---
_id: '8728'
abstract:
- lang: eng
text: Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are
two standard formalisms in system analysis. Their main associated quantitative
objectives are hitting probabilities, discounted sum, and mean payoff. Although
there are many techniques for computing these objectives in general MCs/MDPs,
they have not been thoroughly studied in terms of parameterized algorithms, particularly
when treewidth is used as the parameter. This is in sharp contrast to qualitative
objectives for MCs, MDPs and graph games, for which treewidth-based algorithms
yield significant complexity improvements. In this work, we show that treewidth
can also be used to obtain faster algorithms for the quantitative problems. For
an MC with n states and m transitions, we show that each of the classical quantitative
objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition
of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for
each objective on MDPs, where κ is the number of strategy-iteration refinements
required for the given input and objective. Finally, we make an experimental evaluation
of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark
suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms
outperform existing well-established methods by one or more orders of magnitude.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ali
full_name: Asadi, Ali
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Kiarash
full_name: Mohammadi, Kiarash
last_name: Mohammadi
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster
algorithms for quantitative analysis of MCs and MDPs with small treewidth. In:
Automated Technology for Verification and Analysis. Vol 12302. Springer
Nature; 2020:253-270. doi:10.1007/978-3-030-59152-6_14'
apa: 'Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., & Pavlogiannis,
A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small
treewidth. In Automated Technology for Verification and Analysis (Vol.
12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. https://doi.org/10.1007/978-3-030-59152-6_14'
chicago: Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi,
and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs
and MDPs with Small Treewidth.” In Automated Technology for Verification and
Analysis, 12302:253–70. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-59152-6_14.
ieee: A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis,
“Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,”
in Automated Technology for Verification and Analysis, Hanoi, Vietnam,
2020, vol. 12302, pp. 253–270.
ista: 'Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020.
Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth.
Automated Technology for Verification and Analysis. ATVA: Automated Technology
for Verification and Analysis, LNCS, vol. 12302, 253–270.'
mla: Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and
MDPs with Small Treewidth.” Automated Technology for Verification and Analysis,
vol. 12302, Springer Nature, 2020, pp. 253–70, doi:10.1007/978-3-030-59152-6_14.
short: A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis,
in:, Automated Technology for Verification and Analysis, Springer Nature, 2020,
pp. 253–270.
conference:
end_date: 2020-10-23
location: Hanoi, Vietnam
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2020-10-19
date_created: 2020-11-06T07:30:05Z
date_published: 2020-10-12T00:00:00Z
date_updated: 2026-10-30T23:30:47Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-59152-6_14
external_id:
isi:
- '000723555700014'
file:
- access_level: open_access
checksum: ae83f27e5b189d5abc2e7514f1b7e1b5
content_type: application/pdf
creator: dernst
date_created: 2020-11-06T07:41:03Z
date_updated: 2020-11-06T07:41:03Z
file_id: '8729'
file_name: 2020_LNCS_ATVA_Asadi_accepted.pdf
file_size: 726648
relation: main_file
success: 1
file_date_updated: 2020-11-06T07:41:03Z
fulldoi: https://doi.org/10.1007/978-3-030-59152-6_14
has_accepted_license: '1'
intvolume: ' 12302'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 253-270
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies
publication: Automated Technology for Verification and Analysis
publication_identifier:
eisbn:
- '9783030591526'
eissn:
- 1611-3349
isbn:
- '9783030591519'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12302
year: '2020'
...
---
_id: '8089'
abstract:
- lang: eng
text: "We consider the classical problem of invariant generation for programs with
polynomial assignments and focus on synthesizing invariants that are a conjunction
of strict polynomial inequalities. We present a sound and semi-complete method
based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize
positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side,
the worst-case complexity of our approach is subexponential, whereas the worst-case
complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential.
Even when restricted to linear invariants, the best previous complexity for complete
invariant generation is exponential (Colon et al, CAV 2003). On the practical
side, we reduce the invariant generation problem to quadratic programming (QCLP),
which is a classical optimization problem with many industrial solvers. We demonstrate
the applicability of our approach by providing experimental results on several
academic benchmarks. To the best of our knowledge, the only previous invariant
generation method that provides completeness guarantees for invariants consisting
of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination
and cannot even handle toy programs such as our running example."
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
citation:
ama: 'Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation
for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969'
apa: 'Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020).
Polynomial invariant generation for non-deterministic recursive programs. In Proceedings
of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation
(pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969'
chicago: Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan
Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive
Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming
Language Design and Implementation, 672–87. Association for Computing Machinery,
2020. https://doi.org/10.1145/3385412.3385969.
ieee: K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial
invariant generation for non-deterministic recursive programs,” in Proceedings
of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation,
London, United Kingdom, 2020, pp. 672–687.
ista: 'Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant
generation for non-deterministic recursive programs. Proceedings of the 41st ACM
SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming
Language Design and Implementation, 672–687.'
mla: Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic
Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming
Language Design and Implementation, Association for Computing Machinery, 2020,
pp. 672–87, doi:10.1145/3385412.3385969.
short: K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings
of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation,
Association for Computing Machinery, 2020, pp. 672–687.
conference:
end_date: 2020-06-20
location: London, United Kingdom
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2020-06-15
date_created: 2020-07-05T22:00:45Z
date_published: 2020-06-11T00:00:00Z
date_updated: 2026-10-30T23:30:47Z
day: '11'
department:
- _id: KrCh
doi: 10.1145/3385412.3385969
external_id:
arxiv:
- '1902.04373'
isi:
- '000614622300045'
fulldoi: https://doi.org/10.1145/3385412.3385969
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.04373
month: '06'
oa: 1
oa_version: Preprint
page: 672-687
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language
Design and Implementation
publication_identifier:
isbn:
- '9781450376136'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Polynomial invariant generation for non-deterministic recursive programs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7810'
abstract:
- lang: eng
text: "Interprocedural data-flow analyses form an expressive and useful paradigm
of numerous static analysis applications, such as live variables analysis, alias
analysis and null pointers analysis. The most widely-used framework for interprocedural
data-flow analysis is IFDS, which encompasses distributive data-flow functions
over a finite domain. On-demand data-flow analyses restrict the focus of the analysis
on specific program locations and data facts. This setting provides a natural
split between (i) an offline (or preprocessing) phase, where the program is partially
analyzed and analysis summaries are created, and (ii) an online (or query) phase,
where analysis queries arrive on demand and the summaries are used to speed up
answering queries.\r\nIn this work, we consider on-demand IFDS analyses where
the queries concern program locations of the same procedure (aka same-context
queries). We exploit the fact that flow graphs of programs have low treewidth
to develop faster algorithms that are space and time optimal for many common data-flow
analyses, in both the preprocessing and the query phase. We also use treewidth
to develop query solutions that are embarrassingly parallelizable, i.e. the total
work for answering each query is split to a number of threads such that each thread
performs only a constant amount of work. Finally, we implement a static analyzer
based on our algorithms, and perform a series of on-demand analysis experiments
on standard benchmarks. Our experimental results show a drastic speed-up of the
queries after only a lightweight preprocessing phase, which significantly outperforms
existing techniques."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly
parallel algorithms for on-demand data-flow analysis. In: European Symposium
on Programming. Vol 12075. Springer Nature; 2020:112-140. doi:10.1007/978-3-030-44914-8_5'
apa: 'Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A.
