works for regular triangulations
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 15
year: '1996'
...
---
_id: '4027'
abstract:
- lang: eng
text: 'Questions about lines in space arise frequently as subproblems in three-dimensional
computational geometry. In this paper we study a number of fundamental combinatorial
and algorithmic problems involving arrangements of n lines in three-dimensional
space. Our main results include: 1. A tight Θ(n2) bound on the maximum combinatorial
description complexity of the set of all oriented lines that have specified orientations
relative to the n given lines. 2. A similar bound of Θ(n3) for the complexity
of the set of all lines passing above the n given lines. 3. A preprocessing procedure
using O(n2+ε) time and storage, for any ε > 0, that builds a structure supporting
O(logn)-time queries for testing if a line lies above all the given lines. 4.
An algorithm that tests the "towering property" in O(n4/3+ε) time, for
any ε > 0: do n given red lines lie all above n given blue lines? The tools
used to obtain these and other results include Plücker coordinates for lines in
space and ε-nets for various geometric range spaces.'
acknowledgement: Work on this paper by Bernard Chazelle has been supported by NSF
Grant CCR-87-00917. Work on this paper by Herbert Edelsbrunner has been supported
by NSF Grant CCR-87-14565. Work on this paper by Leonidas Guibas has been supported
by grants from the Mitsubishi and Toshiba Corporations. Work on this paper by Micha
Sharir has been supported by ONR Grant N00014-87-K-0129, by NSF Grants DCR-83-20085
and CCR-89-01484, and by grants from the U.S.-Israeli Binational Science Foundation,
the NCRD — the Israeli National Council for Research and Development, and the EMET
Fund of the Israeli Academy of Sciences.
article_processing_charge: No
article_type: original
author:
- first_name: Bernard
full_name: Chazelle, Bernard
last_name: Chazelle
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Leonidas
full_name: Guibas, Leonidas
last_name: Guibas
- first_name: Micha
full_name: Sharir, Micha
last_name: Sharir
- first_name: Jorge
full_name: Stolfi, Jorge
last_name: Stolfi
citation:
ama: 'Chazelle B, Edelsbrunner H, Guibas L, Sharir M, Stolfi J. Lines in space:
Combinatorics and algorithms. Algorithmica. 1996;15(5):428-447. doi:10.1007/BF01955043'
apa: 'Chazelle, B., Edelsbrunner, H., Guibas, L., Sharir, M., & Stolfi, J. (1996).
Lines in space: Combinatorics and algorithms. Algorithmica. Springer. https://doi.org/10.1007/BF01955043'
chicago: 'Chazelle, Bernard, Herbert Edelsbrunner, Leonidas Guibas, Micha Sharir,
and Jorge Stolfi. “Lines in Space: Combinatorics and Algorithms.” Algorithmica.
Springer, 1996. https://doi.org/10.1007/BF01955043.'
ieee: 'B. Chazelle, H. Edelsbrunner, L. Guibas, M. Sharir, and J. Stolfi, “Lines
in space: Combinatorics and algorithms,” Algorithmica, vol. 15, no. 5.
Springer, pp. 428–447, 1996.'
ista: 'Chazelle B, Edelsbrunner H, Guibas L, Sharir M, Stolfi J. 1996. Lines in
space: Combinatorics and algorithms. Algorithmica. 15(5), 428–447.'
mla: 'Chazelle, Bernard, et al. “Lines in Space: Combinatorics and Algorithms.”
Algorithmica, vol. 15, no. 5, Springer, 1996, pp. 428–47, doi:10.1007/BF01955043.'
short: B. Chazelle, H. Edelsbrunner, L. Guibas, M. Sharir, J. Stolfi, Algorithmica
15 (1996) 428–447.
date_created: 2018-12-11T12:06:31Z
date_published: 1996-05-01T00:00:00Z
date_updated: 2022-08-09T09:55:46Z
day: '01'
doi: 10.1007/BF01955043
extern: '1'
intvolume: ' 15'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 428 - 447
publication: Algorithmica
publication_identifier:
issn:
- 0178-4617
publication_status: published
publisher: Springer
publist_id: '2100'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Lines in space: Combinatorics and algorithms'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 15
year: '1996'
...
---
_id: '4030'
acknowledgement: article M-Pos412
article_processing_charge: No
author:
- first_name: Jie
full_name: Liang, Jie
last_name: Liang
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Shankar
full_name: Subramaniam, Shankar
last_name: Subramaniam
citation:
ama: Liang J, Edelsbrunner H, Subramaniam S. Effects of Molecular Shape Representations
on Boundary Element Method for Protein Electrostatics Computations. Vol 70.
Cell Press; 1996:A224-A224. doi:10.1016/S0006-3495(96)79664-9
apa: Liang, J., Edelsbrunner, H., & Subramaniam, S. (1996). Effects of molecular
shape representations on boundary element method for protein electrostatics computations.
Fortieth Annual Meeting (Vol. 70, pp. A224–A224). Cell Press. https://doi.org/10.1016/S0006-3495(96)79664-9
chicago: Liang, Jie, Herbert Edelsbrunner, and Shankar Subramaniam. Effects of
Molecular Shape Representations on Boundary Element Method for Protein Electrostatics
Computations. Fortieth Annual Meeting. Vol. 70. Cell Press, 1996. https://doi.org/10.1016/S0006-3495(96)79664-9.
ieee: J. Liang, H. Edelsbrunner, and S. Subramaniam, Effects of molecular shape
representations on boundary element method for protein electrostatics computations,
vol. 70, no. 2, Part 2. Cell Press, 1996, pp. A224–A224.
ista: Liang J, Edelsbrunner H, Subramaniam S. 1996. Effects of molecular shape representations
on boundary element method for protein electrostatics computations, Cell Press,p.
mla: Liang, Jie, et al. “Effects of Molecular Shape Representations on Boundary
Element Method for Protein Electrostatics Computations.” Fortieth Annual Meeting,
vol. 70, no. 2, Part 2, Cell Press, 1996, pp. A224–A224, doi:10.1016/S0006-3495(96)79664-9.
short: J. Liang, H. Edelsbrunner, S. Subramaniam, Effects of Molecular Shape Representations
on Boundary Element Method for Protein Electrostatics Computations, Cell Press,
1996.
date_created: 2018-12-11T12:06:32Z
date_published: 1996-02-19T00:00:00Z
date_updated: 2022-08-08T10:22:38Z
day: '19'
doi: 10.1016/S0006-3495(96)79664-9
extern: '1'
intvolume: ' 70'
issue: 2, Part 2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/S0006349596796649?via%3Dihub
month: '02'
oa: 1
oa_version: None
page: A224 - A224
publication: Fortieth Annual Meeting
publication_status: published
publisher: Cell Press
publist_id: '2097'
status: public
title: Effects of molecular shape representations on boundary element method for protein
electrostatics computations
type: conference_poster
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 70
year: '1996'
...
