---
_id: '1027'
abstract:
- lang: eng
text: The rising prevalence of antibiotic resistant bacteria is an increasingly
serious public health challenge. To address this problem, recent work ranging
from clinical studies to theoretical modeling has provided valuable insights into
the mechanisms of resistance, its emergence and spread, and ways to counteract
it. A deeper understanding of the underlying dynamics of resistance evolution
will require a combination of experimental and theoretical expertise from different
disciplines and new technology for studying evolution in the laboratory. Here,
we review recent advances in the quantitative understanding of the mechanisms
and evolution of antibiotic resistance. We focus on key theoretical concepts and
new technology that enables well-controlled experiments. We further highlight
key challenges that can be met in the near future to ultimately develop effective
strategies for combating resistance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic
resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97.
doi:10.1016/j.copbio.2017.02.013
apa: Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding
of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier.
https://doi.org/10.1016/j.copbio.2017.02.013
chicago: Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative
Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology.
Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013.
ieee: M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding
of antibiotic resistance evolution,” Current Opinion in Biotechnology,
vol. 46. Elsevier, pp. 90–97, 2017.
ista: Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of
antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.
mla: Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding
of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology,
vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.
short: M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017)
90–97.
corr_author: '1'
date_created: 2018-12-11T11:49:45Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2026-04-26T22:30:51Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1016/j.copbio.2017.02.013
ec_funded: 1
external_id:
isi:
- '000408077400015'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:57:57Z
date_updated: 2019-01-18T09:57:57Z
file_id: '5846'
file_name: 2017_CurrentOpinion_Lukaciinova.pdf
file_size: 858338
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:57:57Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 90 - 97
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Current Opinion in Biotechnology
publication_status: published
publisher: Elsevier
publist_id: '6364'
pubrep_id: '801'
quality_controlled: '1'
related_material:
record:
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Toward a quantitative understanding of antibiotic resistance evolution
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2017'
...
---
_id: '704'
abstract:
- lang: eng
text: 'How the organization of genes on a chromosome shapes adaptation is essential
for understanding evolutionary paths. Here, we investigate how adaptation to rapidly
increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance
gene inserted at different positions of the Escherichia coli chromosome. Using
a dual-fluorescence reporter that allows us to distinguish gene amplifications
from other up-mutations, we track in real-time adaptive changes in expression
of the drug-resistance gene. We find that the relative contribution of several
mutation types differs systematically between loci due to properties of neighboring
genes: essentiality, expression, orientation, termination, and presence of duplicates.
These properties determine rate and fitness effects of gene amplification, deletions,
and mutations compromising transcriptional termination. Thus, the adaptive potential
of a gene under selection is a system-property with a complex genetic basis that
is specific for each chromosomal locus, and it can be inferred from detailed functional
and genomic data.'
article_number: e25100
article_processing_charge: No
author:
- first_name: Magdalena
full_name: Steinrück, Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
orcid: 0000-0003-1229-9719
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the
adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100
apa: Steinrück, M., & Guet, C. C. (2017). Complex chromosomal neighborhood effects
determine the adaptive potential of a gene under selection. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.25100
chicago: Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood
Effects Determine the Adaptive Potential of a Gene under Selection.” ELife.
eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25100.
ieee: M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine
the adaptive potential of a gene under selection,” eLife, vol. 6. eLife
Sciences Publications, 2017.
ista: Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine
the adaptive potential of a gene under selection. eLife. 6, e25100.
mla: Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood
Effects Determine the Adaptive Potential of a Gene under Selection.” ELife,
vol. 6, e25100, eLife Sciences Publications, 2017, doi:10.7554/eLife.25100.
short: M. Steinrück, C.C. Guet, ELife 6 (2017).