(2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis.
In European Symposium on Programming (Vol. 12075, pp. 112–140). Dublin,
Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-44914-8_5'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen,
and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand
Data-Flow Analysis.” In European Symposium on Programming, 12075:112–40.
Springer Nature, 2020. https://doi.org/10.1007/978-3-030-44914-8_5.
ieee: K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal
and perfectly parallel algorithms for on-demand data-flow analysis,” in European
Symposium on Programming, Dublin, Ireland, 2020, vol. 12075, pp. 112–140.
ista: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal
and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium
on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140.'
mla: Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for
On-Demand Data-Flow Analysis.” European Symposium on Programming, vol.
12075, Springer Nature, 2020, pp. 112–40, doi:10.1007/978-3-030-44914-8_5.
short: K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European
Symposium on Programming, Springer Nature, 2020, pp. 112–140.
conference:
end_date: 2020-04-30
location: Dublin, Ireland
name: 'ESOP: Programming Languages and Systems'
start_date: 2020-04-25
corr_author: '1'
date_created: 2020-05-10T22:00:50Z
date_published: 2020-04-18T00:00:00Z
date_updated: 2026-10-30T23:30:48Z
day: '18'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-44914-8_5
external_id:
isi:
- '000681656800005'
file:
- access_level: open_access
checksum: 8618b80f4cf7b39a60e61a6445ad9807
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T13:34:48Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7895'
file_name: 2020_LNCS_Chatterjee.pdf
file_size: 651250
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
fulldoi: https://doi.org/10.1007/978-3-030-44914-8_5
has_accepted_license: '1'
intvolume: ' 12075'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 112-140
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies
publication: European Symposium on Programming
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030449131'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Optimal and perfectly parallel algorithms for on-demand data-flow analysis
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: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12075
year: '2020'
...
---
_id: '6918'
abstract:
- lang: eng
text: "We consider the classic problem of Network Reliability. A network is given
together with a source vertex, one or more target vertices, and probabilities
assigned to each of the edges. Each edge of the network is operable with its associated
probability and the problem is to determine the probability of having at least
one source-to-target path that is entirely composed of operable edges. This problem
is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve
the Network Reliability problem when the treewidth of the underlying network is
small. We also show our algorithm’s applicability for real-world transit networks
that have small treewidth, including the metro networks of major cities, such
as London and Tokyo. Our algorithm leverages tree decompositions to shrink the
original graph into much smaller graphs, for which reliability can be efficiently
and exactly computed using a brute force method. To the best of our knowledge,
this is the first exact algorithm for Network Reliability that can scale to handle
real-world instances of the problem."
acknowledgement: We are grateful to the anonymous reviewers for their comments, which
significantly improved the present work. The research was partially supported by
the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London
Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian
Academy of Sciences (ÖAW).
article_number: '106665'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Fatemeh
full_name: Mohammadi, Fatemeh
last_name: Mohammadi
citation:
ama: Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability
in small treewidth. Reliability Engineering and System Safety. 2020;193.
doi:10.1016/j.ress.2019.106665
apa: Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing
network reliability in small treewidth. Reliability Engineering and System
Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665
chicago: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm
for Computing Network Reliability in Small Treewidth.” Reliability Engineering
and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665.
ieee: A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network
reliability in small treewidth,” Reliability Engineering and System Safety,
vol. 193. Elsevier, 2020.
ista: Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network
reliability in small treewidth. Reliability Engineering and System Safety. 193,
106665.
mla: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for
Computing Network Reliability in Small Treewidth.” Reliability Engineering
and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665.
short: A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety
193 (2020).
date_created: 2019-09-29T22:00:44Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2026-10-30T23:30:47Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.ress.2019.106665
external_id:
arxiv:
- '1712.09692'
isi:
- '000501641400050'
fulldoi: https://doi.org/10.1016/j.ress.2019.106665
intvolume: ' 193'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.09692
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: Reliability Engineering and System Safety
publication_identifier:
issn:
- 0951-8320
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: An efficient algorithm for computing network reliability in small treewidth
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 193
year: '2020'
...
---
_id: '8569'
abstract:
- lang: eng
text: Concerted radial migration of newly born cortical projection neurons, from
their birthplace to their final target lamina, is a key step in the assembly of
the cerebral cortex. The cellular and molecular mechanisms regulating the specific
sequential steps of radial neuronal migration in vivo are however still unclear,
let alone the effects and interactions with the extracellular environment. In
any in vivo context, cells will always be exposed to a complex extracellular environment
consisting of (1) secreted factors acting as potential signaling cues, (2) the
extracellular matrix, and (3) other cells providing cell–cell interaction through
receptors and/or direct physical stimuli. Most studies so far have described and
focused mainly on intrinsic cell-autonomous gene functions in neuronal migration
but there is accumulating evidence that non-cell-autonomous-, local-, systemic-,
and/or whole tissue-wide effects substantially contribute to the regulation of
radial neuronal migration. These non-cell-autonomous effects may differentially
affect cortical neuron migration in distinct cellular environments. However, the
cellular and molecular natures of such non-cell-autonomous mechanisms are mostly
unknown. Furthermore, physical forces due to collective migration and/or community
effects (i.e., interactions with surrounding cells) may play important roles in
neocortical projection neuron migration. In this concise review, we first outline
distinct models of non-cell-autonomous interactions of cortical projection neurons
along their radial migration trajectory during development. We then summarize
experimental assays and platforms that can be utilized to visualize and potentially
probe non-cell-autonomous mechanisms. Lastly, we define key questions to address
in the future.
acknowledgement: AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy
of Sciences. This work also received support from IST Austria institutional funds;
the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.
article_number: '574382'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection
neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental
Biology. 2020;8(9). doi:10.3389/fcell.2020.574382
apa: Hansen, A. H., & Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms
in radial projection neuron migration in the developing cerebral cortex. Frontiers
in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2020.574382
chicago: Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms
in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers
in Cell and Developmental Biology. Frontiers, 2020. https://doi.org/10.3389/fcell.2020.574382.
ieee: A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial
projection neuron migration in the developing cerebral cortex,” Frontiers in
Cell and Developmental Biology, vol. 8, no. 9. Frontiers, 2020.