---
_id: '4031'
acknowledgement: article W-AM-L6
article_processing_charge: No
author:
- first_name: Jie
full_name: Liang, Jie
last_name: Liang
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Sudhakar
full_name: Pamidghantam, Sudhakar
last_name: Pamidghantam
- first_name: Shankar
full_name: Subramaniam, Shankar
last_name: Subramaniam
citation:
ama: 'Liang J, Edelsbrunner H, Pamidghantam S, Subramaniam S. Analytical Method
for Molecular Shapes: Area, Volume, Cavities, Interface and Pockets. Vol 70.
Cell Press; 1996:A377-A377. doi:10.1016/S0006-3495(96)79670-4'
apa: 'Liang, J., Edelsbrunner, H., Pamidghantam, S., & Subramaniam, S. (1996).
Analytical method for molecular shapes: Area, volume, cavities, interface and
pockets. Fortieth Annual Meeting (Vol. 70, pp. A377–A377). Cell Press.
https://doi.org/10.1016/S0006-3495(96)79670-4'
chicago: 'Liang, Jie, Herbert Edelsbrunner, Sudhakar Pamidghantam, and Shankar Subramaniam.
Analytical Method for Molecular Shapes: Area, Volume, Cavities, Interface and
Pockets. Fortieth Annual Meeting. Vol. 70. Cell Press, 1996. https://doi.org/10.1016/S0006-3495(96)79670-4.'
ieee: 'J. Liang, H. Edelsbrunner, S. Pamidghantam, and S. Subramaniam, Analytical
method for molecular shapes: Area, volume, cavities, interface and pockets,
vol. 70, no. 2, Part 2. Cell Press, 1996, pp. A377–A377.'
ista: 'Liang J, Edelsbrunner H, Pamidghantam S, Subramaniam S. 1996. Analytical
method for molecular shapes: Area, volume, cavities, interface and pockets, Cell
Press,p.'
mla: 'Liang, Jie, et al. “Analytical Method for Molecular Shapes: Area, Volume,
Cavities, Interface and Pockets.” Fortieth Annual Meeting, vol. 70, no.
2, Part 2, Cell Press, 1996, pp. A377–A377, doi:10.1016/S0006-3495(96)79670-4.'
short: 'J. Liang, H. Edelsbrunner, S. Pamidghantam, S. Subramaniam, Analytical Method
for Molecular Shapes: Area, Volume, Cavities, Interface and Pockets, Cell Press,
1996.'
date_created: 2018-12-11T12:06:32Z
date_published: 1996-02-21T00:00:00Z
date_updated: 2022-08-08T10:21:56Z
day: '21'
doi: 10.1016/S0006-3495(96)79670-4
extern: '1'
intvolume: ' 70'
issue: 2, Part 2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/S0006349596796704?via%3Dihub
month: '02'
oa: 1
oa_version: None
page: A377 - A377
publication: Fortieth Annual Meeting
publication_status: published
publisher: Cell Press
publist_id: '2098'
status: public
title: 'Analytical method for molecular shapes: Area, volume, cavities, interface
and pockets'
type: conference_poster
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 70
year: '1996'
...
---
_id: '4142'
abstract:
- lang: eng
text: 'Mutations giving rise to anatomical defects in the inner ear have been isolated
in a large scale screen for mutations causing visible abnormalities in the zebrafish
embryo (Haffter, P., Granato, M., Brand, M. et al. (1996) Development 123, 1-36).
58 mutants have been classified as having a primary ear phenotype; these fall
into several phenotypic classes, affecting presence or size of the otoliths, size
and shape of the otic vesicle and formation of the semicircular canals, and define
at least 20 complementation groups. Mutations in seven genes cause loss of one
or both otoliths, but do not appear to affect development of other structures
within the ear. Mutations in seven genes affect morphology and patterning of the
inner ear epithelium, including formation of the semicircular canals and, in some,
development of sensory patches (maculae and cristae). Within this class, dog-eared
mutants show abnormal development of semicircular canals and lack cristae within
the ear, while in van gogh, semicircular canals fail to form altogether, resulting
in a tiny otic vesicle containing a single sensory patch. Both these mutants show
defects in the expression of homeobox genes within the otic vesicle. In a further
class of mutants, ear size is affected while patterning appears to be relatively
normal; mutations in three genes cause expansion of the otic vesicle, while in
little ears and microtic, the ear is abnormally small, but still contains all
five sensory patches, as in the wild type. Many of the ear and otolith mutants
show an expected behavioural phenotype: embryos fail to balance correctly, and
may swim on their sides, upside down, or in circles. Several mutants with similar
balance defects have also been isolated that have no obvious structural ear defect,
but that may include mutants with vestibular dysfunction of the inner ear (Granato,
M., van Eeden, F. J. M., Schach, U. et al. (1996) Development, 123, 399-413,).
Mutations in 19 genes causing primary defects in other structures also show an
ear defect. In particular, ear phenotypes are often found in conjunction with
defects of neural crest derivatives (pigment cells and/or cartilaginous elements
of the jaw). At least one mutant, dog-eared, shows defects in both the ear and
another placodally derived sensory system, the lateral line, while hypersensitive
mutants have additional trunk lateral line organs.'
acknowledgement: T. T. W. thanks all members of the Tübingen fish and fly groups for
their hospitality and generosity during her visits to the laboratory. We thank Julian
Lewis, in whose laboratory much of this work was carried out, for many helpful discussions
and suggestions, Catherine Haddon for advice on wild-type ear development and techniques,
and Stephen Massey for fish husbandry in Oxford. We are grateful to Julian Lewis,
Catherine Haddon, Nick Monk and Patrick Blader for comments on the manuscript, and
to Trevor Jowett, Tom Schilling,Eric Weinberg and Monte Westerfield for providing
cDNAs. We also thank Jarema Malicki and Wolfgang Driever for making some of the
Boston otolith mutants available before publication. T. T. W. thanks the EMBO (ASTF
7668; ASTF 7918), the Imperial Cancer Research Fund and the Wellcome Trust (03643/Z/92)
for support.
