---
_id: '1125'
abstract:
- lang: eng
text: "Natural environments are never constant but subject to spatial and temporal
change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial
to understand the\r\nimpact of environmental variation on evolutionary processes.
In this thesis, I present\r\nthree topics that share the common theme of environmental
variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst,
I show how a temporally fluctuating environment gives rise to second-order\r\nselection
on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations
are adapted to their environment, mutation rates are minimized. I argue\r\nthat
a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly
subjected to diverse environmental challenges, and I outline implications of\r\nthe
presented results to antibiotic treatment strategies.\r\nSecond, I discuss my
work on the evolution of dispersal. Besides reproducing\r\nknown results about
the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes
in dispersal type frequencies as a source for selection for increased\r\npropensities
to disperse. This concept contains effects of relatedness that are known\r\nto
promote dispersal, and I explain how it identifies other forces selecting for
dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances
of phenotypic traits under multivariate stabilizing\r\nselection. For the case
of constant environments, I generalize known formulae of\r\nequilibrium variances
to multiple traits and discuss how the genetic variance of a focal\r\ntrait is
influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary
work aiming at including environmental fluctuations in the form of moving\r\ntrait
optima into the model."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Evolutionary proccesses in variable emvironments. 2016.
apa: Novak, S. (2016). Evolutionary proccesses in variable emvironments.
Institute of Science and Technology Austria.
chicago: Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute
of Science and Technology Austria, 2016.
ieee: S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of
Science and Technology Austria, 2016.
ista: Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute
of Science and Technology Austria.
mla: Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments.
Institute of Science and Technology Austria, 2016.
short: S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-09-07T11:55:53Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
- access_level: closed
checksum: 81dcc838dfcf7aa0b1a27ecf4fe2da4e
content_type: application/pdf
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language:
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month: '07'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6235'
related_material:
record:
- id: '2023'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolutionary proccesses in variable emvironments
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1130'
abstract:
- lang: eng
text: "In this thesis we present a computer-aided programming approach to concurrency.
Our approach helps the programmer by automatically fixing concurrency-related
bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive
scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are
program behaviours that are incorrect w.r.t. a specification. We consider both
user-provided explicit specifications in the form of assertion\r\nstatements in
the code as well as an implicit specification. The implicit specification is inferred
from the non-preemptive behaviour. Let us consider sequences of calls that the
program makes to an external interface. The implicit specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of sequences produced under a non-preemptive scheduler. We consider several
semantics-preserving fixes that go beyond atomic sections typically explored in
the synchronisation synthesis literature. Our synthesis is able to place locks,
barriers and wait-signal statements and last, but not least reorder independent
statements. The latter may be useful if a thread is released to early, e.g., before
some initialisation is completed. We guarantee that our synthesis does not introduce
deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective
function. We dub our solution trace-based synchronisation synthesis and it is
loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis
works by discovering a trace that is incorrect w.r.t. the specification and identifying
ordering constraints crucial to trigger the specification violation. Synchronisation
may be placed immediately (greedy approach) or delayed until all incorrect traces
are found (non-greedy approach). For the non-greedy approach we construct a set
of global constraints over synchronisation placements. Each model of the global
constraints set corresponds to a correctness-ensuring synchronisation placement.
The placement that is optimal w.r.t. the given objective function is chosen as
the synchronisation solution. We evaluate our approach on a number of realistic
(albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions
of the drivers with known concurrency-related bugs. For the experiments with an
explicit specification we added assertions that would detect the bugs in the experiments.
Device drivers lend themselves to implicit specification, where the device and
the operating system are the external interfaces. Our experiments demonstrate
that our synthesis method is precise and efficient. We implemented objective functions
for coarse-grained and fine-grained locking and observed that different synchronisation
placements are produced for our experiments, favouring e.g. a minimal number of
synchronisation operations or maximum concurrency."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Tarrach T. Automatic synthesis of synchronisation primitives for concurrent
programs. 2016. doi:10.15479/at:ista:1130
apa: Tarrach, T. (2016). Automatic synthesis of synchronisation primitives for
concurrent programs. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1130
chicago: Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for
Concurrent Programs.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/at:ista:1130.
ieee: T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent
programs,” Institute of Science and Technology Austria, 2016.