ista: Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection
neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental
Biology. 8(9), 574382.
mla: Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in
Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers
in Cell and Developmental Biology, vol. 8, no. 9, 574382, Frontiers, 2020,
doi:10.3389/fcell.2020.574382.
short: A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology
8 (2020).
corr_author: '1'
date_created: 2020-09-26T06:11:07Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2026-10-30T23:30:49Z
day: '25'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3389/fcell.2020.574382
ec_funded: 1
external_id:
isi:
- '000577915900001'
pmid:
- '33102480'
file:
- access_level: open_access
checksum: 01f731824194c94c81a5da360d997073
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T13:11:17Z
date_updated: 2020-09-28T13:11:17Z
file_id: '8584'
file_name: 2020_Frontiers_Hansen.pdf
file_size: 5527139
relation: main_file
success: 1
file_date_updated: 2020-09-28T13:11:17Z
fulldoi: https://doi.org/10.3389/fcell.2020.574382
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular mechanisms of radial neuronal migration
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
issn:
- 2296-634X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
related_material:
record:
- id: '9962'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Non-cell-autonomous mechanisms in radial projection neuron migration in the
developing cerebral cortex
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2020'
...
---
_id: '7161'
abstract:
- lang: eng
text: In this paper, we introduce an inertial projection-type method with different
updating strategies for solving quasi-variational inequalities with strongly monotone
and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions,
we establish different strong convergence results for the proposed algorithm.
Primary numerical experiments demonstrate the potential applicability of our scheme
compared with some related methods in the literature.
acknowledgement: We are grateful to the anonymous referees and editor whose insightful
comments helped to considerably improve an earlier version of this paper. The research
of the first author is supported by an ERC Grant from the Institute of Science and
Technology (IST).
article_processing_charge: No
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Aviv
full_name: Gibali, Aviv
last_name: Gibali
- first_name: Simone
full_name: Sagratella, Simone
last_name: Sagratella
citation:
ama: Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving
quasi-variational inequalities in real Hilbert spaces. Journal of Optimization
Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6
apa: Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type
methods for solving quasi-variational inequalities in real Hilbert spaces. Journal
of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6
chicago: Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type
Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal
of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6.
ieee: Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods
for solving quasi-variational inequalities in real Hilbert spaces,” Journal
of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894,
2020.
ista: Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for
solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization
Theory and Applications. 184, 877–894.
mla: Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational
Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications,
vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6.
short: Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications
184 (2020) 877–894.
date_created: 2019-12-09T21:33:44Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2024-11-04T13:52:44Z
day: '01'
ddc:
- '518'
- '510'
- '515'
department:
- _id: VlKo
doi: 10.1007/s10957-019-01616-6
ec_funded: 1
external_id:
isi:
- '000511805200009'
file:
- access_level: open_access
checksum: 9f6dc6c6bf2b48cb3a2091a9ed5feaf2
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T10:40:27Z
date_updated: 2021-03-16T23:30:04Z
embargo: 2021-03-15
file_id: '8647'
file_name: 2020_JourOptimizationTheoryApplic_Shehu.pdf
file_size: 332641
relation: main_file
file_date_updated: 2021-03-16T23:30:04Z
fulldoi: https://doi.org/10.1007/s10957-019-01616-6
has_accepted_license: '1'
intvolume: ' 184'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 877–894
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Journal of Optimization Theory and Applications
publication_identifier:
eissn:
- 1573-2878
issn:
- 0022-3239
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inertial projection-type methods for solving quasi-variational inequalities
in real Hilbert spaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 184
year: '2020'
...
---
_id: '8532'
abstract:
- lang: eng
text: The molecular anatomy of synapses defines their characteristics in transmission
and plasticity. Precise measurements of the number and distribution of synaptic
proteins are important for our understanding of synapse heterogeneity within and
between brain regions. Freeze–fracture replica immunogold electron microscopy
enables us to analyze them quantitatively on a two-dimensional membrane surface.
Here, we introduce Darea software, which utilizes deep learning for analysis of
replica images and demonstrate its usefulness for quick measurements of the pre-
and postsynaptic areas, density and distribution of gold particles at synapses
in a reproducible manner. We used Darea for comparing glutamate receptor and calcium
channel distributions between hippocampal CA3-CA1 spine synapses on apical and
basal dendrites, which differ in signaling pathways involved in synaptic plasticity.
We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic
size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA)
receptors with size. Interestingly, AMPA and NMDA receptors are segregated within
postsynaptic sites and negatively correlated in density among both apical and
basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels
show similar densities in apical and basal synapses with distributions consistent
with an exclusion zone model of calcium channel-release site topography.
acknowledgement: "This research was funded by Austrian Academy of Sciences, DOC fellowship
to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human
Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner
for technical support."
article_number: '6737'
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Matthew J
full_name: Case, Matthew J
id: 44B7CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Case
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y,
Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture
replica images applied to glutamate receptors and calcium channels at hippocampal
synapses. International Journal of Molecular Sciences. 2020;21(18). doi:10.3390/ijms21186737
apa: Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J.,
Fukazawa, Y., & Shigemoto, R. (2020). Deep learning-assisted high-throughput
analysis of freeze-fracture replica images applied to glutamate receptors and
calcium channels at hippocampal synapses. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms21186737
chicago: Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari,
Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted
High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate
Receptors and Calcium Channels at Hippocampal Synapses.” International Journal
of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21186737.
ieee: D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y.
Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of
freeze-fracture replica images applied to glutamate receptors and calcium channels
at hippocampal synapses,” International Journal of Molecular Sciences,
vol. 21, no. 18. MDPI, 2020.
ista: Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y,
Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture
replica images applied to glutamate receptors and calcium channels at hippocampal
synapses. International Journal of Molecular Sciences. 21(18), 6737.
mla: Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis
of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels
at Hippocampal Synapses.” International Journal of Molecular Sciences,
vol. 21, no. 18, 6737, MDPI, 2020, doi:10.3390/ijms21186737.
short: D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y.
Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).
corr_author: '1'
date_created: 2020-09-20T22:01:35Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2026-10-30T23:30:51Z
day: '14'
ddc:
- '570'
department:
- _id: RySh
doi: 10.3390/ijms21186737
ec_funded: 1
external_id:
isi:
- '000579945300001'
file:
- access_level: open_access
checksum: 2e4f62f3cfe945b7391fc3070e5a289f
content_type: application/pdf
creator: dernst
date_created: 2020-09-21T14:08:58Z
date_updated: 2020-09-21T14:08:58Z
file_id: '8551'
file_name: 2020_JournMolecSciences_Kleindienst.pdf
file_size: 5748456
relation: main_file
success: 1
file_date_updated: 2020-09-21T14:08:58Z
fulldoi: https://doi.org/10.3390/ijms21186737
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 25D32BC0-B435-11E9-9278-68D0E5697425
name: Mechanism of formation and maintenance of input side-dependent asymmetry in
the hippocampus
- _id: 26436750-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '785907'
name: Human Brain Project Specific Grant Agreement 2
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '9562'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Deep learning-assisted high-throughput analysis of freeze-fracture replica
images applied to glutamate receptors and calcium channels at hippocampal synapses
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '7426'
abstract:
- lang: eng
text: This paper presents a novel abstraction technique for analyzing Lyapunov and
asymptotic stability of polyhedral switched systems. A polyhedral switched system
is a hybrid system in which the continuous dynamics is specified by polyhedral
differential inclusions, the invariants and guards are specified by polyhedral
sets and the switching between the modes do not involve reset of variables. A
finite state weighted graph abstracting the polyhedral switched system is constructed
from a finite partition of the state–space, such that the satisfaction of certain
graph conditions, such as the absence of cycles with product of weights on the
edges greater than (or equal) to 1, implies the stability of the system. However,
the graph is in general conservative and hence, the violation of the graph conditions
does not imply instability. If the analysis fails to establish stability due to
the conservativeness in the approximation, a counterexample (cycle with product
of edge weights greater than or equal to 1) indicating a potential reason for
the failure is returned. Further, a more precise approximation of the switched
system can be constructed by considering a finer partition of the state–space
in the construction of the finite weighted graph. We present experimental results
on analyzing stability of switched systems using the above method.
article_number: '100856'
article_processing_charge: No
article_type: original
author:
- first_name: Miriam
full_name: Garcia Soto, Miriam
id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Soto
orcid: 0000−0003−2936−5719
- first_name: Pavithra
full_name: Prabhakar, Pavithra
last_name: Prabhakar
citation:
ama: 'Garcia Soto M, Prabhakar P. Abstraction based verification of stability of
polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5).
doi:10.1016/j.nahs.2020.100856'
apa: 'Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification
of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems.
Elsevier. https://doi.org/10.1016/j.nahs.2020.100856'
chicago: 'Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification
of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems.
Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856.'
ieee: 'M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability
of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol.
36, no. 5. Elsevier, 2020.'
ista: 'Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability
of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.'
mla: 'Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification
of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems,
vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856.'
short: 'M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).'
corr_author: '1'
date_created: 2020-02-02T23:00:59Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2026-07-28T12:57:27Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1016/j.nahs.2020.100856
external_id:
isi:
- '000528828600003'
file:
- access_level: open_access
checksum: 560abfddb53f9fe921b6744f59f2cfaa
content_type: application/pdf
creator: dernst
date_created: 2020-10-21T13:16:45Z
date_updated: 2022-05-16T22:30:04Z
embargo: 2022-05-15
file_id: '8688'
file_name: 2020_NAHS_GarciaSoto.pdf
file_size: 818774
relation: main_file
file_date_updated: 2022-05-16T22:30:04Z
fulldoi: https://doi.org/10.1016/j.nahs.2020.100856
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_identifier:
issn:
- 1751-570X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abstraction based verification of stability of polyhedral switched systems
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2020'
...
---
_id: '7680'
abstract:
- lang: eng
text: "Proteins and their complex dynamic interactions regulate cellular mechanisms
from sensing and transducing extracellular signals, to mediating genetic responses,
and sustaining or changing cell morphology. To manipulate these protein-protein
interactions (PPIs) that govern the behavior and fate of cells, synthetically
constructed, genetically encoded tools provide the means to precisely target proteins
of interest (POIs), and control their subcellular localization and activity in
vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger
that does not activate any other endogenous process, thereby allowing manipulation
of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain
from plants, algae and bacteria are re-purposed and genetically fused to POIs.
Illumination with light of a specific wavelength triggers a conformational change
that can mediate PPIs, such as dimerization or oligomerization. By using light
as a trigger, these tools can be activated with high spatial and temporal precision,
on subcellular and millisecond scales. Chemogenetic tools consist of protein domains
that recognize and bind small molecules. By genetic fusion to POIs, these domains
can mediate PPIs upon addition of their specific ligands, which are often synthetically
designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost
optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding
to red, blue or near-UV light, leaving a striking gap in the green band of the
visible light spectrum. Among both optogenetic and chemogenetic tools, there is
an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination,
rely on covalent linkage and subsequent enzymatic cleavage or initially result
in protein clustering of unknown stoichiometry.\r\nThis work describes how the
recently structurally and photochemically characterized green-light responsive
cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed
to function as a green-light responsive optogenetic tool. In contrast to previously
engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI
already upon expression, which can be rapidly disrupted by illumination. This
was employed to mimic inhibition of constitutive activity of a growth factor receptor,
and successfully implement for cell signalling in mammalian cells and in vivo
to rescue development in zebrafish. This work further describes the development
and application of a chemically induced de-dimerizer (CDD) based on a recently
identified and structurally described bacterial oxyreductase. CDD forms a dimer
upon expression in absence of its cofactor, the flavin derivative F420. Safety
and of domain expression and ligand exposure are demonstrated in vitro and in
vivo in zebrafish. The system is further applied to inhibit cell signalling output
from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire
of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing
previously not utilized cues. In the future, they can readily be combined with
existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
orcid: 0000-0002-6709-2195
citation:
ama: Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of
cellular signals. 2020. doi:10.15479/AT:ISTA:7680
apa: Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680
chicago: Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic
Inhibition of Cellular Signals.” Institute of Science and Technology Austria,
2020. https://doi.org/10.15479/AT:ISTA:7680.
ieee: S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals,” Institute of Science and Technology Austria, 2020.
ista: Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals. Institute of Science and Technology Austria.
mla: Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition
of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.
short: S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition
of Cellular Signals, Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-04-24T16:00:51Z
date_published: 2020-04-24T00:00:00Z
date_updated: 2026-08-12T09:19:22Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7680
file:
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month: '04'
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publisher: Institute of Science and Technology Austria
related_material:
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relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
OA_place: publisher
_id: '8620'
abstract:
- lang: eng
text: "The development of the human brain occurs through a tightly regulated series
of dynamic and adaptive processes during prenatal and postnatal life. A disruption
of this strictly orchestrated series of events can lead to a number of neurodevelopmental
conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common,
etiologically and phenotypically heterogeneous group of disorders sharing the
core symptoms of social interaction and communication deficits and restrictive
and repetitive interests and behaviors. They are estimated to affect one in 59
individuals in the U.S. and, over the last three decades, mutations in more than
a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet,
for the vast majority of these ASD-risk genes their role during brain development
and precise molecular function still remain elusive.\r\nDe novo loss of function
mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In
the study described here, we used Cul3 mouse models to evaluate the consequences
of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice
exhibit deficits in motor coordination as well as ASD-relevant social and cognitive
impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display
cortical lamination abnormalities due to defective migration of post-mitotic excitatory
neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line
with the observed abnormal cortical organization, Cul3 heterozygous deletion is
associated with decreased spontaneous excitatory and inhibitory activity in the
cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion
protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal
proteins in Cul3 mutant neural cells results in atypical organization of the actin
mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult
mice does not induce the majority of the behavioral defects observed in constitutive
Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn
conclusion, our data indicate that Cul3 plays a critical role in the regulation
of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral
abnormalities are primarily due to dosage sensitive Cul3 functions at early brain
developmental stages."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: I would like to especially thank Armel Nicolas from the Proteomics
and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to
thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka,
Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line
maintenance and their great support.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
citation:
ama: Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis.