article_processing_charge: No
article_type: original
author:
- first_name: Tanya
full_name: Whitfield, Tanya
last_name: Whitfield
- first_name: Michael
full_name: Granato, Michael
last_name: Granato
- first_name: Fredericus
full_name: Van Eeden, Fredericus
last_name: Van Eeden
- first_name: Ursula
full_name: Schach, Ursula
last_name: Schach
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
- first_name: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
- first_name: Pascal
full_name: Haffter, Pascal
last_name: Haffter
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
- 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: Yunjin
full_name: Jiang, Yunjin
last_name: Jiang
- first_name: Donald
full_name: Kane, Donald
last_name: Kane
- first_name: Robert
full_name: Kelsh, Robert
last_name: Kelsh
- first_name: Mary
full_name: Mullins, Mary
last_name: Mullins
- first_name: Jörg
full_name: Odenthal, Jörg
last_name: Odenthal
- first_name: Christiane
full_name: Nüsslein Volhard, Christiane
last_name: Nüsslein Volhard
citation:
ama: Whitfield T, Granato M, Van Eeden F, et al. Mutations affecting development
of the zebrafish inner ear and lateral line. Development. 1996;123:241-254.
doi:10.1242/dev.123.1.241
apa: Whitfield, T., Granato, M., Van Eeden, F., Schach, U., Brand, M., Furutani
Seiki, M., … Nüsslein Volhard, C. (1996). Mutations affecting development of the
zebrafish inner ear and lateral line. Development. Company of Biologists.
https://doi.org/10.1242/dev.123.1.241
chicago: Whitfield, Tanya, Michael Granato, Fredericus Van Eeden, Ursula Schach,
Michael Brand, Makoto Furutani Seiki, Pascal Haffter, et al. “Mutations Affecting
Development of the Zebrafish Inner Ear and Lateral Line.” Development.
Company of Biologists, 1996. https://doi.org/10.1242/dev.123.1.241.
ieee: T. Whitfield et al., “Mutations affecting development of the zebrafish
inner ear and lateral line,” Development, vol. 123. Company of Biologists,
pp. 241–254, 1996.
ista: Whitfield T, Granato M, Van Eeden F, Schach U, Brand M, Furutani Seiki M,
Haffter P, Hammerschmidt M, Heisenberg C-PJ, Jiang Y, Kane D, Kelsh R, Mullins
M, Odenthal J, Nüsslein Volhard C. 1996. Mutations affecting development of the
zebrafish inner ear and lateral line. Development. 123, 241–254.
mla: Whitfield, Tanya, et al. “Mutations Affecting Development of the Zebrafish
Inner Ear and Lateral Line.” Development, vol. 123, Company of Biologists,
1996, pp. 241–54, doi:10.1242/dev.123.1.241.
short: T. Whitfield, M. Granato, F. Van Eeden, U. Schach, M. Brand, M. Furutani
Seiki, P. Haffter, M. Hammerschmidt, C.-P.J. Heisenberg, Y. Jiang, D. Kane, R.
Kelsh, M. Mullins, J. Odenthal, C. Nüsslein Volhard, Development 123 (1996) 241–254.
date_created: 2018-12-11T12:07:11Z
date_published: 1996-12-01T00:00:00Z
date_updated: 2022-08-08T08:45:59Z
day: '01'
doi: 10.1242/dev.123.1.241
extern: '1'
external_id:
pmid:
- '9007244'
intvolume: ' 123'
language:
- iso: eng
month: '12'
oa_version: None
page: 241 - 254
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1979'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutations affecting development of the zebrafish inner ear and lateral line
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 123
year: '1996'
...
---
_id: '4151'
abstract:
- lang: eng
text: 'Jaws and branchial arches together are a basic, segmented feature of the
vertebrate head, Seven arches develop in the zebrafish embryo (Danio rerio), derived
largely from neural crest cells that form the cartilaginous skeleton, In this
and the following paper we describe the phenotypes of 109 arch mutants, focusing
here on three classes that affect the posterior pharyngeal arches, including the
hyoid and five gill-bearing arches, In lockjaw, the hyoid arch is strongly reduced
and subsets of branchial arches do not develop, Mutants of a large second class,
designated the flathead group, lack several adjacent branchial arches and their
associated cartilages. Five alleles at the flathead locus all lead to larvae that
lack arches 4-6, Among 34 other flathead group members complementation tests are
incomplete, but at least six unique phenotypes can be distinguished, These all
delete continuous stretches of adjacent branchial arches and unpaired cartilages
in the ventral midline, Many show cell death in the midbrain, from which some
neural crest precursors of the arches originate, lockjaw and a few mutants in
the flathead group, including pistachio, affect both jaw cartilage and pigmentation,
reflecting essential functions of these genes in at least two neural crest lineages,
Mutants of a third class, including boxer, dackel and pincher, affect pectoral
fins and axonal trajectories in the brain, as well as the arches. Their skeletal
phenotypes suggest that they disrupt cartilage morphogenesis in all arches, Our
results suggest that there are sets of genes that: (1) specify neural crest cells
in groups of adjacent head segments, and (2) function in common genetic pathways
in a variety of tissues including the brain, pectoral fins and pigment cells as
well as pharyngeal arches.'
acknowledgement: We thank Drs Charles Kimmel, Philip Ingham, Paula Mabee and members
of the Ingham lab for critical comments on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Schilling, Thomas
last_name: Schilling
- first_name: Tatjana
full_name: Piotrowski, Tatjana
last_name: Piotrowski
- first_name: Heiner
full_name: Grandel, Heiner
last_name: Grandel
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
- 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: Yunjin
full_name: Jiang, Yunjin
last_name: Jiang
- first_name: Dirk
full_name: Beuchle, Dirk
last_name: Beuchle
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
- first_name: Donald
full_name: Kane, Donald
last_name: Kane
- first_name: Mary
full_name: Mullins, Mary
last_name: Mullins
- first_name: Fredericus
full_name: Van Eeden, Fredericus
last_name: Van Eeden
- first_name: Robert
full_name: Kelsh, Robert
last_name: Kelsh
- first_name: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
- first_name: Michael
full_name: Granato, Michael
last_name: Granato
- first_name: Pascal
full_name: Haffter, Pascal
last_name: Haffter
- first_name: Jörg
full_name: Odenthal, Jörg
last_name: Odenthal
- first_name: Rachel
full_name: Warga, Rachel
last_name: Warga
- first_name: Torsten
full_name: Trowe, Torsten
last_name: Trowe
- first_name: Christiane
full_name: Nüsslein Volhard, Christiane
last_name: Nüsslein Volhard
citation:
ama: 'Schilling T, Piotrowski T, Grandel H, et al. Jaw and branchial arch mutants
in zebrafish I: Branchial arches. Development. 1996;123(1):329-344. doi:10.1242/dev.123.1.329'
apa: 'Schilling, T., Piotrowski, T., Grandel, H., Brand, M., Heisenberg, C.-P. J.,
Jiang, Y., … Nüsslein Volhard, C. (1996). Jaw and branchial arch mutants in zebrafish
I: Branchial arches. Development. Company of Biologists. https://doi.org/10.1242/dev.123.1.329'
chicago: 'Schilling, Thomas, Tatjana Piotrowski, Heiner Grandel, Michael Brand,
Carl-Philipp J Heisenberg, Yunjin Jiang, Dirk Beuchle, et al. “Jaw and Branchial
Arch Mutants in Zebrafish I: Branchial Arches.” Development. Company of
Biologists, 1996. https://doi.org/10.1242/dev.123.1.329.'
