---
_id: '4255'
abstract:
- lang: eng
text: 'Humans and their closest evolutionary relatives, the chimpanzees, differ
in ∼1.24% of their genomic DNA sequences. The fraction of these changes accumulated
during the speciation processes that have separated the two lineages may be of
special relevance in understanding the basis of their differences. We analyzed
human and chimpanzee sequence data to search for the patterns of divergence and
polymorphism predicted by a theoretical model of speciation. According to the
model, positively selected changes should accumulate in chromosomes that present
fixed structural differences, such as inversions, between the two species. Protein
evolution was more than 2.2 times faster in chromosomes that had undergone structural
rearrangements compared with colinear chromosomes. Also, nucleotide variability
is slightly lower in rearranged chromosomes. These patterns of divergence and
polymorphism may be, at least in part, the molecular footprint of speciation events
in the human and chimpanzee lineages. '
article_processing_charge: No
article_type: original
author:
- first_name: Arcadio
full_name: Navarro, Arcadio
last_name: Navarro
- 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: Navarro A, Barton NH. Chromosomal speciation and molecular divergence -- Accelerated
evolution in rearranged chromosomes. Science. 2003;300(5617):321-324. doi:10.1126/science.1080600
apa: Navarro, A., & Barton, N. H. (2003). Chromosomal speciation and molecular
divergence -- Accelerated evolution in rearranged chromosomes. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1080600
chicago: Navarro, Arcadio, and Nicholas H Barton. “Chromosomal Speciation and Molecular
Divergence -- Accelerated Evolution in Rearranged Chromosomes.” Science.
American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1080600 .
ieee: A. Navarro and N. H. Barton, “Chromosomal speciation and molecular divergence
-- Accelerated evolution in rearranged chromosomes,” Science, vol. 300,
no. 5617. American Association for the Advancement of Science, pp. 321–324, 2003.
ista: Navarro A, Barton NH. 2003. Chromosomal speciation and molecular divergence
-- Accelerated evolution in rearranged chromosomes. Science. 300(5617), 321–324.
mla: Navarro, Arcadio, and Nicholas H. Barton. “Chromosomal Speciation and Molecular
Divergence -- Accelerated Evolution in Rearranged Chromosomes.” Science,
vol. 300, no. 5617, American Association for the Advancement of Science, 2003,
pp. 321–24, doi:10.1126/science.1080600
.
short: A. Navarro, N.H. Barton, Science 300 (2003) 321–324.
date_created: 2018-12-11T12:07:53Z
date_published: 2003-04-11T00:00:00Z
date_updated: 2024-02-26T13:37:51Z
day: '11'
doi: '10.1126/science.1080600 '
extern: '1'
external_id:
pmid:
- ' 12690198'
intvolume: ' 300'
issue: '5617'
language:
- iso: eng
month: '04'
oa_version: None
page: 321 - 324
pmid: 1
publication: Science
publication_identifier:
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '1841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosomal speciation and molecular divergence -- Accelerated evolution in
rearranged chromosomes
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 300
year: '2003'
...
---
_id: '4256'
abstract:
- lang: eng
text: Artificial Life models may shed new light on the long-standing challenge for
evolutionary biology of explaining the origins of complex organs. Real progress
on this issue, however, requires Artificial Life researchers to take seriously
the tools and insights from population genetics.
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: Willem
full_name: Zuidema, Willem
last_name: Zuidema
citation:
ama: Barton NH, Zuidema W. The erratic path towards complexity. Current Biology.
2003;13(16):R649-R651. doi:10.1016/S0960-9822(03)00573-6
apa: Barton, N. H., & Zuidema, W. (2003). The erratic path towards complexity.
Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(03)00573-6
chicago: Barton, Nicholas H, and Willem Zuidema. “The Erratic Path towards Complexity.”
Current Biology. Cell Press, 2003. https://doi.org/10.1016/S0960-9822(03)00573-6.
ieee: N. H. Barton and W. Zuidema, “The erratic path towards complexity,” Current
Biology, vol. 13, no. 16. Cell Press, pp. R649–R651, 2003.
ista: Barton NH, Zuidema W. 2003. The erratic path towards complexity. Current Biology.
13(16), R649–R651.
mla: Barton, Nicholas H., and Willem Zuidema. “The Erratic Path towards Complexity.”
Current Biology, vol. 13, no. 16, Cell Press, 2003, pp. R649–51, doi:10.1016/S0960-9822(03)00573-6.
short: N.H. Barton, W. Zuidema, Current Biology 13 (2003) R649–R651.
date_created: 2018-12-11T12:07:53Z
date_published: 2003-08-19T00:00:00Z
date_updated: 2024-01-23T09:41:33Z
day: '19'
doi: 10.1016/S0960-9822(03)00573-6
extern: '1'
intvolume: ' 13'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: Published Version
page: R649 - R651
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
publist_id: '1838'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The erratic path towards complexity
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 13
year: '2003'
...
---
_id: '4257'
abstract:
- lang: eng
text: Variation within a species may be structured both geographically and by genetic
background. We review the effects of such structuring on neutral variants, using
a framework based on the coalescent process. Short-term effects of sex differences
and age structure can be averaged out using fast timescale approximations, allowing
a simple general treatment of effective population size and migration. We consider
the effects of geographic structure on variation within and between local populations,
first in general terms, and then for specific migration models. We discuss the
close parallels between geographic structure and stable types of genetic structure
caused by selection, including balancing selection and background selection. The
effects of departures from stability, such as selective sweeps and population
bottlenecks, are also described. Methods for distinguishing population history
from the effects of ongoing gene flow are discussed. We relate the theoretical
results to observed patterns of variation in natural populations.
article_processing_charge: No
article_type: original
author:
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Deborah
full_name: Charlesworth, Deborah
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, Charlesworth D, Barton NH. The effects of genetic and geographic
structure on neutral variation. Annual Review of Ecology and Systematics.
2003;34:99-125. doi:10.1146/annurev.ecolsys.34.011802.132359
apa: Charlesworth, B., Charlesworth, D., & Barton, N. H. (2003). The effects
of genetic and geographic structure on neutral variation. Annual Review of
Ecology and Systematics. Annual Reviews. https://doi.org/10.1146/annurev.ecolsys.34.011802.132359
chicago: Charlesworth, Brian, Deborah Charlesworth, and Nicholas H Barton. “The
Effects of Genetic and Geographic Structure on Neutral Variation.” Annual Review
of Ecology and Systematics. Annual Reviews, 2003. https://doi.org/10.1146/annurev.ecolsys.34.011802.132359.
ieee: B. Charlesworth, D. Charlesworth, and N. H. Barton, “The effects of genetic
and geographic structure on neutral variation,” Annual Review of Ecology and
Systematics, vol. 34. Annual Reviews, pp. 99–125, 2003.
ista: Charlesworth B, Charlesworth D, Barton NH. 2003. The effects of genetic and
geographic structure on neutral variation. Annual Review of Ecology and Systematics.
34, 99–125.
mla: Charlesworth, Brian, et al. “The Effects of Genetic and Geographic Structure
on Neutral Variation.” Annual Review of Ecology and Systematics, vol. 34,
Annual Reviews, 2003, pp. 99–125, doi:10.1146/annurev.ecolsys.34.011802.132359.
short: B. Charlesworth, D. Charlesworth, N.H. Barton, Annual Review of Ecology and
Systematics 34 (2003) 99–125.
date_created: 2018-12-11T12:07:53Z
date_published: 2003-11-01T00:00:00Z
date_updated: 2024-01-23T10:15:44Z
day: '01'
doi: 10.1146/annurev.ecolsys.34.011802.132359
extern: '1'
intvolume: ' 34'
language:
- iso: eng
month: '11'
oa_version: None
page: 99 - 125
publication: Annual Review of Ecology and Systematics
publication_identifier:
issn:
- 1543-592X
publication_status: published
publisher: Annual Reviews
publist_id: '1839'
quality_controlled: '1'
status: public
title: The effects of genetic and geographic structure on neutral variation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 34
year: '2003'
...
---
_id: '4338'
abstract:
- lang: eng
text: 'Mosaic hybrid zones arise when ecologically differentiated taxa hybridize
across a network of habitat patches. Frequent interbreeding across a small-scale
patchwork can erode species differences that might have been preserved in a clinal
hybrid zone. In particular, the rapid breakdown of neutral divergence sets an
upper limit to the time for which differences at marker loci can persist. We present
here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina
bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our
20 × 20 km study area, we detected no evidence of a clinal transition but found
a strong association between aquatic habitat and mean allele frequencies at four
molecular markers. In particular, pure populations of B. bombina in ponds appear
to cause massive introgression into the surrounding B. variegata gene pool found
in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid
populations was remarkably similar to those of a previously studied transect near
Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote
deficit and linkage disequilibrium in each country are similar. In Apahida, the
observed strong linkage disequilibria should stem from an imperfect habitat preference
that guides most (but not all) adults into the habitats to which they are adapted.