2020. doi:10.15479/AT:ISTA:8620
apa: Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder
pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620
chicago: Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder
Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620.
ieee: J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,”
Institute of Science and Technology Austria, 2020.
ista: Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder
pathogenesis. Institute of Science and Technology Austria.
mla: Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder
Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.
short: J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis,
Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-10-07T14:53:13Z
date_published: 2020-10-12T00:00:00Z
date_updated: 2026-08-12T09:55:08Z
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supervisor:
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full_name: Novarino, Gaia
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last_name: Novarino
orcid: 0000-0002-7673-7178
title: Illuminating the role of Cul3 in autism spectrum disorder pathogenesis
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2020'
...
---
_id: '7800'
abstract:
- lang: eng
text: De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3
(CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models
to evaluate the consequences of Cul3 mutations in vivo. Our results show that
Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as
ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical
lamination abnormalities due to defective neuronal migration and reduced numbers
of excitatory and inhibitory neurons. In line with the observed abnormal columnar
organization, Cul3 haploinsufficiency is associated with decreased spontaneous
excitatory and inhibitory activity in the cortex. At the molecular level, employing
a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and
adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal
proteins in Cul3 mutant neuronal cells results in atypical organization of the
actin mesh at the cell leading edge, likely causing the observed migration deficits.
In contrast to these important functions early in development, Cul3 deficiency
appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency
in adult mice does not result in the behavioral defects observed in constitutive
Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has
a critical role in the regulation of cytoskeletal proteins and neuronal migration
and that ASD-associated defects and behavioral abnormalities are primarily due
to Cul3 functions at early developmental stages.
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Zoe
full_name: Dobler, Zoe
id: D23090A2-9057-11EA-883A-A8396FC7A38F
last_name: Dobler
- first_name: Emanuele
full_name: Cacci, Emanuele
last_name: Cacci
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein
homeostasis and cell migration during a critical window of brain development.
bioRxiv. doi:10.1101/2020.01.10.902064
apa: Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer,
C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development. bioRxiv.
https://doi.org/10.1101/2020.01.10.902064
chicago: Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan,
Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates
Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of
Brain Development.” BioRxiv, n.d. https://doi.org/10.1101/2020.01.10.902064 .
ieee: J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development,” bioRxiv.
.
ista: Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger
C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton
protein homeostasis and cell migration during a critical window of brain development.
bioRxiv, 10.1101/2020.01.10.902064
.
mla: Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis
and Cell Migration during a Critical Window of Brain Development.” BioRxiv,
doi:10.1101/2020.01.10.902064
.
short: J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer,
C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv
(n.d.).
corr_author: '1'
das_tickbox: '1'
date_created: 2020-05-05T14:31:33Z
date_published: 2020-01-11T00:00:00Z
date_updated: 2026-10-30T23:30:54Z
day: '11'
ddc:
- '570'
department:
- _id: JoDa
- _id: GaNo
- _id: LifeSc
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month: '01'
oa: 1
oa_version: Preprint
project:
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relation: later_version
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relation: dissertation_contains
status: public
status: public
title: Cul3 regulates cytoskeleton protein homeostasis and cell migration during a
critical window of brain development
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
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short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8131'
abstract:
- lang: eng
text: The possibility to generate construct valid animal models enabled the development
and testing of therapeutic strategies targeting the core features of autism spectrum
disorders (ASDs). At the same time, these studies highlighted the necessity of
identifying sensitive developmental time windows for successful therapeutic interventions.
Animal and human studies also uncovered the possibility to stratify the variety
of ASDs in molecularly distinct subgroups, potentially facilitating effective
treatment design. Here, we focus on the molecular pathways emerging as commonly
affected by mutations in diverse ASD-risk genes, on their role during critical
windows of brain development and the potential treatments targeting these biological
processes.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD
treatments. Current Opinion in Genetics & Development. 2020;65(12):126-137.
doi:10.1016/j.gde.2020.06.004
apa: Basilico, B., Morandell, J., & Novarino, G. (2020). Molecular mechanisms
for targeted ASD treatments. Current Opinion in Genetics & Development.
Elsevier. https://doi.org/10.1016/j.gde.2020.06.004
chicago: Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms
for Targeted ASD Treatments.” Current Opinion in Genetics & Development.
Elsevier, 2020. https://doi.org/10.1016/j.gde.2020.06.004.
ieee: B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted
ASD treatments,” Current Opinion in Genetics & Development, vol. 65,
no. 12. Elsevier, pp. 126–137, 2020.
ista: Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted
ASD treatments. Current Opinion in Genetics & Development. 65(12), 126–137.
mla: Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.”
Current Opinion in Genetics & Development, vol. 65, no. 12, Elsevier,
2020, pp. 126–37, doi:10.1016/j.gde.2020.06.004.
short: B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics &
Development 65 (2020) 126–137.
corr_author: '1'
date_created: 2020-07-19T22:00:58Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2026-10-30T23:30:54Z
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ddc:
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department:
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doi: 10.1016/j.gde.2020.06.004
ec_funded: 1
external_id:
isi:
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title: Molecular mechanisms for targeted ASD treatments
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name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
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short: CC BY-NC-ND (4.0)
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volume: 65
year: '2020'
...
---
_id: '9198'
abstract:
- lang: eng
text: "The optimization of multilayer neural networks typically leads to a solution\r\nwith
zero training error, yet the landscape can exhibit spurious local minima\r\nand
the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon:
we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization
makes the landscape of multilayer neural networks\r\napproximately connected and
thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions
are connected via a piecewise linear\r\npath, and the increase in loss along this
path vanishes as the number of\r\nneurons grows large. This result is a consequence
of the fact that the\r\nparameters found by SGD are increasingly dropout stable
as the network becomes\r\nwider. We show that, if we remove part of the neurons
(and suitably rescale the\r\nremaining ones), the change in loss is independent
of the total number of\r\nneurons, and it depends only on how many neurons are
left. Our results exhibit\r\na mild dependence on the input dimension: they are
dimension-free for two-layer\r\nnetworks and depend linearly on the dimension
for multilayer networks. We\r\nvalidate our theoretical findings with numerical
experiments for different\r\narchitectures and classification tasks."
acknowledgement: M. Mondelli was partially supported by the 2019 LopezLoreta Prize.