ieee: 'T. Schilling et al., “Jaw and branchial arch mutants in zebrafish
I: Branchial arches,” Development, vol. 123, no. 1. Company of Biologists,
pp. 329–344, 1996.'
ista: 'Schilling T, Piotrowski T, Grandel H, Brand M, Heisenberg C-PJ, Jiang Y,
Beuchle D, Hammerschmidt M, Kane D, Mullins M, Van Eeden F, Kelsh R, Furutani
Seiki M, Granato M, Haffter P, Odenthal J, Warga R, Trowe T, Nüsslein Volhard
C. 1996. Jaw and branchial arch mutants in zebrafish I: Branchial arches. Development.
123(1), 329–344.'
mla: 'Schilling, Thomas, et al. “Jaw and Branchial Arch Mutants in Zebrafish I:
Branchial Arches.” Development, vol. 123, no. 1, Company of Biologists,
1996, pp. 329–44, doi:10.1242/dev.123.1.329.'
short: T. Schilling, T. Piotrowski, H. Grandel, M. Brand, C.-P.J. Heisenberg, Y.
Jiang, D. Beuchle, M. Hammerschmidt, D. Kane, M. Mullins, F. Van Eeden, R. Kelsh,
M. Furutani Seiki, M. Granato, P. Haffter, J. Odenthal, R. Warga, T. Trowe, C.
Nüsslein Volhard, Development 123 (1996) 329–344.
date_created: 2018-12-11T12:07:15Z
date_published: 1996-12-01T00:00:00Z
date_updated: 2022-08-08T08:41:00Z
day: '01'
doi: 10.1242/dev.123.1.329
extern: '1'
external_id:
pmid:
- '9007253'
intvolume: ' 123'
issue: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 329 - 344
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1968'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Jaw and branchial arch mutants in zebrafish I: Branchial arches'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 123
year: '1996'
...
---
_id: '4154'
abstract:
- lang: eng
text: As part of a large scale chemical mutagenesis screen of the zebrafish (Danio
rerio) genome, we have identified 33 mutants with defects in hematopoiesis, Complementation
analysis placed 32 of these mutants into 17 complementation groups, The allelism
of the remaining 1 blood mutant is currently unresolved, We have categorized these
blood mutants into four phenotypic classes based on analyses of whole embryos
and isolated blood cells, as well as by in situ hybridization using the hematopoietic
transcription factors GATA-1 and GATA-2, Embryos mutant for the gene moonshine
have few if any proerythroblasts visible on the day circulation begins and normal
erythroid cell differentiation is blocked as determined by staining for hemoglobin
and GATA-1 expression, Mutations in five genes, chablis, frascati, merlot, retsina,
thunderbird and two possibly unique mutations cause a progressive decrease in
the number of blood cells during the first 5 days of development, Mutations in
another seven genes, chardonnay, chianti, grenache, sauternes, weibherbst and
zinfandel, and two additional mutations result in hypochromic blood cells which
also decrease in number as development proceeds, Several of these mutants have
immature cells in the circulation, indicating a block in normal erythroid development.
The mutation in zinfandel is dominant, and 2-day old heterozygous carriers fail
to express detectable levels of hemoglobin and have decreasing numbers of circulating
cells during the first 5 days of development, Mutations in two genes, freixenet
and yquem, result in the animals that are photosensitive with autofluorescent
blood, similar to that found in the human congenital porphyrias, The collection
of mutants presented here represent several steps required for normal erythropoiesis,
The analysis of these mutants provides a powerful approach towards defining the
molecular mechanisms involved in vertebrate hematopoietic development.
acknowledgement: 'We thank Leonard Zon for his generous support of D. G. R. and A.
B., for critical review of this manuscript and for many helpful discussions. We
also thank Lauren Barone and Stephen Pratt for technical assistance. D. G. R. is
a postdoctoral fellow of the Howard Hughes Medical Institute. '
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Ransom, David
last_name: Ransom
- first_name: Pascal
full_name: Haffter, Pascal
last_name: Haffter
- first_name: Jörg
full_name: Odenthal, Jörg
last_name: Odenthal
- first_name: Alison
full_name: Brownlie, Alison
last_name: Brownlie
- first_name: Elisabeth
full_name: Vogelsang, Elisabeth
last_name: Vogelsang
- first_name: Robert
full_name: Kelsh, Robert
last_name: Kelsh
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
- first_name: Fredericus
full_name: Van Eeden, Fredericus
last_name: Van Eeden
- first_name: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
- first_name: Michael
full_name: Granato, Michael
last_name: Granato
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
- 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: Yunjin
full_name: Jiang, Yunjin
last_name: Jiang
- first_name: Donald
full_name: Kane, Donald
last_name: Kane
- first_name: Mary
full_name: Mullins, Mary
last_name: Mullins
- first_name: Christiane
full_name: Nüsslein Volhard, Christiane
last_name: Nüsslein Volhard
citation:
ama: Ransom D, Haffter P, Odenthal J, et al. Characterization of zebrafish mutants
with defects in embryonic hematopoiesis. Development. 1996;123(1):311-319.
doi:10.1242/dev.123.1.311
apa: Ransom, D., Haffter, P., Odenthal, J., Brownlie, A., Vogelsang, E., Kelsh,
R., … Nüsslein Volhard, C. (1996). Characterization of zebrafish mutants with
defects in embryonic hematopoiesis. Development. Company of Biologists.
https://doi.org/10.1242/dev.123.1.311
chicago: Ransom, David, Pascal Haffter, Jörg Odenthal, Alison Brownlie, Elisabeth
Vogelsang, Robert Kelsh, Michael Brand, et al. “Characterization of Zebrafish
Mutants with Defects in Embryonic Hematopoiesis.” Development. Company
of Biologists, 1996. https://doi.org/10.1242/dev.123.1.311.