corr_author: '1'
date_created: 2018-12-11T11:48:01Z
date_published: 2017-07-25T00:00:00Z
date_updated: 2026-04-26T22:30:55Z
day: '25'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.7554/eLife.25100
external_id:
isi:
- '000406183700001'
file:
- access_level: open_access
checksum: 6b908b5db9f61f6820ebd7f8fa815571
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:54Z
date_updated: 2020-07-14T12:47:48Z
file_id: '4975'
file_name: IST-2017-890-v1+1_elife-25100-v1.pdf
file_size: 2092088
relation: main_file
- access_level: open_access
checksum: ca21530389b720243552678125fdba35
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:55Z
date_updated: 2020-07-14T12:47:48Z
file_id: '4976'
file_name: IST-2017-890-v1+2_elife-25100-figures-v1.pdf
file_size: 3428681
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6990'
pubrep_id: '890'
quality_controlled: '1'
related_material:
record:
- id: '5564'
relation: popular_science
status: public
- id: '26'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Complex chromosomal neighborhood effects determine the adaptive potential of
a gene under selection
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2017'
...
---
_id: '1024'
abstract:
- lang: eng
text: The history of auxin and cytokinin biology including the initial discoveries
by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt
(1919) is a beautiful demonstration of unceasing continuity of research. Novel
findings are integrated into existing hypotheses and models and deepen our understanding
of biological principles. At the same time new questions are triggered and hand
to hand with this new methodologies are developed to address these new challenges.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
orcid: 0000-0003-3638-1426
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Hurny A, Benková E. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1
apa: Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin
biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1
chicago: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.
ieee: A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,”
Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29,
2017.
ista: Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 1569, 1–29.
mla: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer,
2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.
short: A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017)
1–29.
corr_author: '1'
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2026-04-26T22:30:54Z
day: '17'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1007/978-1-4939-6831-2_1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:18Z
date_updated: 2019-10-15T07:47:05Z
file_id: '5068'
file_name: IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf
file_size: 840646
relation: main_file
file_date_updated: 2019-10-15T07:47:05Z
has_accepted_license: '1'
intvolume: ' 1569'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 29
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Auxins and Cytokinins in Plant Biology
publication_identifier:
issn:
- 1064-3745
publication_status: published
publisher: Springer
publist_id: '6369'
pubrep_id: '1019'
quality_controlled: '1'
related_material:
record:
- id: '539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Methodological advances in auxin and cytokinin biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1569
year: '2017'
...
---
_id: '679'
abstract:
- lang: eng
text: Protective responses against pathogens require a rapid mobilization of resting
neutrophils and the timely removal of activated ones. Neutrophils are exceptionally
short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged
neutrophils is regulated differently from that in the circulating steady-state
pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing
protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated
infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient
neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection
site. In the context of myeloid-specific deletion of Ttp, the potentiation of
neutrophil deployment protected mice against lethal soft tissue infection with
Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome
analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically
associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not
other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher
Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP.
The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable
to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates
that posttranscriptional gene regulation by TTP schedules the termination of the
antimicrobial engagement of neutrophils. The balancing role of TTP comes at the
cost of an increased risk of bacterial infections.
acknowledgement: This work was supported by grants from the Austrian Science Fund
(FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union
Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN)
for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement
PITN-GA-2012-316682; and by a joint research cluster initiative of the University
of Vienna and the Medical University of Vienna.
article_processing_charge: No
author:
- first_name: Florian
full_name: Ebner, Florian
last_name: Ebner
- first_name: Vitaly
full_name: Sedlyarov, Vitaly
last_name: Sedlyarov
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Masa
full_name: Ivin, Masa
last_name: Ivin
- first_name: Franz
full_name: Kratochvill, Franz
last_name: Kratochvill
- first_name: Nina
full_name: Gratz, Nina
last_name: Gratz
- first_name: Lukas
full_name: Kenner, Lukas
last_name: Kenner
- first_name: Andreas
full_name: Villunger, Andreas
last_name: Villunger
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Pavel
full_name: Kovarik, Pavel
last_name: Kovarik
citation:
ama: Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin
schedules apoptosis of pathogen-engaged neutrophils during bacterial infection.
The Journal of Clinical Investigation. 2017;127(6):2051-2065. doi:10.1172/JCI80631
apa: Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N.,
… Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis
of pathogen-engaged neutrophils during bacterial infection. The Journal of
Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI80631
chicago: Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill,
Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik.