ista: Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent
programs. Institute of Science and Technology Austria.
mla: Tarrach, Thorsten. Automatic Synthesis of Synchronisation Primitives for
Concurrent Programs. Institute of Science and Technology Austria, 2016, doi:10.15479/at:ista:1130.
short: T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent
Programs, Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-07T00:00:00Z
date_updated: 2023-09-07T11:57:01Z
day: '07'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
- _id: GradSch
doi: 10.15479/at:ista:1130
ec_funded: 1
file:
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checksum: 319a506831650327e85376db41fc1094
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:39:32Z
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content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:14:38Z
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url: http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf
month: '07'
oa: 1
oa_version: Published Version
page: '151'
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6230'
related_material:
record:
- id: '1729'
relation: part_of_dissertation
status: public
- id: '2218'
relation: part_of_dissertation
status: public
- id: '2445'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Automatic synthesis of synchronisation primitives for concurrent programs
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1122'
abstract:
- lang: eng
text: "Computer graphics is an extremely exciting field for two reasons. On the
one hand,\r\nthere is a healthy injection of pragmatism coming from the visual
effects industry\r\nthat want robust algorithms that work so they can produce
results at an increasingly\r\nfrantic pace. On the other hand, they must always
try to push the envelope and\r\nachieve the impossible to wow their audiences
in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism,
and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance
that it will pan into something\r\nuseful.\r\nWater simulation has been in visual
effects for decades, however it still remains\r\nextremely challenging because
of its high computational cost and difficult artdirectability.\r\nThe work in
this thesis tries to address some of these difficulties.\r\nSpecifically, we make
the following three novel contributions to the state-of-the-art\r\nin water simulation
for visual effects.\r\nFirst, we develop the first algorithm that can convert
any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art
methods at the time\r\ncould only handle surfaces with fixed connectivity, but
we are the first to be able to\r\nhandle surfaces that merge and split apart.
This is important for water simulation\r\npractitioners, because it allows them
to convert splashy water surfaces extracted\r\nfrom particles or simulated using
grid-based level sets into triangle meshes that can\r\nbe either textured and
enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm
to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions
of human performances.\r\nSecond, we formulate a surface-based energy that measures
the deviation of a\r\nwater surface froma physically valid state. Such discrepancies
arise when there is a\r\nmismatch in the degrees of freedom between the water
surface and the underlying\r\nphysics solver. This commonly happens when practitioners
use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution
grid-based surfaces\r\nare combined with low-resolution physics. Following the
direction of steepest\r\ndescent on our surface-based energy, we can either smooth
these artifacts or turn\r\nthem into high-resolution waves by interpreting the
energy as a physical potential.\r\nThird, we extend state-of-the-art techniques
in non-reflecting boundaries to handle spatially and time-varying background flows.
This allows a novel new\r\nworkflow where practitioners can re-simulate part of
an existing simulation, such\r\nas removing a solid obstacle, adding a new splash
or locally changing the resolution.\r\nSuch changes can easily lead to new waves
in the re-simulated region that would\r\nreflect off of the new simulation boundary,
effectively ruining the illusion of a\r\nseamless simulation boundary between
the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure
that such waves are absorbed."
acknowledgement: "First and foremost I would like to thank Chris. I have been incredibly
lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right
thing in all walks of\r\nlife is something I admire and aspire to. I also really
appreciate the fact that when\r\nworking with you it felt like we were equals. I
think we had a very synergetic work\r\nrelationship: I learned immensely from you,
but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would
like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working
with you. You showed me how to persevere and keep morale\r\nhigh when things were
looking the most bleak before the deadline. You are an\r\nincredible motivator and
super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker
games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing
you by asking about your guitar playing that one\r\ntime. You really are quite awesome!
Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch
researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also
like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have
learned so much. The excellent discussions we had in reading\r\ngroups and research
meetings really helped me become a better researcher!\r\nNext, I would like to thank
all the amazing people that I met during my PhD\r\nstudies, both at IST Austria,
in Vienna and elsewhere. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
citation:
ama: Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016.
doi:10.15479/AT:ISTA:th_640
apa: Bojsen-Hansen, M. (2016). Tracking, correcting and absorbing water surface
waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_640
chicago: Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface
Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:th_640.
ieee: M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,”
Institute of Science and Technology Austria, 2016.
ista: Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves.