ieee: D. Ransom et al., “Characterization of zebrafish mutants with defects
in embryonic hematopoiesis,” Development, vol. 123, no. 1. Company of Biologists,
pp. 311–319, 1996.
ista: Ransom D, Haffter P, Odenthal J, Brownlie A, Vogelsang E, Kelsh R, Brand M,
Van Eeden F, Furutani Seiki M, Granato M, Hammerschmidt M, Heisenberg C-PJ, Jiang
Y, Kane D, Mullins M, Nüsslein Volhard C. 1996. Characterization of zebrafish
mutants with defects in embryonic hematopoiesis. Development. 123(1), 311–319.
mla: Ransom, David, et al. “Characterization of Zebrafish Mutants with Defects in
Embryonic Hematopoiesis.” Development, vol. 123, no. 1, Company of Biologists,
1996, pp. 311–19, doi:10.1242/dev.123.1.311.
short: D. Ransom, P. Haffter, J. Odenthal, A. Brownlie, E. Vogelsang, R. Kelsh,
M. Brand, F. Van Eeden, M. Furutani Seiki, M. Granato, M. Hammerschmidt, C.-P.J.
Heisenberg, Y. Jiang, D. Kane, M. Mullins, C. Nüsslein Volhard, Development 123
(1996) 311–319.
date_created: 2018-12-11T12:07:16Z
date_published: 1996-12-01T00:00:00Z
date_updated: 2022-08-08T08:23:35Z
day: '01'
doi: 10.1242/dev.123.1.311
extern: '1'
external_id:
pmid:
- '9007251'
intvolume: ' 123'
issue: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 311 - 319
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1966'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characterization of zebrafish mutants with defects in embryonic hematopoiesis
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 123
year: '1996'
...
---
_id: '4156'
abstract:
- lang: eng
text: 'In a large scale screen for mutants that affect the early development of
the zebrafish, 109 mutants were found that cause defects in the formation of the
jaw and the more posterior pharyngeal arches, Here we present the phenotypic description
and results of the complementation analysis of mutants belonging to two major
classes: (1) mutants with defects in the mandibular and hyoid arches and (2) mutants
with defects in cartilage differentiation and growth in all arches, Mutations
in four of the genes identified during the screen show specific defects in the
first two arches and leave the more posterior pharyngeal arches largely unaffected
(schmerle, sucker, hoover and sturgeon). In these mutants ventral components of
the mandibular and hyoid arches are reduced (Meckel''s cartilage and ceratohyal
cartilage) whereas dorsal structures (palato-quadrate and hyosymplectic cartilages)
are of normal size or enlarged, Thus, mutations in single genes cause defects
in the formation of first and second arch structures but also differentially affect
development of the dorsal and ventral structures within one arch. In 27 mutants
that define at least 8 genes, the differentiation of cartilage and growth is affected.
In hammerhead mutants particularly the mesodermally derived cartilages are reduced,
whereas jellyfish mutant larvae are characterized by a severe reduction of all
cartilaginous elements, leaving only two pieces in the position of the ceratohyal
cartilages. In all other mutant larvae all skeletal elements are present, but
consist of smaller and disorganized chondrocytes. These mutants also exhibit shortened
heads and reduced pectoral fins. In homozygous knorrig embryos, tumor-like outgrowths
of chondrocytes occur along the edges of all cartilaginous elements. The mutants
presented here may be valuable tools for elucidating the genetic mechanisms that
underlie the development of the mandibular and the hyoid arches, as well as the
process of cartilage differentiation.'
acknowledgement: We would like to thank Siegfried Roth, Stefan Schulte-Merker and
Tanya Whitfield for critically reading the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Tatjana
full_name: Piotrowski, Tatjana
last_name: Piotrowski
- first_name: Thomas
full_name: Schilling, Thomas
last_name: Schilling
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
- first_name: Yunjin
full_name: Jiang, Yunjin
last_name: Jiang
- 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: Dirk
full_name: Beuchle, Dirk
last_name: Beuchle
- first_name: Heiner
full_name: Grandel, Heiner
last_name: Grandel
- first_name: Fredericus
full_name: Van Eeden, Fredericus
last_name: Van Eeden
- first_name: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
- first_name: Michael
full_name: Granato, Michael
last_name: Granato
- first_name: Pascal
full_name: Haffter, Pascal
last_name: Haffter
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
- first_name: Donald
full_name: Kane, Donald
last_name: Kane
- first_name: Robert
full_name: Kelsh, Robert
last_name: Kelsh
- first_name: Mary
full_name: Mullins, Mary
last_name: Mullins
- first_name: Jörg
full_name: Odenthal, Jörg
last_name: Odenthal
- first_name: Rachel
full_name: Warga, Rachel
last_name: Warga
- first_name: Christiane
full_name: Nüsslein Volhard, Christiane
last_name: Nüsslein Volhard
citation:
ama: 'Piotrowski T, Schilling T, Brand M, et al. Jaw and branchial arch mutants
in zebrafish II: Anterior arches and cartilage differentiation. Development.
1996;123(1):345-356. doi:10.1242/dev.123.1.345'
apa: 'Piotrowski, T., Schilling, T., Brand, M., Jiang, Y., Heisenberg, C.-P. J.,
Beuchle, D., … Nüsslein Volhard, C. (1996). Jaw and branchial arch mutants in
zebrafish II: Anterior arches and cartilage differentiation. Development.
Company of Biologists. https://doi.org/10.1242/dev.123.1.345'
chicago: 'Piotrowski, Tatjana, Thomas Schilling, Michael Brand, Yunjin Jiang, Carl-Philipp
J Heisenberg, Dirk Beuchle, Heiner Grandel, et al. “Jaw and Branchial Arch Mutants
in Zebrafish II: Anterior Arches and Cartilage Differentiation.” Development.
Company of Biologists, 1996. https://doi.org/10.1242/dev.123.1.345.'
ieee: 'T. Piotrowski et al., “Jaw and branchial arch mutants in zebrafish
II: Anterior arches and cartilage differentiation,” Development, vol. 123,
no. 1. Company of Biologists, pp. 345–356, 1996.'
ista: 'Piotrowski T, Schilling T, Brand M, Jiang Y, Heisenberg C-PJ, Beuchle D,
Grandel H, Van Eeden F, Furutani Seiki M, Granato M, Haffter P, Hammerschmidt
M, Kane D, Kelsh R, Mullins M, Odenthal J, Warga R, Nüsslein Volhard C. 1996.