In the absence of a clinal structure, the inferred migration rate between habitats
implies that associations between selected loci and neutral markers should break
down rapidly. Although plausible selection strengths can maintain differentiation
at those loci adapting the toads to either permanent or temporary breeding sites,
the divergence at neutral markers must be transient. The hybrid zone may be approaching
a state in which the gene pools are homogenized at all but the selected loci,
not dissimilar from an early stage of sympatric divergence.'
acknowledgement: "We thank G. Mara and T. Galbena for enthusiastic field\r\nassistance,
A. Hofmann and R. Sieglstetter for access to their\r\nunpublished data, B. Fo¨rg-Brey
and G. Praetzel for help in\r\nthe lab. Helpful comments on a previous version of
the man-\r\nuscript were provided by R. Ennos, J. Szymura, F. Balloux,\r\nJ. Bridle,
L. Kruuk, F. Bonhomme, M. Arnold, and two anon-\r\nymous reviewers. We also thank
A. Pinggera for providing\r\nthe cover illustration. This work was supported by
Natural\r\nEnvironment Research Council studentships to THV and TRS\r\nand Deutsche
Forschungsgemeinschaft grant Nu 51/2-1 to BN."
article_processing_charge: No
article_type: original
author:
- first_name: Timothy
full_name: Vines, Timothy
last_name: Vines
- first_name: S C
full_name: Kohler, S C
last_name: Kohler
- first_name: M
full_name: Thiel, M
last_name: Thiel
- first_name: Ioan
full_name: Ghira, Ioan
last_name: Ghira
- first_name: T R
full_name: Sands, T R
last_name: Sands
- first_name: Catriona
full_name: Maccallum, Catriona
last_name: Maccallum
- 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: Beate
full_name: Nürnberger, Beate
last_name: Nürnberger
citation:
ama: Vines T, Kohler SC, Thiel M, et al. On the maintenance of reproductive isolation
in a mosaic hybrid zone between the toads Bombina bombina and B. variegata. Evolution.
2003;57(8):1876-1888. doi:10.1111/j.0014-3820.2003.tb00595.x
apa: Vines, T., Kohler, S. C., Thiel, M., Ghira, I., Sands, T. R., Maccallum, C.,
… Nürnberger, B. (2003). On the maintenance of reproductive isolation in a mosaic
hybrid zone between the toads Bombina bombina and B. variegata. Evolution.
Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2003.tb00595.x
chicago: Vines, Timothy, S C Kohler, M Thiel, Ioan Ghira, T R Sands, Catriona Maccallum,
Nicholas H Barton, and Beate Nürnberger. “On the Maintenance of Reproductive Isolation
in a Mosaic Hybrid Zone between the Toads Bombina Bombina and B. Variegata.” Evolution.
Wiley-Blackwell, 2003. https://doi.org/10.1111/j.0014-3820.2003.tb00595.x.
ieee: T. Vines et al., “On the maintenance of reproductive isolation in a
mosaic hybrid zone between the toads Bombina bombina and B. variegata,” Evolution,
vol. 57, no. 8. Wiley-Blackwell, pp. 1876–1888, 2003.
ista: Vines T, Kohler SC, Thiel M, Ghira I, Sands TR, Maccallum C, Barton NH, Nürnberger
B. 2003. On the maintenance of reproductive isolation in a mosaic hybrid zone
between the toads Bombina bombina and B. variegata. Evolution. 57(8), 1876–1888.
mla: Vines, Timothy, et al. “On the Maintenance of Reproductive Isolation in a Mosaic
Hybrid Zone between the Toads Bombina Bombina and B. Variegata.” Evolution,
vol. 57, no. 8, Wiley-Blackwell, 2003, pp. 1876–88, doi:10.1111/j.0014-3820.2003.tb00595.x.
short: T. Vines, S.C. Kohler, M. Thiel, I. Ghira, T.R. Sands, C. Maccallum, N.H.
Barton, B. Nürnberger, Evolution 57 (2003) 1876–1888.
date_created: 2018-12-11T12:08:20Z
date_published: 2003-08-01T00:00:00Z
date_updated: 2024-01-23T09:16:43Z
day: '01'
doi: 10.1111/j.0014-3820.2003.tb00595.x
extern: '1'
intvolume: ' 57'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1876 - 1888
publication: Evolution
publication_identifier:
issn:
- 0014-3820
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1692'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the maintenance of reproductive isolation in a mosaic hybrid zone between
the toads Bombina bombina and B. variegata
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 57
year: '2003'
...
---
_id: '4348'
abstract:
- lang: eng
text: Many questions in evolutionary biology are best addressed by comparing traits
in different species. Often such studies involve mapping characters on phylogenetic
trees. Mapping characters on trees allows the nature, number, and timing of the
transformations to be identified. The parsimony method is the only method available
for mapping morphological characters on phylogenies. Although the parsimony method
often makes reasonable reconstructions of the history of a character, it has a
number of limitations. These limitations include the inability to consider more
than a single change along a branch on a tree and the uncoupling of evolutionary
time from amount of character change. We extended a method described by Nielsen
(2002, Syst. Biol. 51:729-739) to the mapping of morphological characters under
continuous-time Markov models and demonstrate here the utility of the method for
mapping characters on trees and for identifying character correlation.
acknowledgement: "We thank J. Kohn, D. Stern, and M. Hart for sending the alignments\r\nused
in this study. J.P.H. was supported by NSF grants DEB-0075406\r\nand MCB-0075404.
R.N. was supported by NSF grant DEB-0089487."
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Huelsenbeck, John
last_name: Huelsenbeck
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Huelsenbeck J, Nielsen R, Bollback JP. Stochastic mapping of morphological
characters. Systematic Biology. 2003;52(2):131-158. doi:10.1080/10635150390192780
apa: Huelsenbeck, J., Nielsen, R., & Bollback, J. P. (2003). Stochastic mapping
of morphological characters. Systematic Biology. Oxford University Press.
https://doi.org/10.1080/10635150390192780
chicago: Huelsenbeck, John, Rasmus Nielsen, and Jonathan P Bollback. “Stochastic
Mapping of Morphological Characters.” Systematic Biology. Oxford University
Press, 2003. https://doi.org/10.1080/10635150390192780.
ieee: J. Huelsenbeck, R. Nielsen, and J. P. Bollback, “Stochastic mapping of morphological
characters,” Systematic Biology, vol. 52, no. 2. Oxford University Press,
pp. 131–158, 2003.
ista: Huelsenbeck J, Nielsen R, Bollback JP. 2003. Stochastic mapping of morphological
characters. Systematic Biology. 52(2), 131–158.
mla: Huelsenbeck, John, et al. “Stochastic Mapping of Morphological Characters.”
Systematic Biology, vol. 52, no. 2, Oxford University Press, 2003, pp.
131–58, doi:10.1080/10635150390192780.
short: J. Huelsenbeck, R. Nielsen, J.P. Bollback, Systematic Biology 52 (2003) 131–158.
date_created: 2018-12-11T12:08:24Z
date_published: 2003-04-01T00:00:00Z
date_updated: 2024-01-23T09:10:59Z
day: '01'
doi: 10.1080/10635150390192780
extern: '1'
external_id:
pmid:
- '12746144 '
intvolume: ' 52'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 131 - 158
pmid: 1
publication: Systematic Biology
publication_identifier:
issn:
- '0039-7989 '
publication_status: published
publisher: Oxford University Press
publist_id: '1111'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic mapping of morphological characters
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 52
year: '2003'
...
---
_id: '4350'
abstract:
- lang: eng
text: 'The phylogeny of Crocodylia offers an unusual twist on the usual molecules
versus morphology story. The true gharial (Gavialis gangeticus) and the false
gharial (Tomistoma schlegelii), as their common names imply, have appeared in
all cladistic morphological analyses as distantly related species, convergent
upon a similar morphology. In contrast, all previous molecular studies have shown
them to be sister taxa. We present the first phylogenetic study of Crocodylia
using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator
mississippiensis to facilitate primer design and then sequenced an 1,100-base
pair fragment that includes both coding and noncoding regions and informative
indels for one species in each extant crocodylian genus and six avian outgroups.
Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference
all strongly agreed on the same tree, which is identical to the tree found in
previous molecular analyses: Gavialis and Tomistoma are sister taxa and together
are the sister group of Crocodylidae. Kishino-Hasegawa tests rejected the morphological
tree in favor of the molecular tree. We excluded long-branch attraction and variation
in base composition among taxa as explanations for this topology. To explore the
causes of discrepancy between molecular and morphological estimates of crocodylian
phylogeny, we examined puzzling features of the morphological data using a priori
partitions of the data based on anatomical regions and investigated the effects
of different coding schemes for two obvious morphological similarities of the
two gharials.'
acknowledgement: "We thank Lou Densmore and Herb Dessauer for crocodylian tissue\r\nsamples.
Dave Swofford, Jim Wilgenbusch, and Kevin de Queiroz gave\r\nus much helpful advice.
Dave also allowed us to use an experimental\r\nversion of PAUP∗ with partitioned
likelihood, and Jim also provided\r\nprograms to make possible partitioned model
KH tests. Chris Brochu\r\nand Lou Densmore sent us preprints of their papers in
press, and Chris\r\nprovided an unpublished version of his morphological data set.
Allan\r\nBaker, Lou Densmore, and an anonymous reviewer provided useful\r\ncomments
on the manuscript. We especially wish to acknowledge Chris\r\nBrochu’s help; although
we remain in disagreement on many points,\r\nhis comments on several previous drafts
have greatly improved this\r\npaper."