The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed
Algorithms and Systems Lab for providing computational resources.
article_processing_charge: No
arxiv: 1
author:
- first_name: Aleksandr
full_name: Shevchenko, Aleksandr
id: F2B06EC2-C99E-11E9-89F0-752EE6697425
last_name: Shevchenko
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of
SGD solutions for over-parameterized neural networks. In: Proceedings of the
37th International Conference on Machine Learning. Vol 119. ML Research Press;
2020:8773-8784.'
apa: Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout
stability of SGD solutions for over-parameterized neural networks. In Proceedings
of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784).
ML Research Press.
chicago: Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and
Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In
Proceedings of the 37th International Conference on Machine Learning, 119:8773–84.
ML Research Press, 2020.
ieee: A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability
of SGD solutions for over-parameterized neural networks,” in Proceedings of
the 37th International Conference on Machine Learning, 2020, vol. 119, pp.
8773–8784.
ista: Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability
of SGD solutions for over-parameterized neural networks. Proceedings of the 37th
International Conference on Machine Learning. vol. 119, 8773–8784.
mla: Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout
Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings
of the 37th International Conference on Machine Learning, vol. 119, ML Research
Press, 2020, pp. 8773–84.
short: A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference
on Machine Learning, ML Research Press, 2020, pp. 8773–8784.
date_created: 2021-02-25T09:36:22Z
date_published: 2020-07-13T00:00:00Z
date_updated: 2026-10-30T23:31:02Z
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title: Landscape connectivity and dropout stability of SGD solutions for over-parameterized
neural networks
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 119
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '8707'
abstract:
- lang: eng
text: Dynamic changes in the three-dimensional (3D) organization of chromatin are
associated with central biological processes, such as transcription, replication
and development. Therefore, the comprehensive identification and quantification
of these changes is fundamental to understanding of evolutionary and regulatory
mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity
(CHESS), an algorithm for the comparison of chromatin contact maps and automatic
differential feature extraction. We demonstrate the robustness of CHESS to experimental
variability and showcase its biological applications on (1) interspecies comparisons
of syntenic regions in human and mouse models; (2) intraspecies identification
of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific
aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and
(4) the systematic identification of chromatin contact differences in high-resolution
Capture-C data. In summary, CHESS is a computationally efficient method for the
comparison and classification of changes in chromatin contact data.
acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society,
the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome
Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the
DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project
no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN
to J.M.V.) and the Medical Research Council in the UK. This research was partially
funded by the European Union’s H2020 Framework Programme through the European Research
Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio
de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R.
The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia,
Innovación y Universidades to the European Molecular Biology Laboratory partnership,
the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208,
the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación
y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya
through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing
by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from
the European Regional Development Fund corresponding to the 2014–2020 Smart Growth
Operating Program. S.G. thanks the support from the Company of Biologists (grant
no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship
programme.'
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: ' Galan, Silvia'
last_name: ' Galan'
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
- first_name: Kai
full_name: Kruse, Kai
last_name: Kruse
- first_name: Noelia
full_name: Díaz, Noelia
last_name: Díaz
- first_name: Marc A
full_name: Marti-Renom, Marc A
last_name: Marti-Renom
- first_name: Juan M
full_name: Vaquerizas, Juan M
last_name: Vaquerizas
citation:
ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS
enables quantitative comparison of chromatin contact data and automatic feature
extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y
apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas,
J. M. (2020). CHESS enables quantitative comparison of chromatin contact data
and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y
chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom,
and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature,
2020. https://doi.org/10.1038/s41588-020-00712-y.
ieee: S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M.
Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and
automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature,
pp. 1247–1255, 2020.
ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020.
CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction. Nature Genetics. 52, 1247–1255.
mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer
Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.
short: S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas,
Nature Genetics 52 (2020) 1247–1255.
date_created: 2020-10-25T23:01:20Z
date_published: 2020-10-19T00:00:00Z
date_updated: 2026-10-30T23:31:11Z
day: '19'
department:
- _id: FyKo
doi: 10.1038/s41588-020-00712-y
external_id:
isi:
- '000579693500004'
pmid:
- '33077914'
fulldoi: https://doi.org/10.1038/s41588-020-00712-y
intvolume: ' 52'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pmc.ncbi.nlm.nih.gov/articles/PMC7610641/
month: '10'
oa: 1
oa_version: Submitted Version
page: 1247-1255
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '18642'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2020'
...
---
_id: '11062'
abstract:
- lang: eng
text: Most neurons are not replaced during an animal’s lifetime. This nondividing
state is characterized by extreme longevity and age-dependent decline of key regulatory
proteins. To study the lifespans of cells and proteins in adult tissues, we combined
isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping,
we show that liver and pancreas are composed of cells with vastly different ages,
many as old as the animal. Strikingly, we also found that a subset of fibroblasts
and endothelial cells, both known for their replicative potential, are characterized
by the absence of cell division during adulthood. In addition, we show that the
primary cilia of beta cells and neurons contains different structural regions
with vastly different lifespans. Based on these results, we propose that age mosaicism
across multiple scales is a fundamental principle of adult tissue, cell, and protein
complex organization.
article_processing_charge: No
article_type: original
author:
- first_name: Rafael
full_name: Arrojo e Drigo, Rafael
last_name: Arrojo e Drigo
- first_name: Varda
full_name: Lev-Ram, Varda
last_name: Lev-Ram
- first_name: Swati
full_name: Tyagi, Swati
last_name: Tyagi
- first_name: Ranjan
full_name: Ramachandra, Ranjan
last_name: Ramachandra
- first_name: Thomas
full_name: Deerinck, Thomas
last_name: Deerinck
- first_name: Eric
full_name: Bushong, Eric
last_name: Bushong
- first_name: Sebastien
full_name: Phan, Sebastien
last_name: Phan
- first_name: Victoria
full_name: Orphan, Victoria
last_name: Orphan
- first_name: Claude
full_name: Lechene, Claude
last_name: Lechene
- first_name: Mark H.
full_name: Ellisman, Mark H.