Jaw and branchial arch mutants in zebrafish II: Anterior arches and cartilage
differentiation. Development. 123(1), 345–356.'
mla: 'Piotrowski, Tatjana, et al. “Jaw and Branchial Arch Mutants in Zebrafish II:
Anterior Arches and Cartilage Differentiation.” Development, vol. 123,
no. 1, Company of Biologists, 1996, pp. 345–56, doi:10.1242/dev.123.1.345.'
short: T. Piotrowski, T. Schilling, M. Brand, Y. Jiang, C.-P.J. Heisenberg, D. Beuchle,
H. Grandel, F. Van Eeden, M. Furutani Seiki, M. Granato, P. Haffter, M. Hammerschmidt,
D. Kane, R. Kelsh, M. Mullins, J. Odenthal, R. Warga, C. Nüsslein Volhard, Development
123 (1996) 345–356.
date_created: 2018-12-11T12:07:17Z
date_published: 1996-12-01T00:00:00Z
date_updated: 2022-08-08T08:13:07Z
day: '01'
doi: 10.1242/dev.123.1.345
extern: '1'
external_id:
pmid:
- '9007254 '
intvolume: ' 123'
issue: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 345 - 356
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1963'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Jaw and branchial arch mutants in zebrafish II: Anterior arches and cartilage
differentiation'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 123
year: '1996'
...
---
_id: '4164'
abstract:
- lang: eng
text: In a large-scale screen for mutants with defects in embryonic development
we identified 17 genes (65 mutants) specifically required for the development
of xanthophores, We provide evidence that these genes are required for three different
aspects of xanthophore development, (1) Pigment cell formation and migration (pfeffer
and salt); (2) pigment synthesis (edison, yobo, yocca and brie) and (3) pigment
translocation (esrom, tilsit and tofu). The number of xanthophore cells that appear
in the body is reduced in embryos with mutations in the two genes, salt and pfeffer.
In heterozygous and homozygous salt and pfeffer adults, the melanophore stripes
are interrupted, indicating that xanthophore cells have an important function
in adult melanophore pattern formation, Most other genes affect only larval pigmentation,
In embryos mutant for edison, yobo, yocca and brie, differences in pteridine synthesis
can be observed under UV light and by thin-layer chromatography. Homozygous mutant
females of yobo show a recessive maternal effect, Embryonic development is slowed
down and embryos display head and tail truncations, Xanthophores in larvae mutant
in the three genes esrom, tilsit and tofu appear less spread out, In addition,
these mutants display a defect in retinotectal axon pathfinding, These mutations
may affect xanthophore pigment distribution within the cells or xanthophore cell
shape, Mutations in seven genes affecting xanthophore pigmentation remain unclassified.
acknowledgement: We thank Silke Rudolph for technical assistance, Joel Wilson and
Cornelia Fricke for their help in the fish work and the thin layer chromatography,
and Darren Gilmour for help with the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Jörg
full_name: Odenthal, Jörg
last_name: Odenthal
- first_name: Karin
full_name: Rossnagel, Karin
last_name: Rossnagel
- first_name: Pascal
full_name: Haffter, Pascal
last_name: Haffter
- first_name: Robert
full_name: Kelsh, Robert
last_name: Kelsh
- first_name: Elisabeth
full_name: Vogelsang, Elisabeth
last_name: Vogelsang
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
- first_name: Fredericus
full_name: Van Eeden, Fredericus
last_name: Van Eeden
- first_name: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
- first_name: Michael
full_name: Granato, Michael
last_name: Granato
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
- 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: Yunjin
full_name: Jiang, Yunjin
last_name: Jiang
- first_name: Donald
full_name: Kane, Donald
last_name: Kane
- first_name: Mary
full_name: Mullins, Mary
last_name: Mullins
- first_name: Christiane
full_name: Nüsslein Volhard, Christiane
last_name: Nüsslein Volhard
citation:
ama: Odenthal J, Rossnagel K, Haffter P, et al. Mutations affecting xanthophore
pigmentation in the zebrafish, Danio rerio. Development. 1996;123(1):391-398.
doi:10.1242/dev.123.1.391
apa: Odenthal, J., Rossnagel, K., Haffter, P., Kelsh, R., Vogelsang, E., Brand,
M., … Nüsslein Volhard, C. (1996). Mutations affecting xanthophore pigmentation
in the zebrafish, Danio rerio. Development. Company of Biologists. https://doi.org/10.1242/dev.123.1.391
chicago: Odenthal, Jörg, Karin Rossnagel, Pascal Haffter, Robert Kelsh, Elisabeth
Vogelsang, Michael Brand, Fredericus Van Eeden, et al. “Mutations Affecting Xanthophore
Pigmentation in the Zebrafish, Danio Rerio.” Development. Company of Biologists,
1996. https://doi.org/10.1242/dev.123.1.391.
ieee: J. Odenthal et al., “Mutations affecting xanthophore pigmentation in
the zebrafish, Danio rerio,” Development, vol. 123, no. 1. Company of Biologists,
pp. 391–398, 1996.
ista: Odenthal J, Rossnagel K, Haffter P, Kelsh R, Vogelsang E, Brand M, Van Eeden
F, Furutani Seiki M, Granato M, Hammerschmidt M, Heisenberg C-PJ, Jiang Y, Kane
D, Mullins M, Nüsslein Volhard C. 1996. Mutations affecting xanthophore pigmentation
in the zebrafish, Danio rerio. Development. 123(1), 391–398.
mla: Odenthal, Jörg, et al. “Mutations Affecting Xanthophore Pigmentation in the
Zebrafish, Danio Rerio.” Development, vol. 123, no. 1, Company of Biologists,
1996, pp. 391–98, doi:10.1242/dev.123.1.391.
short: J. Odenthal, K. Rossnagel, P. Haffter, R. Kelsh, E. Vogelsang, M. Brand,
F. Van Eeden, M. Furutani Seiki, M. Granato, M. Hammerschmidt, C.-P.J. Heisenberg,
Y. Jiang, D. Kane, M. Mullins, C. Nüsslein Volhard, Development 123 (1996) 391–398.
date_created: 2018-12-11T12:07:20Z
date_published: 1996-12-01T00:00:00Z
date_updated: 2022-08-08T08:08:51Z
day: '01'
doi: 10.1242/dev.123.1.391
extern: '1'
external_id:
pmid:
- '9007257 '
intvolume: ' 123'
issue: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 391 - 398
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1955'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutations affecting xanthophore pigmentation in the zebrafish, Danio rerio
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 123
year: '1996'
...