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Harshman, John
last_name: Harshman
- first_name: Christopher
full_name: Huddleston, Christopher
last_name: Huddleston
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Thomas
full_name: Parsons, Thomas
last_name: Parsons
- first_name: Michael
full_name: Braun, Michael
last_name: Braun
citation:
ama: 'Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. True and false
gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 2003;52(3):386-402.
doi:10.1080/10635150390197028'
apa: 'Harshman, J., Huddleston, C., Bollback, J. P., Parsons, T., & Braun, M.
(2003). True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic
Biology. Oxford University Press. https://doi.org/10.1080/10635150390197028'
chicago: 'Harshman, John, Christopher Huddleston, Jonathan P Bollback, Thomas Parsons,
and Michael Braun. “True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia.”
Systematic Biology. Oxford University Press, 2003. https://doi.org/10.1080/10635150390197028.'
ieee: 'J. Harshman, C. Huddleston, J. P. Bollback, T. Parsons, and M. Braun, “True
and false gharials: A nuclear gene phylogeny of crocodylia,” Systematic Biology,
vol. 52, no. 3. Oxford University Press, pp. 386–402, 2003.'
ista: 'Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. 2003. True and
false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 52(3),
386–402.'
mla: 'Harshman, John, et al. “True and False Gharials: A Nuclear Gene Phylogeny
of Crocodylia.” Systematic Biology, vol. 52, no. 3, Oxford University Press,
2003, pp. 386–402, doi:10.1080/10635150390197028.'
short: J. Harshman, C. Huddleston, J.P. Bollback, T. Parsons, M. Braun, Systematic
Biology 52 (2003) 386–402.
date_created: 2018-12-11T12:08:24Z
date_published: 2003-06-01T00:00:00Z
date_updated: 2024-01-23T08:53:58Z
day: '01'
doi: 10.1080/10635150390197028
extern: '1'
external_id:
pmid:
- ' 12775527'
intvolume: ' 52'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 386 - 402
pmid: 1
publication: Systematic Biology
publication_identifier:
issn:
- '0039-7989 '
publication_status: published
publisher: Oxford University Press
publist_id: '1110'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'True and false gharials: A nuclear gene phylogeny of crocodylia'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 52
year: '2003'
...
---
_id: '4416'
abstract:
- lang: eng
text: "Methods for the formal specification and verification of systems are indispensible
for the development of complex yet correct systems. In formal verification, the
designer describes the system in a modeling language with a well-defined semantics,
and this system description is analyzed against a set of correctness requirements.
Model checking is an algorithmic technique to check that a system description
indeed satisfies correctness requirements given as logical specifications. While
successful in hardware verification, the potential for model checking for software
and embedded systems has not yet been realized. This is because traditional model
checking focuses on systems modeled as finite state-transition graphs. While a
natural model for hardware (especially synchronous hardware), state-transition
graphs often do not capture software and embedded systems at an appropriate level
of granularity. This dissertation considers two orthogonal extensions to finite
state-transition graphs making model checking techniques applicable to both a
wider class of systems and a wider class of properties.\r\n\r\nThe first direction
is an extension to infinite-state structures finitely represented using constraints
and operations on constraints. Infinite state arises when we wish to model variables
with unbounded range (e.g., integers), or data structures, or real time. We provide
a uniform framework of symbolic region algebras to study model checking of infinite-state
systems. We also provide sufficient language-independent termination conditions
for symbolic model checking algorithms on infinite state systems.\r\n\r\nThe second
direction supplements verification with game theoretic reasoning. Games are natural
models for interactions between components. We study game theoretic behavior with
winning conditions given by temporal logic objectives both in the deterministic
and in the probabilistic context. For deterministic games, we provide an extremal
model characterization of fixpoint algorithms that link solutions of verification
problems to solutions for games. For probabilistic games we study fixpoint characterization
of winning probabilities for games with omega-regular winning objectives, and
construct (epsilon-)optimal winning strategies."
article_processing_charge: No
author:
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: Majumdar R. Symbolic algorithms for verification and control. 2003:1-201.
apa: Majumdar, R. (2003). Symbolic algorithms for verification and control.
University of California, Berkeley.
chicago: Majumdar, Ritankar. “Symbolic Algorithms for Verification and Control.”
University of California, Berkeley, 2003.
ieee: R. Majumdar, “Symbolic algorithms for verification and control,” University
of California, Berkeley, 2003.
ista: Majumdar R. 2003. Symbolic algorithms for verification and control. University
of California, Berkeley.
mla: Majumdar, Ritankar. Symbolic Algorithms for Verification and Control.
University of California, Berkeley, 2003, pp. 1–201.
short: R. Majumdar, Symbolic Algorithms for Verification and Control, University
of California, Berkeley, 2003.
date_created: 2018-12-11T12:08:44Z
date_published: 2003-12-01T00:00:00Z
date_updated: 2021-01-12T07:56:49Z
day: '01'
extern: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 1 - 201
publication_status: published
publisher: University of California, Berkeley
publist_id: '313'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Symbolic algorithms for verification and control
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2003'
...
---
_id: '4425'
abstract:
- lang: eng
text: "Giotto provides a time-triggered programmer’s model for the implementation
of embedded control systems with hard real-time constraints. Giotto’s precise
semantics and predictabil- ity make it suitable for safety-critical applications.\r\nGiotto
is based around the idea that time-triggered task invocation together with time-triggered
mode switching can form a useful programming model for real-time systems. To substantiate
this claim, we describe the use of Giotto to refactor the software of a small,
autonomous helicopter. The ease with which Giotto expresses the existing software
provides evidence that Giotto is an appropriate programming language for control
systems.\r\nSince Giotto is a real-time programming language, ensuring that Giotto
programs meet their deadlines is crucial. To study precedence-constrained Giotto
scheduling, we first examine single-mode, single-processor scheduling. We extend
to an infinite, periodic setting the classical problem of meeting deadlines for
a set of tasks with release times, deadlines, precedence constraints, and preemption.
We then develop an algorithm for scheduling Giotto programs on a single processor
by representing Giotto programs as instances of the extended scheduling problem.\r\nNext,
we study multi-mode, single-processor Giotto scheduling. This problem is different
from classical scheduling problems, since in our precedence-constrained approach,
the deadlines of tasks may vary depending on the mode switching behavior of the
program. We present conditional scheduling models which capture this varying-deadline
behavior. We develop polynomial-time algorithms for some conditional scheduling
models, and prove oth- ers to be computationally hard. We show how to represent
multi-mode Giotto programs as instances of the model, resulting in an algorithm
for scheduling multi-mode Giotto programs on a single processor.\r\nFinally, we
show that the problem of scheduling Giotto programs for multiple net- worked processors
is strongly NP-hard."
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Horowitz, Benjamin
last_name: Horowitz
citation:
ama: 'Horowitz B. Giotto: A time-triggered language for embedded programming. 2003:1-237.'
apa: 'Horowitz, B. (2003). Giotto: A time-triggered language for embedded programming.
University of California, Berkeley.'
chicago: 'Horowitz, Benjamin. “Giotto: A Time-Triggered Language for Embedded Programming.”
University of California, Berkeley, 2003.'
ieee: 'B. Horowitz, “Giotto: A time-triggered language for embedded programming,”
University of California, Berkeley, 2003.'
ista: 'Horowitz B. 2003. Giotto: A time-triggered language for embedded programming.
University of California, Berkeley.'
mla: 'Horowitz, Benjamin. Giotto: A Time-Triggered Language for Embedded Programming.
University of California, Berkeley, 2003, pp. 1–237.'
short: 'B. Horowitz, Giotto: A Time-Triggered Language for Embedded Programming,
University of California, Berkeley, 2003.'
date_created: 2018-12-11T12:08:47Z
date_published: 2003-10-01T00:00:00Z
date_updated: 2021-01-12T07:56:53Z
day: '01'
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 1 - 237
publication_status: published
publisher: University of California, Berkeley
publist_id: '305'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: 'Giotto: A time-triggered language for embedded programming'
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2003'
...
---
_id: '4460'
abstract:
- lang: eng
text: "Symbolic model checking, which enables the automatic verification of large
systems, proceeds by calculating expressions that represent state sets. Traditionally,
symbolic model-checking tools are based on back- ward state traversal; their basic
operation is the function pre, which, given a set of states, returns the set of
all predecessor states. This is because specifiers usually employ formalisms with
future-time modalities, which are naturally evaluated by iterating applications
of pre. It has been shown experimentally that symbolic model checking can perform
significantly better if it is based, instead, on forward state traversal; in this
case, the basic operation is the function post, which, given a set of states,
returns the set of all successor states. This is because forward state traversal
can ensure that only parts of the state space that are reachable from an initial
state and relevant for the satisfaction or violation of the specification are
explored; that is, errors can be detected as soon as possible.\r\nIn this paper,
we investigate which specifications can be checked by symbolic forward state traversal.
We formulate the problems of symbolic backward and forward model checking by means
of two μ-calculi. The pre-μ calculus is based on the pre operation, and the post-μ
calculus is based on the post operation. These two μ-calculi induce query logics,
which augment fixpoint expressions with a boolean emptiness query. Using query
logics, we are able to relate and compare the symbolic backward and forward approaches.