last_name: Ellisman
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Arrojo e Drigo R, Lev-Ram V, Tyagi S, et al. Age mosaicism across multiple
scales in adult tissues. Cell Metabolism. 2019;30(2):343-351.e3. doi:10.1016/j.cmet.2019.05.010
apa: Arrojo e Drigo, R., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T.,
Bushong, E., … Hetzer, M. (2019). Age mosaicism across multiple scales in adult
tissues. Cell Metabolism. Elsevier. https://doi.org/10.1016/j.cmet.2019.05.010
chicago: Arrojo e Drigo, Rafael, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra,
Thomas Deerinck, Eric Bushong, Sebastien Phan, et al. “Age Mosaicism across Multiple
Scales in Adult Tissues.” Cell Metabolism. Elsevier, 2019. https://doi.org/10.1016/j.cmet.2019.05.010.
ieee: R. Arrojo e Drigo et al., “Age mosaicism across multiple scales in
adult tissues,” Cell Metabolism, vol. 30, no. 2. Elsevier, p. 343–351.e3,
2019.
ista: Arrojo e Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E,
Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer M. 2019. Age mosaicism across
multiple scales in adult tissues. Cell Metabolism. 30(2), 343–351.e3.
mla: Arrojo e Drigo, Rafael, et al. “Age Mosaicism across Multiple Scales in Adult
Tissues.” Cell Metabolism, vol. 30, no. 2, Elsevier, 2019, p. 343–351.e3,
doi:10.1016/j.cmet.2019.05.010.
short: R. Arrojo e Drigo, V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E.
Bushong, S. Phan, V. Orphan, C. Lechene, M.H. Ellisman, M. Hetzer, Cell Metabolism
30 (2019) 343–351.e3.
date_created: 2022-04-07T07:45:21Z
date_published: 2019-08-06T00:00:00Z
date_updated: 2025-12-15T10:02:11Z
day: '06'
department:
- _id: MaHe
doi: 10.1016/j.cmet.2019.05.010
extern: '1'
external_id:
pmid:
- '31178361'
fulldoi: https://doi.org/10.1016/j.cmet.2019.05.010
intvolume: ' 30'
issue: '2'
keyword:
- Cell Biology
- Molecular Biology
- Physiology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cmet.2019.05.010
month: '08'
oa: 1
oa_version: Published Version
page: 343-351.e3
pmid: 1
publication: Cell Metabolism
publication_identifier:
issn:
- 1550-4131
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Age mosaicism across multiple scales in adult tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2019'
...
---
_id: '27'
abstract:
- lang: eng
text: The cerebral cortex is composed of a large variety of distinct cell-types
including projection neurons, interneurons and glial cells which emerge from distinct
neural stem cell (NSC) lineages. The vast majority of cortical projection neurons
and certain classes of glial cells are generated by radial glial progenitor cells
(RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis
and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated
in a profound deterministic manner. In this review we focus on recent advances
based mainly on correlative phenotypic data emerging from functional genetic studies
in mice. We establish hypotheses to test in future research and outline a conceptual
framework how epigenetic cues modulate the generation of cell-type diversity during
cortical development. This article is protected by copyright. All rights reserved.
acknowledgement: " This work was supported by IST Austria institutional funds; NÖ
Forschung und Bildung \r\nn[f+b] (C13-002) to SH; a program grant from
\ the Human Frontiers Science Program (RGP0053/2014) to SH; the People
\ Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the European
\ Research Council (ERC) under the European Union’s Horizon 2020 research
\ and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n"
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation
of cell type diversity in the cerebral cortex. Journal of Neurochemistry.
2019;149(1):12-26. doi:10.1111/jnc.14601
apa: Amberg, N., Laukoter, S., & Hippenmeyer, S. (2019). Epigenetic cues modulating
the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry.
Wiley. https://doi.org/10.1111/jnc.14601
chicago: Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues
Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal
of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14601.
ieee: N. Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the
generation of cell type diversity in the cerebral cortex,” Journal of Neurochemistry,
vol. 149, no. 1. Wiley, pp. 12–26, 2019.
ista: Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the
generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry.
149(1), 12–26.
mla: Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type
Diversity in the Cerebral Cortex.” Journal of Neurochemistry, vol. 149,
no. 1, Wiley, 2019, pp. 12–26, doi:10.1111/jnc.14601.
short: N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019)
12–26.
corr_author: '1'
date_created: 2018-12-11T11:44:14Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2025-04-14T07:43:05Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1111/jnc.14601
ec_funded: 1
external_id:
isi:
- '000462680200002'
file:
- access_level: open_access
checksum: db027721a95d36f5de36aadcd0bdf7e6
content_type: application/pdf
creator: kschuh
date_created: 2020-01-07T13:35:52Z
date_updated: 2020-07-14T12:45:45Z
file_id: '7239'
file_name: 2019_Wiley_Amberg.pdf
file_size: 889709
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
fulldoi: https://doi.org/10.1111/jnc.14601
has_accepted_license: '1'
intvolume: ' 149'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 12-26
project:
- _id: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Journal of Neurochemistry
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Epigenetic cues modulating the generation of cell type diversity in the cerebral
cortex
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 149
year: '2019'
...
---
_id: '301'
abstract:
- lang: eng
text: A representation formula for solutions of stochastic partial differential
equations with Dirichlet boundary conditions is proved. The scope of our setting
is wide enough to cover the general situation when the backward characteristics
that appear in the usual formulation are not even defined in the Itô sense.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: István
full_name: Gyöngy, István
last_name: Gyöngy
citation:
ama: Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems.
Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003
apa: Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic
Dirichlet problems. Stochastic Processes and Their Applications. Elsevier.
https://doi.org/10.1016/j.spa.2018.04.003
chicago: Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic
Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier,
2019. https://doi.org/10.1016/j.spa.2018.04.003.
ieee: M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet
problems,” Stochastic Processes and their Applications, vol. 129, no. 3.
Elsevier, pp. 995–1012, 2019.
ista: Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet
problems. Stochastic Processes and their Applications. 129(3), 995–1012.
mla: Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet
Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3,
Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003.
short: M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129
(2019) 995–1012.
date_created: 2018-12-11T11:45:42Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:20:49Z
day: '01'
department:
- _id: JaMa
doi: 10.1016/j.spa.2018.04.003
external_id:
arxiv:
- '1611.04177'
isi:
- '000458945300012'
fulldoi: https://doi.org/10.1016/j.spa.2018.04.003
intvolume: ' 129'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.04177
month: '03'
oa: 1
oa_version: Preprint
page: 995-1012
publication: Stochastic Processes and their Applications
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Feynman–Kac formula for stochastic Dirichlet problems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 129
year: '2019'
...