“The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged
Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation.
American Society for Clinical Investigation, 2017. https://doi.org/10.1172/JCI80631.
ieee: F. Ebner et al., “The RNA-binding protein tristetraprolin schedules
apoptosis of pathogen-engaged neutrophils during bacterial infection,” The
Journal of Clinical Investigation, vol. 127, no. 6. American Society for Clinical
Investigation, pp. 2051–2065, 2017.
ista: Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L,
Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin
schedules apoptosis of pathogen-engaged neutrophils during bacterial infection.
The Journal of Clinical Investigation. 127(6), 2051–2065.
mla: Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis
of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of
Clinical Investigation, vol. 127, no. 6, American Society for Clinical Investigation,
2017, pp. 2051–65, doi:10.1172/JCI80631.
short: F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L.
Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation
127 (2017) 2051–2065.
date_created: 2018-12-11T11:47:53Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2026-04-26T22:30:56Z
day: '01'
department:
- _id: MiSi
doi: 10.1172/JCI80631
external_id:
isi:
- '000402620800008'
pmid:
- '28504646'
intvolume: ' 127'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/
month: '06'
oa: 1
oa_version: Submitted Version
page: 2051 - 2065
pmid: 1
project:
- _id: 25985A36-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T00817-B21
name: The biochemical basis of PAR polarization
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: The Journal of Clinical Investigation
publication_identifier:
issn:
- 0021-9738
publication_status: published
publisher: American Society for Clinical Investigation
publist_id: '7038'
quality_controlled: '1'
related_material:
record:
- id: '12401'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged
neutrophils during bacterial infection
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 127
year: '2017'
...
---
_id: '676'
abstract:
- lang: eng
text: The segregation of different cell types into distinct tissues is a fundamental
process in metazoan development. Differences in cell adhesion and cortex tension
are commonly thought to drive cell sorting by regulating tissue surface tension
(TST). However, the role that differential TST plays in cell segregation within
the developing embryo is as yet unclear. Here, we have analyzed the role of differential
TST for germ layer progenitor cell segregation during zebrafish gastrulation.
Contrary to previous observations that differential TST drives germ layer progenitor
cell segregation in vitro, we show that germ layers display indistinguishable
TST within the gastrulating embryo, arguing against differential TST driving germ
layer progenitor cell segregation in vivo. We further show that the osmolarity
of the interstitial fluid (IF) is an important factor that influences germ layer
TST in vivo, and that lower osmolarity of the IF compared with standard cell culture
medium can explain why germ layers display differential TST in culture but not
in vivo. Finally, we show that directed migration of mesendoderm progenitors is
required for germ layer progenitor cell segregation and germ layer formation.
article_processing_charge: No
article_type: original
author:
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Jim
full_name: Veldhuis, Jim
last_name: Veldhuis
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Wayne
full_name: Brodland, Wayne
last_name: Brodland
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates
the action of differential tissue surface tension in progenitor cell segregation
during gastrulation. Development. 2017;144(10):1798-1806. doi:10.1242/dev.144964
apa: Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W.,
& Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the
action of differential tissue surface tension in progenitor cell segregation during
gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.144964
chicago: Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître,
Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity
Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell
Segregation during Gastrulation.” Development. Company of Biologists, 2017.
https://doi.org/10.1242/dev.144964.
ieee: G. Krens et al., “Interstitial fluid osmolarity modulates the action
of differential tissue surface tension in progenitor cell segregation during gastrulation,”
Development, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.
ista: Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg
C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential
tissue surface tension in progenitor cell segregation during gastrulation. Development.
144(10), 1798–1806.
mla: Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action
of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.”
Development, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806,
doi:10.1242/dev.144964.
short: G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J.