In particular, we prove that all ω-regular (linear-time) specifications can be
expressed as post-μ queries, and therefore checked using symbolic forward state
traversal. On the other hand, we show that there are simple branching-time specifications
that cannot be checked in this way."
acknowledgement: This research was supported in part by the SRC contract 99-TJ-683.003
and the NSF grant CCR-9988172.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: Henzinger TA, Kupferman O, Qadeer S. From pre-historic to post-modern symbolic
model checking. Formal Methods in System Design. 2003;23(3):303-327. doi:10.1023/A:1026228213080
apa: Henzinger, T. A., Kupferman, O., & Qadeer, S. (2003). From pre-historic
to post-modern symbolic model checking. Formal Methods in System Design.
Springer. https://doi.org/10.1023/A:1026228213080
chicago: Henzinger, Thomas A, Orna Kupferman, and Shaz Qadeer. “From Pre-Historic
to Post-Modern Symbolic Model Checking.” Formal Methods in System Design.
Springer, 2003. https://doi.org/10.1023/A:1026228213080.
ieee: T. A. Henzinger, O. Kupferman, and S. Qadeer, “From pre-historic to post-modern
symbolic model checking,” Formal Methods in System Design, vol. 23, no.
3. Springer, pp. 303–327, 2003.
ista: Henzinger TA, Kupferman O, Qadeer S. 2003. From pre-historic to post-modern
symbolic model checking. Formal Methods in System Design. 23(3), 303–327.
mla: Henzinger, Thomas A., et al. “From Pre-Historic to Post-Modern Symbolic Model
Checking.” Formal Methods in System Design, vol. 23, no. 3, Springer, 2003,
pp. 303–27, doi:10.1023/A:1026228213080.
short: T.A. Henzinger, O. Kupferman, S. Qadeer, Formal Methods in System Design
23 (2003) 303–327.
date_created: 2018-12-11T12:08:58Z
date_published: 2003-06-20T00:00:00Z
date_updated: 2024-01-10T11:50:31Z
day: '20'
doi: 10.1023/A:1026228213080
extern: '1'
intvolume: ' 23'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 303 - 327
publication: Formal Methods in System Design
publication_identifier:
issn:
- 0925-9856
publication_status: published
publisher: Springer
publist_id: '268'
quality_controlled: '1'
scopus_import: '1'
status: public
title: From pre-historic to post-modern symbolic model checking
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 23
year: '2003'
...
---
_id: '4462'
abstract:
- lang: eng
text: 'A major hurdle in the algorithmic verification and control of systems is
the need to find suitable abstract models, which omit enough details to overcome
the state-explosion problem, but retain enough details to exhibit satisfaction
or controllability with respect to the specification. The paradigm of counterexample-guided
abstraction refinement suggests a fully automatic way of finding suitable abstract
models: one starts with a coarse abstraction, attempts to verify or control the
abstract model, and if this attempt fails and the abstract counterexample does
not correspond to a concrete counterexample, then one uses the spurious counterexample
to guide the refinement of the abstract model. We present a counterexample-guided
refinement algorithm for solving ω-regular control objectives. The main difficulty
is that in control, unlike in verification, counterexamples are strategies in
a game between system and controller. In the case that the controller has no choices,
our scheme subsumes known counterexample-guided refinement algorithms for the
verification of ω-regular specifications. Our algorithm is useful in all situations
where ω-regular games need to be solved, such as supervisory control, sequential
and program synthesis, and modular verification. The algorithm is fully symbolic,
and therefore applicable also to infinite-state systems.'
acknowledgement: This research was supported in part by the DARPA SEC grant F33615-C-98-3614,
the ONR grant N00014-02-1-0671, and the NSF grants CCR-9988172, CCR-0085949, and
CCR-0225610.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R. Counterexample-guided control. In: Proceedings
of the 30th International Colloquium on Automata, Languages and Programming.
Vol 2719. Springer; 2003:886-902. doi:10.1007/3-540-45061-0_69'
apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2003). Counterexample-guided
control. In Proceedings of the 30th International Colloquium on Automata, Languages
and Programming (Vol. 2719, pp. 886–902). Eindhoven, The Netherlands: Springer.
https://doi.org/10.1007/3-540-45061-0_69'
chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Counterexample-Guided
Control.” In Proceedings of the 30th International Colloquium on Automata,
Languages and Programming, 2719:886–902. Springer, 2003. https://doi.org/10.1007/3-540-45061-0_69.
ieee: T. A. Henzinger, R. Jhala, and R. Majumdar, “Counterexample-guided control,”
in Proceedings of the 30th International Colloquium on Automata, Languages
and Programming, Eindhoven, The Netherlands, 2003, vol. 2719, pp. 886–902.
ista: 'Henzinger TA, Jhala R, Majumdar R. 2003. Counterexample-guided control. Proceedings
of the 30th International Colloquium on Automata, Languages and Programming. ICALP:
Automata, Languages and Programming, LNCS, vol. 2719, 886–902.'
mla: Henzinger, Thomas A., et al. “Counterexample-Guided Control.” Proceedings
of the 30th International Colloquium on Automata, Languages and Programming,
vol. 2719, Springer, 2003, pp. 886–902, doi:10.1007/3-540-45061-0_69.
short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, Proceedings of the 30th International
Colloquium on Automata, Languages and Programming, Springer, 2003, pp. 886–902.
conference:
end_date: 2003-07-04
location: Eindhoven, The Netherlands
name: 'ICALP: Automata, Languages and Programming'
start_date: 2003-06-30
date_created: 2018-12-11T12:08:58Z
date_published: 2003-06-25T00:00:00Z
date_updated: 2024-01-10T11:19:41Z
day: '25'
doi: 10.1007/3-540-45061-0_69
extern: '1'
intvolume: ' 2719'
language:
- iso: eng
month: '06'
oa_version: None
page: 886 - 902
publication: Proceedings of the 30th International Colloquium on Automata, Languages
and Programming
publication_identifier:
isbn:
- '9783540404934'
publication_status: published
publisher: Springer
publist_id: '265'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counterexample-guided control
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2719
year: '2003'
...
---
_id: '4463'
abstract:
- lang: eng
text: We present an algorithm called TAR (“Thread-modular Abstraction Refinement”)
for model checking safety properties of concurrent software. The TAR algorithm
uses thread-modular assume-guarantee reasoning to overcome the exponential complexity
in the control state of multithreaded programs. Thread modularity means that TAR
explores the state space of one thread at a time, making assumptions about how
the environment can interfere. The TAR algorithm uses counterexample-guided predicate-abstraction
refinement to overcome the usually infinite complexity in the data state of C
programs. A successive approximation scheme automatically infers the necessary
precision on data variables as well as suitable environment assumptions. The scheme
is novel in that transition relations are approximated from above, while at the
same time environment assumptions are approximated from below. In our software
verification tool BLAST we have implemented a fully automatic race checker for
multithreaded C programs which is based on the TAR algorithm. This tool has verified
a wide variety of commonly used locking idioms, including locking schemes that
are not amenable to existing dynamic and static race checkers such as ERASER or
WARLOCK.
acknowledgement: This work was supported in part by the NSF grants CCR-0085949 and
CCR-0234690, the DARPA grant F33615-00-C-1693, and the MARCO grant 98-DT-660.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Qadeer S. Thread-modular abstraction refinement.
In: Proceedings of the 15th International Conference on Computer Aided Verification.
Vol 2725. Springer; 2003:262-274. doi:10.1007/978-3-540-45069-6_27'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Qadeer, S. (2003). Thread-modular
abstraction refinement. In Proceedings of the 15th International Conference
on Computer Aided Verification (Vol. 2725, pp. 262–274). Boulder, CO, USA:
Springer. https://doi.org/10.1007/978-3-540-45069-6_27'
chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Shaz Qadeer.
“Thread-Modular Abstraction Refinement.” In Proceedings of the 15th International
Conference on Computer Aided Verification, 2725:262–74. Springer, 2003. https://doi.org/10.1007/978-3-540-45069-6_27.
ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and S. Qadeer, “Thread-modular abstraction
refinement,” in Proceedings of the 15th International Conference on Computer
Aided Verification, Boulder, CO, USA, 2003, vol. 2725, pp. 262–274.
ista: 'Henzinger TA, Jhala R, Majumdar R, Qadeer S. 2003. Thread-modular abstraction
refinement. Proceedings of the 15th International Conference on Computer Aided
Verification. CAV: Computer Aided Verification, LNCS, vol. 2725, 262–274.'
mla: Henzinger, Thomas A., et al. “Thread-Modular Abstraction Refinement.” Proceedings
of the 15th International Conference on Computer Aided Verification, vol.
2725, Springer, 2003, pp. 262–74, doi:10.1007/978-3-540-45069-6_27.
short: T.A. Henzinger, R. Jhala, R. Majumdar, S. Qadeer, in:, Proceedings of the
15th International Conference on Computer Aided Verification, Springer, 2003,
pp. 262–274.
conference:
end_date: 2003-07-12
location: Boulder, CO, USA
name: 'CAV: Computer Aided Verification'
start_date: 2003-07-08
date_created: 2018-12-11T12:08:59Z
date_published: 2003-06-27T00:00:00Z
date_updated: 2024-01-10T11:05:53Z
day: '27'
doi: 10.1007/978-3-540-45069-6_27
extern: '1'
intvolume: ' 2725'
language:
- iso: eng
month: '06'
oa_version: None
page: 262 - 274
publication: Proceedings of the 15th International Conference on Computer Aided Verification
publication_identifier:
isbn:
- '9783540405245'
publication_status: published
publisher: Springer
publist_id: '266'
quality_controlled: '1'
status: public
title: Thread-modular abstraction refinement
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2725
year: '2003'
...