---
_id: '12190'
abstract:
- lang: eng
text: Meiotic crossover frequency varies within genomes, which influences genetic
diversity and adaptation. In turn, genetic variation within populations can act
to modify crossover frequency in cis and trans. To identify genetic variation
that controls meiotic crossover frequency, we screened Arabidopsis accessions
using fluorescent recombination reporters. We mapped a genetic modifier of crossover
frequency in Col × Bur populations of Arabidopsis to a premature stop codon within
TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase
II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare
variant found in the British Isles, originating in South-West Ireland. Using genetics,
genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers,
with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq)
from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas
its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting
gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread
transcriptional changes, including in genes that regulate the meiotic cell cycle
and recombination. Therefore, TAF4b duplication is associated with acquisition
of meiocyte-specific expression and promotion of germline transcription, which
act directly or indirectly to elevate crossovers. This identifies a novel mode
of meiotic recombination control via a general transcription factor.
acknowledgement: "We thank Gregory Copenhaver (University of North Carolina), Avraham
Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for
FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash
University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon
(INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for
access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.),
European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’
(BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and
X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.;
StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Emma J.
full_name: Lawrence, Emma J.
last_name: Lawrence
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Andrew J.
full_name: Tock, Andrew J.
last_name: Tock
- first_name: Christophe
full_name: Lambing, Christophe
last_name: Lambing
- first_name: Alexander R.
full_name: Blackwell, Alexander R.
last_name: Blackwell
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Ian R.
full_name: Henderson, Ian R.
last_name: Henderson
citation:
ama: Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084
apa: Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng,
X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.06.084
chicago: Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander
R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED
FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.”
Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.06.084.
ieee: E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis,” Current
Biology, vol. 29, no. 16. Elsevier, p. 2676–2686.e3, 2019.
ista: Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR.
2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover
and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.
mla: Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls
Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology,
vol. 29, no. 16, Elsevier, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.
short: E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R.
Henderson, Current Biology 29 (2019) 2676–2686.e3.
date_created: 2023-01-16T09:16:33Z
date_published: 2019-08-19T00:00:00Z
date_updated: 2025-01-14T14:31:02Z
day: '19'
department:
- _id: XiFe
doi: 10.1016/j.cub.2019.06.084
extern: '1'
external_id:
pmid:
- '31378616'
fulldoi: https://doi.org/10.1016/j.cub.2019.06.084
intvolume: ' 29'
issue: '16'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2676-2686.e3
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and
germline transcription in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2019'
...
---
_id: '12192'
abstract:
- lang: eng
text: Transposable elements (TEs), the movement of which can damage the genome,
are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in
the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis
thaliana. However, the extent and mechanism of this activation are unknown. Here
we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed
DNA demethylation. We further demonstrate that DEMETER access to some of these
TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically
expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent
mechanism. We demonstrate that H1 is required for heterochromatin condensation
in plant cells and show that H1 overexpression creates heterochromatic foci in
the VC progenitor cell. Taken together, our results demonstrate that the natural
depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation,
heterochromatin relaxation, and TE activation.
acknowledgement: We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP
vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder)
for their assistance with microscopy, and the Norwich BioScience Institute Partnership
Computing infrastructure for Science Group for High Performance Computing resources.
This work was funded by a Biotechnology and Biological Sciences Research Council
(BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research
Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers
by the Gatsby Charitable Foundation (SH and XF).
article_number: '42530'
article_processing_charge: No
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells
causes DNA demethylation, heterochromatin decondensation and transposon activation.
eLife. 2019;8. doi:10.7554/elife.42530
apa: He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of
histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation
and transposon activation. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.42530
chicago: He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion
of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation
and Transposon Activation.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.42530.
ieee: S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1
in sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation,” eLife, vol. 8. eLife Sciences Publications, 2019.
ista: He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in
sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation. eLife. 8, 42530.
mla: He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA
Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife,
vol. 8, 42530, eLife Sciences Publications, 2019, doi:10.7554/elife.42530.
short: S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).
date_created: 2023-01-16T09:17:21Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2025-01-14T14:31:41Z
day: '28'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.7554/elife.42530
extern: '1'
external_id:
unknown:
- '31135340'
file:
- access_level: open_access
checksum: ea6b89c20d59e5eb3646916fe5d568ad
content_type: application/pdf
creator: alisjak
date_created: 2023-02-07T09:42:46Z
date_updated: 2023-02-07T09:42:46Z
file_id: '12525'
file_name: 2019_elife_He.pdf
file_size: 2493837
relation: main_file
success: 1
file_date_updated: 2023-02-07T09:42:46Z
fulldoi: https://doi.org/10.7554/elife.42530
has_accepted_license: '1'
intvolume: ' 8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin
decondensation and transposon activation
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2019'
...
---
_id: '13067'
abstract:
- lang: eng
text: Genetic incompatibilities contribute to reproductive isolation between many
diverging populations, but it is still unclear to what extent they play a role
if divergence happens with gene flow. In contact zones between the "Crab" and
"Wave" ecotypes of the snail Littorina saxatilis divergent selection forms strong
barriers to gene flow, while the role of postzygotic barriers due to selection
against hybrids remains unclear. High embryo abortion rates in this species could
indicate the presence of such barriers. Postzygotic barriers might include genetic
incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation,
both expected to be most pronounced in contact zones. In addition, embryo abortion
might reflect physiological stress on females and embryos independent of any genetic
stress. We examined all embryos of >500 females sampled outside and inside
contact zones of three populations in Sweden. Females' clutch size ranged from
0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean
12%). We described female genotypes by using a hybrid index based on hundreds
of SNPs differentiated between ecotypes with which we characterised female genotypes.
We also calculated female SNP heterozygosity and inversion karyotype. Clutch size
did not vary with female hybrid index and abortion rates were only weakly related
to hybrid index in two sites but not at all in a third site. No additional variation
in abortion rate was explained by female SNP heterozygosity, but increased female
inversion heterozygosity added slightly to increased abortion. Our results show
only weak and probably biologically insignificant postzygotic barriers contributing
to ecotype divergence and the high and variable abortion rates were marginally,
if at all, explained by hybrid index of females.
article_processing_charge: No
author:
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Zuzanna
full_name: Zagrodzka, Zuzanna
last_name: Zagrodzka
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo
abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019.
doi:10.5061/DRYAD.TB2RBNZWK'
apa: 'Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R.
(2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between
Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK'
chicago: 'Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and
Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow
between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.'
ieee: 'K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data
from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?” Dryad, 2019.'
ista: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from:
Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?,
Dryad, 10.5061/DRYAD.TB2RBNZWK.'
mla: 'Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic
Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.'
short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).
date_created: 2023-05-23T16:36:27Z
date_published: 2019-12-02T00:00:00Z
date_updated: 2025-07-10T11:54:22Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.TB2RBNZWK
fulldoi: https://doi.org/10.5061/DRYAD.TB2RBNZWK
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.tb2rbnzwk
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '7205'
relation: used_in_publication
status: public
status: public
title: 'Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...