Heisenberg, Development 144 (2017) 1798–1806.
corr_author: '1'
date_created: 2018-12-11T11:47:52Z
date_published: 2017-05-15T00:00:00Z
date_updated: 2026-04-26T22:31:00Z
day: '15'
ddc:
- '570'
department:
- _id: Bio
- _id: CaHe
doi: 10.1242/dev.144964
external_id:
isi:
- '000402275900007'
pmid:
- '28512197'
file:
- access_level: open_access
checksum: bc25125fb664706cdf180e061429f91d
content_type: application/pdf
creator: dernst
date_created: 2019-09-24T06:56:22Z
date_updated: 2020-07-14T12:47:39Z
file_id: '6905'
file_name: 2017_Development_Krens.pdf
file_size: 8194516
relation: main_file
file_date_updated: 2020-07-14T12:47:39Z
has_accepted_license: '1'
intvolume: ' 144'
isi: 1
issue: '10'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1798 - 1806
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '7047'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
- id: '50'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Interstitial fluid osmolarity modulates the action of differential tissue surface
tension in progenitor cell segregation during gastrulation
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 144
year: '2017'
...
---
_id: '661'
abstract:
- lang: eng
text: During embryonic development, mechanical forces are essential for cellular
rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish
embryo, friction forces are generated at the interface between anterior axial
mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole
and neurectoderm progenitors moving in the opposite direction towards the vegetal
pole of the embryo. These friction forces lead to global rearrangement of cells
within the neurectoderm and determine the position of the neural anlage. Using
a combination of experiments and simulations, we show that this process depends
on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated
adhesion between those tissues. Our data thus establish the emergence of friction
forces at the interface between moving tissues as a critical force-generating
process shaping the embryo.
acknowledged_ssus:
- _id: SSU
article_processing_charge: No
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Zsuzsa
full_name: Ákos, Zsuzsa
last_name: Ákos
- first_name: Silvia
full_name: Grigolon, Silvia
last_name: Grigolon
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Verena
full_name: Ruprecht, Verena
last_name: Ruprecht
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Ekaterina
full_name: Papusheva, Ekaterina
id: 41DB591E-F248-11E8-B48F-1D18A9856A87
last_name: Papusheva
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Tamás
full_name: Vicsek, Tamás
last_name: Vicsek
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage.
Nature Cell Biology. 2017;19:306-317. doi:10.1038/ncb3492
apa: Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D.,
… Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. Nature
Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3492
chicago: Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena
Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural
Anlage.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3492.
ieee: M. Smutny et al., “Friction forces position the neural anlage,” Nature
Cell Biology, vol. 19. Nature Publishing Group, pp. 306–317, 2017.
ista: Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M,
Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction
forces position the neural anlage. Nature Cell Biology. 19, 306–317.
mla: Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” Nature
Cell Biology, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:10.1038/ncb3492.
short: M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M.
Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg,
Nature Cell Biology 19 (2017) 306–317.
corr_author: '1'
date_created: 2018-12-11T11:47:46Z
date_published: 2017-03-27T00:00:00Z
date_updated: 2026-04-26T22:31:00Z
day: '27'
department:
- _id: CaHe
- _id: BjHo
- _id: Bio
doi: 10.1038/ncb3492
ec_funded: 1
external_id:
isi:
- '000397917000009'
pmid:
- '28346437'
intvolume: ' 19'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://europepmc.org/articles/pmc5635970
month: '03'
oa: 1
oa_version: Submitted Version
page: 306 - 317
pmid: 1
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 252ABD0A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I930-B20
name: Control of Epithelial Cell Layer Spreading in Zebrafish
publication: Nature Cell Biology
publication_identifier:
issn:
- 1465-7392
publication_status: published
publisher: Nature Publishing Group
publist_id: '7074'
quality_controlled: '1'
related_material:
record:
- id: '8350'
relation: dissertation_contains
status: public
- id: '50'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Friction forces position the neural anlage
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 19
year: '2017'
...
---
_id: '639'
abstract:
- lang: eng
text: We study the problem of developing efficient approaches for proving worst-case
bounds of non-deterministic recursive programs. Ranking functions are sound and
complete for proving termination and worst-case bounds of non-recursive programs.