---
_id: '4464'
abstract:
- lang: eng
text: We introduce the paradigm of schedule-carrying code (SCC). A hard real-time
program can be executed on a given platform only if there exists a feasible schedule
for the real-time tasks of the program. Traditionally, a scheduler determines
the existence of a feasible schedule according to some scheduling strategy. With
SCC, a compiler proves the existence of a feasible schedule by generating executable
code that is attached to the program and represents its schedule. An SCC executable
is a real-time program that carries its schedule as code, which is produced once
and can be revalidated and executed with each use. We evaluate SCC both in theory
and practice. In theory, we give two scenarios, of nonpreemptive and distributed
scheduling for Giotto programs, where the generation of a feasible schedule is
hard, while the validation of scheduling instructions that are attached to the
programs is easy. In practice, we implement SCC and show that explicit scheduling
instructions can reduce the scheduling overhead up to 35% and can provide an efficient,
flexible, and verifiable means for compiling Giotto programs on complex architectures,
such as the TTA.
acknowledgement: This work was supported by the AFOSR MURI grant F49620-00-1-0327,
the California MICRO grant 01-037, the DARPA grant F33615-C-98-3614, the MARCO grant
98-DT-660, and the NSF grants CCR-0208875, CCR-0085949, and CCR-0225610.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Slobodan
full_name: Matic, Slobodan
last_name: Matic
citation:
ama: 'Henzinger TA, Kirsch C, Matic S. Schedule-carrying code. In: Proceedings
of the 3rd International Conference on Embedded Software. Vol 2855. ACM; 2003:241-256.
doi:10.1007/978-3-540-45212-6_16'
apa: 'Henzinger, T. A., Kirsch, C., & Matic, S. (2003). Schedule-carrying code.
In Proceedings of the 3rd International Conference on Embedded Software
(Vol. 2855, pp. 241–256). Philadelphia, PA, USA: ACM. https://doi.org/10.1007/978-3-540-45212-6_16'
chicago: Henzinger, Thomas A, Christoph Kirsch, and Slobodan Matic. “Schedule-Carrying
Code.” In Proceedings of the 3rd International Conference on Embedded Software,
2855:241–56. ACM, 2003. https://doi.org/10.1007/978-3-540-45212-6_16.
ieee: T. A. Henzinger, C. Kirsch, and S. Matic, “Schedule-carrying code,” in Proceedings
of the 3rd International Conference on Embedded Software, Philadelphia, PA,
USA, 2003, vol. 2855, pp. 241–256.
ista: 'Henzinger TA, Kirsch C, Matic S. 2003. Schedule-carrying code. Proceedings
of the 3rd International Conference on Embedded Software. EMSOFT: Embedded Software
, LNCS, vol. 2855, 241–256.'
mla: Henzinger, Thomas A., et al. “Schedule-Carrying Code.” Proceedings of the
3rd International Conference on Embedded Software, vol. 2855, ACM, 2003, pp.
241–56, doi:10.1007/978-3-540-45212-6_16.
short: T.A. Henzinger, C. Kirsch, S. Matic, in:, Proceedings of the 3rd International
Conference on Embedded Software, ACM, 2003, pp. 241–256.
conference:
end_date: 2003-10-15
location: Philadelphia, PA, USA
name: 'EMSOFT: Embedded Software '
start_date: 2003-10-13
date_created: 2018-12-11T12:08:59Z
date_published: 2003-09-29T00:00:00Z
date_updated: 2024-01-10T11:33:57Z
day: '29'
doi: 10.1007/978-3-540-45212-6_16
extern: '1'
intvolume: ' 2855'
language:
- iso: eng
month: '09'
oa_version: None
page: 241 - 256
publication: Proceedings of the 3rd International Conference on Embedded Software
publication_identifier:
isbn:
- '9783540202233'
publication_status: published
publisher: ACM
publist_id: '267'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Schedule-carrying code
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2855
year: '2003'
...
---
_id: '4465'
abstract:
- lang: eng
text: Giotto is a principled, tool-supported design methodology for implementing
embedded control systems on platforms of possibly distributed sensors, actuators,
CPUs, and networks. Giotto is based on the principle that time-triggered task
invocations plus time-triggered mode switches can form the abstract essence of
programming real-time control systems. Giotto consists of a programming language
with a formal semantics, and a retargetable compiler and runtime library. Giotto
supports the automation of control system design by strictly separating platform-independent
functionality and timing concerns from platform-dependent scheduling and communication
issues. The time-triggered predictability of Giotto makes it particularly suitable
for safety-critical applications with hard real-time constraints. We illustrate
the platform independence and time-triggered execution of Giotto by coordinating
a heterogeneous flock of Intel x86 robots and Lego Mindstorms robots.
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Benjamin
full_name: Horowitz, Benjamin
last_name: Horowitz
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
citation:
ama: 'Henzinger TA, Horowitz B, Kirsch C. Embedded control systems development with
Giotto. In: Software-Enabled Control: Information Technology for Dynamical
Systems. Wiley-Blackwell; 2003:123-146. doi:10.1002/047172288X.ch8'
apa: 'Henzinger, T. A., Horowitz, B., & Kirsch, C. (2003). Embedded control
systems development with Giotto. In Software-Enabled Control: Information Technology
for Dynamical Systems (pp. 123–146). Wiley-Blackwell. https://doi.org/10.1002/047172288X.ch8'
chicago: 'Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Embedded
Control Systems Development with Giotto.” In Software-Enabled Control: Information
Technology for Dynamical Systems, 123–46. Wiley-Blackwell, 2003. https://doi.org/10.1002/047172288X.ch8.'
ieee: 'T. A. Henzinger, B. Horowitz, and C. Kirsch, “Embedded control systems development
with Giotto,” in Software-Enabled Control: Information Technology for Dynamical
Systems, Wiley-Blackwell, 2003, pp. 123–146.'
ista: 'Henzinger TA, Horowitz B, Kirsch C. 2003.Embedded control systems development
with Giotto. In: Software-Enabled Control: Information Technology for Dynamical
Systems. , 123–146.'
mla: 'Henzinger, Thomas A., et al. “Embedded Control Systems Development with Giotto.”
Software-Enabled Control: Information Technology for Dynamical Systems,
Wiley-Blackwell, 2003, pp. 123–46, doi:10.1002/047172288X.ch8.'
short: 'T.A. Henzinger, B. Horowitz, C. Kirsch, in:, Software-Enabled Control: Information
Technology for Dynamical Systems, Wiley-Blackwell, 2003, pp. 123–146.'
date_created: 2018-12-11T12:08:59Z
date_published: 2003-05-20T00:00:00Z
date_updated: 2024-01-08T12:24:01Z
day: '20'
doi: 10.1002/047172288X.ch8
extern: '1'
language:
- iso: eng
month: '05'
oa_version: None
page: 123 - 146
publication: 'Software-Enabled Control: Information Technology for Dynamical Systems'
publication_identifier:
isbn:
- '9780471234364 '
publication_status: published
publisher: Wiley-Blackwell
publist_id: '262'
quality_controlled: '1'
status: public
title: Embedded control systems development with Giotto
type: book_chapter
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '2003'
...
---
_id: '4466'
abstract:
- lang: eng
text: One source of complexity in the μ-calculus is its ability to specify an unbounded
number of switches between universal (AX) and existential (EX) branching modes.
We therefore study the problems of satisfiability, validity, model checking, and
implication for the universal and existential fragments of the μ-calculus, in
which only one branching mode is allowed. The universal fragment is rich enough
to express most specifications of interest, and therefore improved algorithms
are of practical importance. We show that while the satisfiability and validity
problems become indeed simpler for the existential and universal fragments, this
is, unfortunately, not the case for model checking and implication. We also show
the corresponding results for the alternationfree fragment of the μ-calculus,
where no alternations between least and greatest fixed points are allowed. Our
results imply that efforts to find a polynomial-time model-checking algorithm
for the μ-calculus can be replaced by efforts to find such an algorithm for the
universal or existential fragment.
acknowledgement: This work was supported in part by NSF grant CCR-9988172, the AFOSR
MURI grant F49620-00-1-0327, and a Microsoft Research Fellowship.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'Henzinger TA, Kupferman O, Majumdar R. On the universal and existential fragments
of the mu-calculus. In: Proceedings of the 9th International Conference on
Tools and Algorithms for the Construction and Analysis of Systems . Vol 2619.
Springer; 2003:49-64. doi:10.1007/3-540-36577-X_5'
apa: 'Henzinger, T. A., Kupferman, O., & Majumdar, R. (2003). On the universal
and existential fragments of the mu-calculus. In Proceedings of the 9th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems
(Vol. 2619, pp. 49–64). Warsaw, Poland: Springer. https://doi.org/10.1007/3-540-36577-X_5'
chicago: Henzinger, Thomas A, Orna Kupferman, and Ritankar Majumdar. “On the Universal
and Existential Fragments of the Mu-Calculus.” In Proceedings of the 9th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems
, 2619:49–64. Springer, 2003. https://doi.org/10.1007/3-540-36577-X_5.
ieee: T. A. Henzinger, O. Kupferman, and R. Majumdar, “On the universal and existential
fragments of the mu-calculus,” in Proceedings of the 9th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems , Warsaw,
Poland, 2003, vol. 2619, pp. 49–64.
ista: 'Henzinger TA, Kupferman O, Majumdar R. 2003. On the universal and existential
fragments of the mu-calculus. Proceedings of the 9th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems . TACAS:
Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol.