---
_id: '4166'
abstract:
- lang: eng
text: In a large scale screen for mutants with defects in the embryonic development
of the zebrafish we identified mutations in four genes, floating head (flh), memo
(mom), no tail (ntl), and dec, that are required for early notochord formation.
Mutations in flh and ntl have been described previously, while mom and doe are
newly identified genes. Mutant mom embryos lack a notochord in the trunk, and
trunk somites from the right and left side of the embryo fuse underneath the neural
tube. In this respect morn appears similar to flh. In contrast, notochord precursor
cells are present in both ntl and doc embryos. In order to gain a greater understanding
of the phenotypes, we have analysed the expression of several axial mesoderm markers
in mutant embryos of all four genes. In flh and mom, Ntl expression is normal
in the germ ring and tailbud, while the expression of Nd and other notochord markers
in the axial mesodermal region is disrupted. Nd expression is normal in doc embryos
until early semitic stages, when there is a reduction in expression which is first
seen in anterior regions of the embryo. This suggests a function for doc in the
maintenance of ntl expression. Other notochord markers such as twist, sonic hedgehog
and axial are not expressed in the axial mesoderm of ntl embryos, their expression
parallels the expression of ntl in the axial mesoderm of mutant doc,flh and mom
embryos, indicating that ntl is required for the expression of these markers.
The role of doc in the expression of the notochord markers appears indirect via
ntl. Floor plate formation is disrupted in most regions in flh and mom mutant
embryos but is present in mutant ntl and doc embryos. In mutant embryos with strong
ntl alleles the band of cells expressing floor plate markers is broadened. A similar
broadening is also observed in the axial mesoderm underlying the floor plate of
ntl embryos, suggesting a direct involvement of the notochord precursor cells
in floor plate induction. Mutations in al of these four genes result in embryos
lacking a horizontal myoseptum and muscle pioneer cells, both of which are thought
to be induced by the notochord. These somite defects can be traced back to an
impairment of the specification of the adaxial cells during early stages of development.
Transplantation of wild-type cells into mutant doc embryos reveals that wild-type
notochord cells are sufficient to induce horizontal myoseptum formation in the
flanking mutant tissue. Thus dec, like flh and ntl, acts cell autonomously in
the notochord. In addition to the four mutants with defects in early notochord
formation, we have isolated 84 mutants, defining at least 15 genes, with defects
in later stages of notochord development. These are listed in an appendix to this
study.
acknowledgement: We thank Bob Riggleman for providing the twist probe prior to publication,
William Talbot, Anne Melby, Marnie Halpern and Chuck Kimmel for communicating results
prior to publication, Bill Trevarrow for the flhn1 allele, Stefan Schulte-Merker
for providing the ntl antibody, and N. H. Patel for providing the Eng antibody (4D9).
We thank Klaus Trummler, Frank Uhlmann and Mathias Metz for assistance in the analysis
of the ntl alleles, Silke Rudolph for technical assistance, Heike Schauerte for
helping with the in situ hybridization, and Joel Wilson and Cornelia Fricke for
their help with the fish work, and finally Tanya Whitfield, Francisco Pelegri, Darren
Gilmour and Stefan Schulte-Merker for discussion and help with the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Jörg
full_name: Odenthal, Jörg
last_name: Odenthal
- first_name: Pascal
full_name: Haffter, Pascal
last_name: Haffter
- first_name: Elisabeth
full_name: Vogelsang, Elisabeth
last_name: Vogelsang
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
- first_name: Fredericus
full_name: Van Eeden, Fredericus
last_name: Van Eeden
- first_name: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
- first_name: Michael
full_name: Granato, Michael
last_name: Granato
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
- 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: Yunjin
full_name: Jiang, Yunjin
last_name: Jiang
- first_name: Donald
full_name: Kane, Donald
last_name: Kane
- first_name: Robert
full_name: Kelsh, Robert
last_name: Kelsh
- first_name: Mary
full_name: Mullins, Mary
last_name: Mullins
- first_name: Rachel
full_name: Warga, Rachel
last_name: Warga
- first_name: Miguel
full_name: Allende, Miguel
last_name: Allende
- first_name: Eric
full_name: Weinberg, Eric
last_name: Weinberg
- first_name: Christiane
full_name: Nüsslein Volhard, Christiane
last_name: Nüsslein Volhard
citation:
ama: Odenthal J, Haffter P, Vogelsang E, et al. Mutations affecting the formation
of the notochord in the zebrafish, Danio rerio. Development. 1996;123(1):103-115.
doi:10.1242/dev.123.1.103
apa: Odenthal, J., Haffter, P., Vogelsang, E., Brand, M., Van Eeden, F., Furutani
Seiki, M., … Nüsslein Volhard, C. (1996). Mutations affecting the formation of
the notochord in the zebrafish, Danio rerio. Development. Company of Biologists.
https://doi.org/10.1242/dev.123.1.103
chicago: Odenthal, Jörg, Pascal Haffter, Elisabeth Vogelsang, Michael Brand, Fredericus
Van Eeden, Makoto Furutani Seiki, Michael Granato, et al. “Mutations Affecting
the Formation of the Notochord in the Zebrafish, Danio Rerio.” Development.
Company of Biologists, 1996. https://doi.org/10.1242/dev.123.1.103.
ieee: J. Odenthal et al., “Mutations affecting the formation of the notochord
in the zebrafish, Danio rerio,” Development, vol. 123, no. 1. Company of
Biologists, pp. 103–115, 1996.
ista: Odenthal J, Haffter P, Vogelsang E, Brand M, Van Eeden F, Furutani Seiki M,
Granato M, Hammerschmidt M, Heisenberg C-PJ, Jiang Y, Kane D, Kelsh R, Mullins
M, Warga R, Allende M, Weinberg E, Nüsslein Volhard C. 1996. Mutations affecting
the formation of the notochord in the zebrafish, Danio rerio. Development. 123(1),
103–115.
mla: Odenthal, Jörg, et al. “Mutations Affecting the Formation of the Notochord
in the Zebrafish, Danio Rerio.” Development, vol. 123, no. 1, Company of
Biologists, 1996, pp. 103–15, doi:10.1242/dev.123.1.103.
short: J. Odenthal, P. Haffter, E. Vogelsang, M. Brand, F. Van Eeden, M. Furutani
Seiki, M. Granato, M. Hammerschmidt, C.-P.J. Heisenberg, Y. Jiang, D. Kane, R.