First, we apply ranking functions to recursion, resulting in measure functions,
and show that they provide a sound and complete approach to prove worst-case bounds
of non-deterministic recursive programs. Our second contribution is the synthesis
of measure functions in non-polynomial forms. We show that non-polynomial measure
functions with logarithm and exponentiation can be synthesized through abstraction
of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem
using linear programming. While previous methods obtain worst-case polynomial
bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr)
where r is not an integer. We present experimental results to demonstrate that
our approach can efficiently obtain worst-case bounds of classical recursive algorithms
such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive
programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:10.1007/978-3-319-63390-9_3'
apa: 'Chatterjee, K., Fu, H., & Goharshady, A. K. (2017). Non-polynomial worst
case analysis of recursive programs. In R. Majumdar & V. Kunčak (Eds.) (Vol.
10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg,
Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_3'
chicago: Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial
Worst Case Analysis of Recursive Programs.” edited by Rupak Majumdar and Viktor
Kunčak, 10427:41–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_3.
ieee: 'K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis
of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg,
Germany, 2017, vol. 10427, pp. 41–63.'
ista: 'Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis
of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63.'
mla: Chatterjee, Krishnendu, et al. Non-Polynomial Worst Case Analysis of Recursive
Programs. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer,
2017, pp. 41–63, doi:10.1007/978-3-319-63390-9_3.
short: K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.),
Springer, 2017, pp. 41–63.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:47:39Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2026-04-26T22:31:03Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-319-63390-9_3
ec_funded: 1
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
arxiv:
- '1705.00317'
isi:
- '000431900900003'
intvolume: ' 10427'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.00317
month: '01'
oa: 1
oa_version: Submitted Version
page: 41 - 63
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
isbn:
- 978-331963389-3
publication_status: published
publisher: Springer
publist_id: '7149'
quality_controlled: '1'
related_material:
record:
- id: '7014'
relation: later_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Non-polynomial worst case analysis of recursive programs
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10427
year: '2017'
...
---
_id: '949'
abstract:
- lang: eng
text: The notion of treewidth of graphs has been exploited for faster algorithms
for several problems arising in verification and program analysis. Moreover, various
notions of balanced tree decompositions have been used for improved algorithms
supporting dynamic updates and analysis of concurrent programs. In this work,
we present a tool for constructing tree-decompositions of CFGs obtained from Java
methods, which is implemented as an extension to the widely used Soot framework.
The experimental results show that our implementation on real-world Java benchmarks
is very efficient. Our tool also provides the first implementation for balancing
tree-decompositions. In summary, we present the first tool support for exploiting
treewidth in the static analysis problems on Java programs.
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
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- 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, Pavlogiannis A. JTDec: A tool for tree decompositions
in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:10.1007/978-3-319-68167-2_4'
apa: 'Chatterjee, K., Goharshady, A. K., & Pavlogiannis, A. (2017). JTDec: A
tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66).
Presented at the ATVA: Automated Technology for Verification and Analysis, Pune,
India: Springer. https://doi.org/10.1007/978-3-319-68167-2_4'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis.
“JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66.
Springer, 2017. https://doi.org/10.1007/978-3-319-68167-2_4.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for
tree decompositions in soot,” presented at the ATVA: Automated Technology for
Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.'
ista: 'Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree
decompositions in soot. ATVA: Automated Technology for Verification and Analysis,
LNCS, vol. 10482, 59–66.'
mla: 'Chatterjee, Krishnendu, et al. JTDec: A Tool for Tree Decompositions in
Soot. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:10.1007/978-3-319-68167-2_4.'
short: K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer,
2017, pp. 59–66.
conference:
end_date: 2017-10-06
location: Pune, India
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2017-10-03
corr_author: '1'
date_created: 2018-12-11T11:49:22Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2026-04-26T22:31:04Z
day: '01'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.1007/978-3-319-68167-2_4
ec_funded: 1
editor:
- first_name: Deepak
full_name: D'Souza, Deepak
last_name: D'Souza
external_id:
isi:
- '000723567800004'
file:
- access_level: open_access
checksum: a0d9f5f94dc594c4e71e78525c9942f1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:45Z
date_updated: 2020-07-14T12:48:16Z
file_id: '4835'
file_name: IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf
file_size: 948514
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 10482'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 59 - 66
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '6468'
pubrep_id: '845'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'JTDec: A tool for tree decompositions in soot'
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10482
year: '2017'
...