2619, 49–64.'
mla: Henzinger, Thomas A., et al. “On the Universal and Existential Fragments of
the Mu-Calculus.” Proceedings of the 9th International Conference on Tools
and Algorithms for the Construction and Analysis of Systems , vol. 2619, Springer,
2003, pp. 49–64, doi:10.1007/3-540-36577-X_5.
short: T.A. Henzinger, O. Kupferman, R. Majumdar, in:, Proceedings of the 9th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems
, Springer, 2003, pp. 49–64.
conference:
end_date: 2003-04-11
location: Warsaw, Poland
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2003-04-07
date_created: 2018-12-11T12:08:59Z
date_published: 2003-03-14T00:00:00Z
date_updated: 2024-01-08T13:17:35Z
day: '14'
doi: 10.1007/3-540-36577-X_5
extern: '1'
intvolume: ' 2619'
language:
- iso: eng
month: '03'
oa_version: None
page: 49 - 64
publication: 'Proceedings of the 9th International Conference on Tools and Algorithms
for the Construction and Analysis of Systems '
publication_identifier:
isbn:
- '9783540008989'
publication_status: published
publisher: Springer
publist_id: '263'
quality_controlled: '1'
status: public
title: On the universal and existential fragments of the mu-calculus
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2619
year: '2003'
...
---
_id: '4467'
abstract:
- lang: eng
text: 'BLAST (the Berkeley Lazy Abstraction Software verification Tool) is a verification
system for checking safety properties of C programs using automatic property-driven
construction and model checking of software abstractions. Blast implements an
abstract-model check-refine loop to check for reachability of a specified label
in the program. The abstract model is built on the fly using predicate abstraction.
This model is then checked for reachability. If there is no (abstract) path to
the specified error label, Blast reports that the system is safe and produces
a succinct proof. Otherwise, it checks if the path is feasible using symbolic
execution of the program. If the path is feasible, Blast outputs the path as an
error trace, otherwise, it uses the infeasibility of the path to refine the abstract
model. Blast short-circuits the loop from abstraction to verification to refinement,
integrating the three steps tightly through “lazy abstraction” [5]. This integration
can offer significant advantages in performance by avoiding the repetition of
work from one iteration of the loop to the next. '
acknowledgement: This work was supported in part by the NSF grants CCR-0085949 and
CCR-9988172, the DARPA PCES grant F33615-00-C-1693, the MARCO GSRC grant 98-DT-660,
and a Microsoft Research Fellowship.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Grégoire
full_name: Sutre, Grégoire
last_name: Sutre
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. Software verification with BLAST.
In: Proceedings of the 10th International SPIN Workshop . Vol 2648. Springer;
2003:235-239. doi:10.1007/3-540-44829-2_17'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sutre, G. (2003). Software
verification with BLAST. In Proceedings of the 10th International SPIN Workshop
(Vol. 2648, pp. 235–239). Portland, OR, USA: Springer. https://doi.org/10.1007/3-540-44829-2_17'
chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Grégoire Sutre.
“Software Verification with BLAST.” In Proceedings of the 10th International
SPIN Workshop , 2648:235–39. Springer, 2003. https://doi.org/10.1007/3-540-44829-2_17.
ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and G. Sutre, “Software verification
with BLAST,” in Proceedings of the 10th International SPIN Workshop , Portland,
OR, USA, 2003, vol. 2648, pp. 235–239.
ista: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. 2003. Software verification with
BLAST. Proceedings of the 10th International SPIN Workshop . SPIN: Model Checking
Software, LNCS, vol. 2648, 235–239.'
mla: Henzinger, Thomas A., et al. “Software Verification with BLAST.” Proceedings
of the 10th International SPIN Workshop , vol. 2648, Springer, 2003, pp. 235–39,
doi:10.1007/3-540-44829-2_17.
short: T.A. Henzinger, R. Jhala, R. Majumdar, G. Sutre, in:, Proceedings of the
10th International SPIN Workshop , Springer, 2003, pp. 235–239.
conference:
end_date: 2003-05-10
location: Portland, OR, USA
name: 'SPIN: Model Checking Software'
start_date: 2003-05-09
date_created: 2018-12-11T12:09:00Z
date_published: 2003-04-28T00:00:00Z
date_updated: 2024-01-08T14:05:29Z
day: '28'
doi: 10.1007/3-540-44829-2_17
extern: '1'
intvolume: ' 2648'
language:
- iso: eng
month: '04'
oa_version: None
page: 235 - 239
publication: 'Proceedings of the 10th International SPIN Workshop '
publication_identifier:
isbn:
- '9783540401179'
publication_status: published
publisher: Springer
publist_id: '264'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Software verification with BLAST
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2648
year: '2003'
...
---
_id: '4468'
abstract:
- lang: eng
text: Giotto is a high-level programming language for time-triggered control applications.
The authors begin with a conceptual overview of its methodology, discuss the Giotto
helicopter project, and summarize available Giotto implementations.
acknowledgement: We thank Niklaus Wirth and Walter Schaufelberger for their advice
and support of the reengineering effort of the ETH Zurich helicopter control system
using Giotto. This research was supported in part by DARPA SEC grant F33615-C-98–3614,
MARCO GSRC grant 98-DT-660, and AFOSR MURI grant F49620–00-1–0327. A preliminary
version of this article appeared as [1].
article_processing_charge: No
article_type: original
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Marco
full_name: Sanvido, Marco
last_name: Sanvido
- first_name: Wolfgang
full_name: Pree, Wolfgang
last_name: Pree
citation:
ama: Henzinger TA, Kirsch C, Sanvido M, Pree W. From control models to real-time
code using Giotto. IEEE Control Systems Magazine. 2003;23(1):50-64. doi:10.1109/MCS.2003.1172829
apa: Henzinger, T. A., Kirsch, C., Sanvido, M., & Pree, W. (2003). From control
models to real-time code using Giotto. IEEE Control Systems Magazine. IEEE.
https://doi.org/10.1109/MCS.2003.1172829
chicago: Henzinger, Thomas A, Christoph Kirsch, Marco Sanvido, and Wolfgang Pree.
“From Control Models to Real-Time Code Using Giotto.” IEEE Control Systems
Magazine. IEEE, 2003. https://doi.org/10.1109/MCS.2003.1172829.
ieee: T. A. Henzinger, C. Kirsch, M. Sanvido, and W. Pree, “From control models
to real-time code using Giotto,” IEEE Control Systems Magazine, vol. 23,
no. 1. IEEE, pp. 50–64, 2003.
ista: Henzinger TA, Kirsch C, Sanvido M, Pree W. 2003. From control models to real-time
code using Giotto. IEEE Control Systems Magazine. 23(1), 50–64.
mla: Henzinger, Thomas A., et al. “From Control Models to Real-Time Code Using Giotto.”
IEEE Control Systems Magazine, vol. 23, no. 1, IEEE, 2003, pp. 50–64, doi:10.1109/MCS.2003.1172829.
short: T.A. Henzinger, C. Kirsch, M. Sanvido, W. Pree, IEEE Control Systems Magazine
23 (2003) 50–64.
date_created: 2018-12-11T12:09:00Z
date_published: 2003-01-29T00:00:00Z
date_updated: 2024-01-08T10:54:53Z
day: '29'
doi: 10.1109/MCS.2003.1172829
extern: '1'
intvolume: ' 23'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 50 - 64
publication: IEEE Control Systems Magazine
publication_identifier:
issn:
- '1066-033X '
publication_status: published
publisher: IEEE
publist_id: '260'
quality_controlled: '1'
scopus_import: '1'
status: public
title: From control models to real-time code using Giotto
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 23
year: '2003'
...
---
_id: '4469'
abstract:
- lang: eng
text: Giotto provides an abstract programmer's model for the implementation of embedded
control systems with hard real-time constraints. A typical control application
consists of periodic software tasks together with a mode-switching logic for enabling
and disabling tasks. Giotto specifies time-triggered sensor readings, task invocations,
actuator updates, and mode switches independent of any implementation platform.
Giotto can be annotated with platform constraints such as task-to-host mappings,
and task and communication schedules. The annotations are directives for the Giotto
compiler, but they do not alter the functionality and timing of a Giotto program.
By separating the platform-independent from the platform-dependent concerns, Giotto
enables a great deal of flexibility in choosing control platforms as well as a
great deal of automation in the validation and synthesis of control software.