Kelsh, M. Mullins, R. Warga, M. Allende, E. Weinberg, C. Nüsslein Volhard, Development
123 (1996) 103–115.
date_created: 2018-12-11T12:07:21Z
date_published: 1996-12-01T00:00:00Z
date_updated: 2022-08-08T08:06:12Z
day: '01'
doi: 10.1242/dev.123.1.103
extern: '1'
external_id:
pmid:
- '9007233'
intvolume: ' 123'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://journals.biologists.com/dev/article/123/1/103/39325/Mutations-affecting-the-formation-of-the-notochord
month: '12'
oa: 1
oa_version: Published Version
page: 103 - 115
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1954'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutations affecting the formation of the notochord in the zebrafish, Danio
rerio
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 123
year: '1996'
...
---
_id: '4170'
abstract:
- lang: eng
text: We identified 6 genes that are essential for specifying ventral regions of
the early zebrafish embryo, Mutations in these genes cause an expansion of structures
normally derived from dorsal-lateral regions of the blastula at the expense of
ventrally derived structures, A series of phenotypes of varied strengths is observed
with different alleles of these mutants, The weakest phenotype is a reduction
in the ventral tail fin, observed as a dominant phenotype of swirl, piggytail,
and somitabun and a recessive phenotype of min fin, lost-a-fin and some piggytail
alleles, With increasing phenotypic strength, the blood and pronephric anlagen
are also reduced or absent, while the paraxial mesoderm and anterior neuroectoderm
is progressively expanded, In the strong phenotypes, displayed by homozygous embryos
of snailhouse, swirl and somitabun, the somites circle around the embryo and the
midbrain region is expanded laterally, Several mutations in this group of genes
are semidominant as well as recessive indicating a strong dosage sensitivity of
the processes involved, Mutations in the piggytail gene display an unusual dominance
that depends on both a maternal and zygotic heterozygous genotype, while somitabun
is a fully penetrant dominant maternal-effect mutation, The similar and overlapping
phenotypes of mutants of the 6 genes identified suggest that they function in
a common pathway, which begins in oogenesis, but also depends on factors provided
after the onset of zygotic transcription, presumably during blastula stages, This
pathway provides ventral positional information, counteracting the dorsalizing
instructions of the organizer, which is localized in the dorsal shield.
acknowledgement: 'We would like to thank: Eric Weinberg, and David Ransom and Leonard
Zon for providing the myoD and gata1 cDNA clone, respectively, prior to publication;
David Ransom for pointing out the histological blood staining method; J. S. Joly
for the eve1 cDNA clone; Mary Ellen Lane, Siegfried Roth, Stefan Schulte-Merker,
Herbert Steinbeiser for helpful comments on the manuscript; and very special thanks
to Karin Finger-Miller for technical support, as well as to Hans-Martin Maischein,
Amanda Wilson, Jörg Zeller, and Cosima Fabian. This work was supported by an NIH
postdoctoral fellowship to M. C. M.'
article_processing_charge: No
article_type: original
author:
- first_name: Mary
full_name: Mullins, Mary
last_name: Mullins
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
- first_name: Donald
full_name: Kane, Donald
last_name: Kane
- first_name: Jörg
full_name: Odenthal, Jörg
last_name: Odenthal
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
- first_name: Fredericus
full_name: Van Eeden, Fredericus
last_name: Van Eeden
- first_name: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
- first_name: Michael
full_name: Granato, Michael
last_name: Granato
- first_name: Pascal
full_name: Haffter, Pascal
last_name: Haffter
- 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: Yunjin
full_name: Jiang, Yunjin
last_name: Jiang
- first_name: Robert
full_name: Kelsh, Robert
last_name: Kelsh
- first_name: Christiane
full_name: Nüsslein Volhard, Christiane
last_name: Nüsslein Volhard
citation:
ama: 'Mullins M, Hammerschmidt M, Kane D, et al. Genes establishing dorsoventral
pattern formation in the zebrafish embryo: The ventral specifying genes. Development.
1996;123(1):81-93. doi:10.1242/dev.123.1.81'
apa: 'Mullins, M., Hammerschmidt, M., Kane, D., Odenthal, J., Brand, M., Van Eeden,
F., … Nüsslein Volhard, C. (1996). Genes establishing dorsoventral pattern formation
in the zebrafish embryo: The ventral specifying genes. Development. Company
of Biologists. https://doi.org/10.1242/dev.123.1.81'
chicago: 'Mullins, Mary, Matthias Hammerschmidt, Donald Kane, Jörg Odenthal, Michael
Brand, Fredericus Van Eeden, Makoto Furutani Seiki, et al. “Genes Establishing
Dorsoventral Pattern Formation in the Zebrafish Embryo: The Ventral Specifying
Genes.” Development. Company of Biologists, 1996. https://doi.org/10.1242/dev.123.1.81.'
ieee: 'M. Mullins et al., “Genes establishing dorsoventral pattern formation
in the zebrafish embryo: The ventral specifying genes,” Development, vol.
123, no. 1. Company of Biologists, pp. 81–93, 1996.'
ista: 'Mullins M, Hammerschmidt M, Kane D, Odenthal J, Brand M, Van Eeden F, Furutani
Seiki M, Granato M, Haffter P, Heisenberg C-PJ, Jiang Y, Kelsh R, Nüsslein Volhard
C. 1996. Genes establishing dorsoventral pattern formation in the zebrafish embryo:
The ventral specifying genes. Development. 123(1), 81–93.'
mla: 'Mullins, Mary, et al. “Genes Establishing Dorsoventral Pattern Formation in
the Zebrafish Embryo: The Ventral Specifying Genes.” Development, vol.
123, no. 1, Company of Biologists, 1996, pp. 81–93, doi:10.1242/dev.123.1.81.'
short: M. Mullins, M. Hammerschmidt, D. Kane, J. Odenthal, M. Brand, F. Van Eeden,
M. Furutani Seiki, M. Granato, P. Haffter, C.-P.J. Heisenberg, Y. Jiang, R. Kelsh,
C. Nüsslein Volhard, Development 123 (1996) 81–93.
date_created: 2018-12-11T12:07:22Z
date_published: 1996-12-01T00:00:00Z
date_updated: 2022-08-05T12:01:06Z
day: '01'
doi: 10.1242/dev.123.1.81
extern: '1'
external_id:
pmid:
- '9007231'
intvolume: ' 123'
issue: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 81 - 93
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1951'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genes establishing dorsoventral pattern formation in the zebrafish embryo:
The ventral specifying genes'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 123
year: '1996'
...