The time-triggered nature of Giotto achieves timing predictability, which makes
Giotto particularly suitable for safety-critical applications.
acknowledgement: The authors would like to thank R. Majumdar for implementing a prototype
Giotto compiler for Lego Mindstorms robots. They would like to thank D. Derevyanko
and W. Williams for building the Intel x86 robots; and E. Lee and X. Liu for help
with implementing Giotto as a “model of computation” in Ptolemy II [26]. Finally,
they would also like to thank M. Sanvido for his suggestions on the design of the
Giotto drivers; and P. Griffiths for implementing the functionality code of the
electronic throttle controller.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Benjamin
full_name: Horowitz, Benjamin
last_name: Horowitz
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
citation:
ama: 'Henzinger TA, Horowitz B, Kirsch C. Giotto: A time-triggered language for
embedded programming. Proceedings of the IEEE. 2003;91(1):84-99. doi:10.1109/JPROC.2002.805825'
apa: 'Henzinger, T. A., Horowitz, B., & Kirsch, C. (2003). Giotto: A time-triggered
language for embedded programming. Proceedings of the IEEE. IEEE. https://doi.org/10.1109/JPROC.2002.805825'
chicago: 'Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Giotto:
A Time-Triggered Language for Embedded Programming.” Proceedings of the IEEE.
IEEE, 2003. https://doi.org/10.1109/JPROC.2002.805825.'
ieee: 'T. A. Henzinger, B. Horowitz, and C. Kirsch, “Giotto: A time-triggered language
for embedded programming,” Proceedings of the IEEE, vol. 91, no. 1. IEEE,
pp. 84–99, 2003.'
ista: 'Henzinger TA, Horowitz B, Kirsch C. 2003. Giotto: A time-triggered language
for embedded programming. Proceedings of the IEEE. 91(1), 84–99.'
mla: 'Henzinger, Thomas A., et al. “Giotto: A Time-Triggered Language for Embedded
Programming.” Proceedings of the IEEE, vol. 91, no. 1, IEEE, 2003, pp.
84–99, doi:10.1109/JPROC.2002.805825.'
short: T.A. Henzinger, B. Horowitz, C. Kirsch, Proceedings of the IEEE 91 (2003)
84–99.
date_created: 2018-12-11T12:09:00Z
date_published: 2003-01-29T00:00:00Z
date_updated: 2024-01-10T11:55:18Z
day: '29'
doi: 10.1109/JPROC.2002.805825
extern: '1'
intvolume: ' 91'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 84 - 99
publication: Proceedings of the IEEE
publication_identifier:
issn:
- '0018-9219 '
publication_status: published
publisher: IEEE
publist_id: '261'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Giotto: A time-triggered language for embedded programming'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 91
year: '2003'
...
---
_id: '2613'
abstract:
- lang: eng
text: In this investigation, we report identification and characterization of a
95 kDa postsynaptic density protein (PSD-95)/discs-large/ ZO-1 (PDZ) domain-containing
protein termed tamalin, also recently named GRP1-associated scaffold protein (GRASP),
that interacts with group 1 metabotropic glutamate receptors (mGluRs). The yeast
two-hybrid system and in vitro pull-down assays indicated that the PDZ domain-containing,
amino-terminal half of tamalin directly binds to the class I PDZ-binding motif
of group 1 mGluRs. The C-terminal half of tamalin also bound to cytohesins, the
members of guanine nucleotide exchange factors (GEFs) specific for the ADP-ribosylation
factor (ARF) family of small GTP-binding proteins. Tamalin mRNA is expressed predominantly
in the telencephalic region and highly overlaps with the expression of group 1
mGluR mRNAs. Both tamalin and cytohesin-2 were enriched and codistributed with
mGluR1a in postsynaptic membrane fractions. Importantly, recombinant and native
mGluR1a/tamalin/cytohesin-2 complexes were coimmunoprecipitated from transfected
COS-7 cells and rat brain tissue, respectively. Transfection of tamalin and mutant
tamalin lacking a cytohesin-binding domain caused an increase and decrease in
cell-surface expression of mGluR1a in COS-7 cells, respectively. Furthermore,
adenovirus-mediated expression of tamalin and dominant-negative tamalin facilitated
and reduced the neuritic distribution of endogenous mGluR5 in cultured hippocampal
neurons, respectively. The results indicate that tamalin plays a key role in the
association of group 1 mGluRs with the ARF-specific GEF proteins and contributes
to intracellular trafficking and the macromolecular organization of group 1 mGluRs
at synapses.
acknowledgement: This work was supported in part by research grants from the Ministry
of Education, Science and Culture of Japan. We thank Bert Vogelstein for providing
adenoviral recombination vectors and Haruhiko Bito for a gift of the enolase promoter
and technical advice. We are grateful to Atsushi Nishimune and Satoshi Kaneko for
technical advice and Kumlesh K. Dev for careful reading of this manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Jun
full_name: Kitano, Jun
last_name: Kitano
- first_name: Kouji
full_name: Kimura, Kouji
last_name: Kimura
- first_name: Yoshimitsu
full_name: Yamazaki, Yoshimitsu
last_name: Yamazaki
- first_name: Takeshi
full_name: Soda, Takeshi
last_name: Soda
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Yoshiaki
full_name: Nakajima, Yoshiaki
last_name: Nakajima
- first_name: Shigetada
full_name: Nakanishi, Shigetada
last_name: Nakanishi
citation:
ama: Kitano J, Kimura K, Yamazaki Y, et al. Tamalin, a PDZ domain-containing protein,
links a protein complex formation of group 1 metabotropic glutamate receptors
and the guanine nucleotide exchange factor cytohesins. Journal of Neuroscience.
2002;22(4):1280-1289. doi:10.1523/JNEUROSCI.22-04-01280.2002
apa: Kitano, J., Kimura, K., Yamazaki, Y., Soda, T., Shigemoto, R., Nakajima, Y.,
& Nakanishi, S. (2002). Tamalin, a PDZ domain-containing protein, links a
protein complex formation of group 1 metabotropic glutamate receptors and the
guanine nucleotide exchange factor cytohesins. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.22-04-01280.2002
chicago: Kitano, Jun, Kouji Kimura, Yoshimitsu Yamazaki, Takeshi Soda, Ryuichi Shigemoto,
Yoshiaki Nakajima, and Shigetada Nakanishi. “Tamalin, a PDZ Domain-Containing
Protein, Links a Protein Complex Formation of Group 1 Metabotropic Glutamate Receptors
and the Guanine Nucleotide Exchange Factor Cytohesins.” Journal of Neuroscience.
Society for Neuroscience, 2002. https://doi.org/10.1523/JNEUROSCI.22-04-01280.2002.
ieee: J. Kitano et al., “Tamalin, a PDZ domain-containing protein, links
a protein complex formation of group 1 metabotropic glutamate receptors and the
guanine nucleotide exchange factor cytohesins,” Journal of Neuroscience,
vol. 22, no. 4. Society for Neuroscience, pp. 1280–1289, 2002.
ista: Kitano J, Kimura K, Yamazaki Y, Soda T, Shigemoto R, Nakajima Y, Nakanishi
S. 2002. Tamalin, a PDZ domain-containing protein, links a protein complex formation
of group 1 metabotropic glutamate receptors and the guanine nucleotide exchange
factor cytohesins. Journal of Neuroscience. 22(4), 1280–1289.
mla: Kitano, Jun, et al. “Tamalin, a PDZ Domain-Containing Protein, Links a Protein
Complex Formation of Group 1 Metabotropic Glutamate Receptors and the Guanine
Nucleotide Exchange Factor Cytohesins.” Journal of Neuroscience, vol. 22,
no. 4, Society for Neuroscience, 2002, pp. 1280–89, doi:10.1523/JNEUROSCI.22-04-01280.2002.
short: J. Kitano, K. Kimura, Y. Yamazaki, T. Soda, R. Shigemoto, Y. Nakajima, S.
Nakanishi, Journal of Neuroscience 22 (2002) 1280–1289.
date_created: 2018-12-11T11:58:40Z
date_published: 2002-02-15T00:00:00Z
date_updated: 2023-07-25T11:34:46Z
day: '15'
doi: 10.1523/JNEUROSCI.22-04-01280.2002
extern: '1'
external_id:
pmid:
- '11850456'
intvolume: ' 22'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 1280 - 1289
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
publist_id: '4285'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tamalin, a PDZ domain-containing protein, links a protein complex formation
of group 1 metabotropic glutamate receptors and the guanine nucleotide exchange
factor cytohesins
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 22
year: '2002'
...
---
_id: '2614'
abstract:
- lang: eng
text: Metabotropic glutamate receptors (mGluRs) from group III reduce glutamate
release. Because these receptors reduce cAMP levels, we explored whether this
signaling pathway contributes to release inhibition caused by mGluRs with low
affinity for L-2-amino-4-phosphonobutyrate (L-AP4). In biochemical experiments
with the population of cerebrocortical nerve terminals we find that L-AP4 (1 mM)
inhibited the Ca2+dependent-evoked release of glutamate by 25%. This inhibitory
effect was largely prevented by the pertussis toxin but was insensitive to inhibitors
of protein kinase C bisindolylmaleimide and protein kinase A H-89. Furthermore,
this inhibition was associated with reduction in N-type Ca2+ channel activity
in the absence of any detectable change in cAMP levels. In the presence of forskolin,
however, L-AP4 decreased the levels of cAMP. The activation of this additional
signaling pathway was very efficient in counteracting the facilitation of glutamate
release induced either by forskolin or the β-adrenergic receptor agonist isoproterenol.
Imaging experiments to measure Ca2+ dynamics in single nerve terminals showed
that L-AP4 strongly reduced the Ca2+ response in 28% of the nerve terminals. Moreover,
immunochemical experiments showed that 25-35% of the nerve terminals that were
immunopositive to synaptophysin were also immunoreactive to the low affinity L-AP4-sensitive
mGluR7. Then, mGluR7 mediates the inhibition of glutamate release caused by 1
mM L-AP4, primarily by a strong inhibition of Ca2+ channels, although high cAMP
uncovers the receptor ability to decrease cAMP.
acknowledgement: We thank Dr. Enrique Castro from Las Palmas University for critical
reading of the manuscript and M. Sefton for editorial assistance.
article_processing_charge: No
article_type: original
author:
- first_name: Carmelo
full_name: Millán, Carmelo
last_name: Millán
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: José
full_name: Sánchez Prieto, José
last_name: Sánchez Prieto
citation:
ama: Millán C, Luján R, Shigemoto R, Sánchez Prieto J. The inhibition of glutamate
release by metabotropic glutamate receptor 7 affects both [Ca2+]c and cAMP. Evidence
for a strong reduction of Ca2+ entry in single nerve terminals. Journal of
Biological Chemistry. 2002;277(16):14092-14101. doi:10.1074/jbc.M109044200
apa: Millán, C., Luján, R., Shigemoto, R., & Sánchez Prieto, J. (2002). The
inhibition of glutamate release by metabotropic glutamate receptor 7 affects both
[Ca2+]c and cAMP. Evidence for a strong reduction of Ca2+ entry in single nerve
terminals. Journal of Biological Chemistry. American Society for Biochemistry
and Molecular Biology. https://doi.org/10.1074/jbc.M109044200
chicago: Millán, Carmelo, Rafael Luján, Ryuichi Shigemoto, and José Sánchez Prieto.
“The Inhibition of Glutamate Release by Metabotropic Glutamate Receptor 7 Affects
Both [Ca2+]c and CAMP. Evidence for a Strong Reduction of Ca2+ Entry in Single
Nerve Terminals.” Journal of Biological Chemistry. American Society for
Biochemistry and Molecular Biology, 2002. https://doi.org/10.1074/jbc.M109044200.
ieee: C. Millán, R. Luján, R. Shigemoto, and J. Sánchez Prieto, “The inhibition
of glutamate release by metabotropic glutamate receptor 7 affects both [Ca2+]c
and cAMP. Evidence for a strong reduction of Ca2+ entry in single nerve terminals,”
Journal of Biological Chemistry, vol. 277, no. 16. American Society for
Biochemistry and Molecular Biology, pp. 14092–14101, 2002.
ista: Millán C, Luján R, Shigemoto R, Sánchez Prieto J. 2002. The inhibition of
glutamate release by metabotropic glutamate receptor 7 affects both [Ca2+]c and
cAMP. Evidence for a strong reduction of Ca2+ entry in single nerve terminals.
Journal of Biological Chemistry. 277(16), 14092–14101.
mla: Millán, Carmelo, et al. “The Inhibition of Glutamate Release by Metabotropic
Glutamate Receptor 7 Affects Both [Ca2+]c and CAMP. Evidence for a Strong Reduction
of Ca2+ Entry in Single Nerve Terminals.” Journal of Biological Chemistry,
vol. 277, no. 16, American Society for Biochemistry and Molecular Biology, 2002,
pp. 14092–101, doi:10.1074/jbc.M109044200.
short: C. Millán, R. Luján, R. Shigemoto, J. Sánchez Prieto, Journal of Biological
Chemistry 277 (2002) 14092–14101.
date_created: 2018-12-11T11:58:41Z
date_published: 2002-04-19T00:00:00Z
date_updated: 2023-07-25T10:16:44Z
day: '19'
ddc:
- '570'
doi: 10.1074/jbc.M109044200
extern: '1'
external_id:
pmid:
- '11825890'
file:
- access_level: open_access
checksum: 0290fcbbd9153ec654185b0c856f214c
content_type: application/pdf
creator: alisjak
date_created: 2023-07-25T10:13:16Z
date_updated: 2023-07-25T10:13:16Z
file_id: '13309'
file_name: 2002_JBC_Millan.pdf
file_size: 2105520
relation: main_file
success: 1
file_date_updated: 2023-07-25T10:13:16Z
has_accepted_license: '1'
intvolume: ' 277'
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 14092 - 14101
pmid: 1
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '4284'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The inhibition of glutamate release by metabotropic glutamate receptor 7 affects
both [Ca2+]c and cAMP. Evidence for a strong reduction of Ca2+ entry in single nerve
terminals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 277
year: '2002'
...
---
_id: '2615'
abstract:
- lang: eng
text: Taste-mGluR4, cloned from taste tissues, is a truncated variant of brain-expressed
mGluR4a (brain-mGluR4), and is known to be a candidate for the receptor involved
in the umami taste sense. Although the expression patterns of taste- and brain-mGluR4
mRNAs have been demonstrated, no mention has so far been made of the expression
of these two mGluR4 proteins in taste tissues. The present study examined the
expression of taste-mGluR4 and brain-mGluR4 proteins in rat taste tissues by using
a specific antibody for mGluR4a which shared a C-terminus of both taste- and brain-mGluR4,
for immunoblot analysis and immunohistochemistry. Immunoblot analysis showed that
both brain-mGluR4 and taste-mGluR4 were expressed in the taste tissues. Taste-mGluR4
was not detected in the cerebellum. The immunoreactive band for brain-mGluR4 protein
was much stronger than that for taste-mGluR4 protein. In the cryosections of fungiform,
foliate and circumvallate papillae, the antibody against taste-mGluR4 exhibited
intense labeling of the taste pores and taste hairs in all the taste buds of gustatory
papillae examined; the immunoreaction to the antibody against brain-mGluR4 was
more intense at the same sites of the taste buds. The portions of the taste bud
cells below the taste pore and surrounding keratinocytes did not show any immunoreactivities.
The results of the present study strongly suggest that, in addition to taste-mGluR4,
brain-mGluR4 may function even more importantly than the former as a receptor
for glutamate, i.e. the umami taste sensation.
article_processing_charge: No
article_type: original
author:
- first_name: Takashi
full_name: Toyono, Takashi
last_name: Toyono
- first_name: Yuji
full_name: Seta, Yuji
last_name: Seta
- first_name: Shinji
full_name: Sataoka, Shinji
last_name: Sataoka
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Takahiko
full_name: Morotomi, Takahiko
last_name: Morotomi
- first_name: Shintaro
full_name: Kawano, Shintaro
last_name: Kawano
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Kuniaki
full_name: Toyoshima, Kuniaki
last_name: Toyoshima
citation:
ama: Toyono T, Seta Y, Sataoka S, et al. Expression of the metabotropic glutamate
receptor, mGluR4a, in the taste hairs of taste buds in rat gustatory papillae.
Archives of Histology and Cytology. 2002;65(1):91-96. doi:10.1679/aohc.65.91
apa: Toyono, T., Seta, Y., Sataoka, S., Harada, H., Morotomi, T., Kawano, S., …
Toyoshima, K. (2002). Expression of the metabotropic glutamate receptor, mGluR4a,
in the taste hairs of taste buds in rat gustatory papillae. Archives of Histology
and Cytology. Japan Society of Histological Documentation. https://doi.org/10.1679/aohc.65.91
chicago: Toyono, Takashi, Yuji Seta, Shinji Sataoka, Harumi Harada, Takahiko Morotomi,
Shintaro Kawano, Ryuichi Shigemoto, and Kuniaki Toyoshima. “Expression of the
Metabotropic Glutamate Receptor, MGluR4a, in the Taste Hairs of Taste Buds in
Rat Gustatory Papillae.” Archives of Histology and Cytology. Japan Society
of Histological Documentation, 2002. https://doi.org/10.1679/aohc.65.91.
ieee: T. Toyono et al., “Expression of the metabotropic glutamate receptor,
mGluR4a, in the taste hairs of taste buds in rat gustatory papillae,” Archives
of Histology and Cytology, vol. 65, no. 1. Japan Society of Histological Documentation,
pp. 91–96, 2002.
ista: Toyono T, Seta Y, Sataoka S, Harada H, Morotomi T, Kawano S, Shigemoto R,
Toyoshima K. 2002. Expression of the metabotropic glutamate receptor, mGluR4a,
in the taste hairs of taste buds in rat gustatory papillae. Archives of Histology
and Cytology. 65(1), 91–96.
mla: Toyono, Takashi, et al. “Expression of the Metabotropic Glutamate Receptor,
MGluR4a, in the Taste Hairs of Taste Buds in Rat Gustatory Papillae.” Archives
of Histology and Cytology, vol. 65, no. 1, Japan Society of Histological Documentation,
2002, pp. 91–96, doi:10.1679/aohc.65.91.
short: T. Toyono, Y. Seta, S. Sataoka, H. Harada, T. Morotomi, S. Kawano, R. Shigemoto,
K. Toyoshima, Archives of Histology and Cytology 65 (2002) 91–96.
date_created: 2018-12-11T11:58:41Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-07-25T10:00:15Z
day: '01'
doi: 10.1679/aohc.65.91
extern: '1'
external_id:
pmid:
- '12002614'
intvolume: ' 65'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 91 - 96
pmid: 1
publication: Archives of Histology and Cytology
publication_identifier:
issn:
- 0914-9465
publication_status: published
publisher: Japan Society of Histological Documentation
publist_id: '4283'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expression of the metabotropic glutamate receptor, mGluR4a, in the taste hairs
of taste buds in rat gustatory papillae
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 65
year: '2002'
...