Institute of Science and Technology Austria.
mla: Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:th_640.
short: M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves,
Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:16Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2024-02-21T13:50:48Z
day: '15'
ddc:
- '004'
- '005'
- '006'
- '532'
- '621'
degree_awarded: PhD
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:th_640
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:02Z
date_updated: 2018-12-12T10:13:02Z
file_id: '4982'
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language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: '114'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6238'
related_material:
record:
- id: '5558'
relation: other
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: Tracking, correcting and absorbing water surface waves
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1398'
abstract:
- lang: eng
text: Hybrid zones represent evolutionary laboratories, where recombination brings
together alleles in combinations which have not previously been tested by selection.
This provides an excellent opportunity to test the effect of molecular variation
on fitness, and how this variation is able to spread through populations in a
natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for
two loci controlling the distribution of yellow and magenta floral pigments. Where
the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley
in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine
to give striking transgressive variation for flower colour. The sharp transition
in phenotype over ~1km implies strong selection maintaining the hybrid zone. An
indirect assay of pollinator visitation in the field found that pollinators forage
in a positive-frequency dependent manner on Antirrhinum, matching previous data
on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds
demonstrated assortative mating for pigmentation alleles, and that pollinator
behaviour alone is sufficient to explain this pattern. Selection by pollinators
should be sufficiently strong to maintain the hybrid zone, although other mechanisms
may be at work. At a broader scale I examined evolutionary transitions between
yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection
has acted strate that pollinators are a major determinant of reproductive success
and mating patterns in wild Antirrhinum.
acknowledgement: "I am indebted to many people for their support during my PhD, but
I particularly wish to thank Nick Barton for his guidance and intuition, and for
encouraging me to take the time to look beyond the immediate topic of my PhD to
understand the broader context. I am also especially grateful to David Field his
bottomless patience, invaluable advice on experimental design, analysis and scientific
writing, and for tireless work on the population surveys and genomic work without
most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work
with the combined strengths of the groups at The John Innes Centre, University of
Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in
Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank
David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections,
as well as Monique Burrus and Christophe Andalo and a large number of volunteers
for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski
for providing seeds and for her input into the design of the experimental arrays,
and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those
mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous
reviewers for their insightful comments on sections of this manuscript. I also thank
Jana Porsche for her e ff orts in tracking down the more obscure references for
chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted
to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer
and Magnus Nordborg for taking the time to read and evaluate the thesis given a
shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been
the supportive atmosphere of IST. In particular, I have come to appreciate the enormous
support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann
and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for
their enthusiasm and readiness to help where possible in setting up our greenhouse
and experiments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. The role of pollinator-mediated selection in the maintenance of a
flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526
apa: Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526
chicago: Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute
of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 .
ieee: T. Ellis, “The role of pollinator-mediated selection in the maintenance of
a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of
Science and Technology Austria, 2016.
ista: Ellis T. 2016. The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria.
mla: Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute
of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 .
short: T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of
a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-18T00:00:00Z
date_updated: 2024-02-21T13:51:39Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
doi: '10.15479/AT:ISTA:TH_526 '
file:
- access_level: open_access
checksum: a89b17ff27cf92c9a15f6b3d46bd7e53
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:51Z
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- iso: eng
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page: '130'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5809'
pubrep_id: '526'
related_material:
record:
- id: '5553'
relation: popular_science
status: public
- id: '5551'
relation: popular_science
status: public
- id: '5552'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The role of pollinator-mediated selection in the maintenance of a flower color
polymorphism in an Antirrhinum majus hybrid zone
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1131'
abstract:
- lang: eng
text: "Evolution of gene regulation is important for phenotypic evolution and diversity.
Sequence-specific binding of regulatory proteins is one of the key regulatory
mechanisms determining gene expression. Although there has been intense interest
in evolution of regulatory binding sites in the last decades, a theoretical understanding
is far from being complete. In this thesis, I aim at a better understanding of
the evolution of transcriptional regulatory binding sequences by using biophysical
and population genetic models.\r\nIn the first part of the thesis, I discuss how
to formulate the evolutionary dynamics of binding se- quences in a single isolated
binding site and in promoter/enhancer regions. I develop a theoretical framework
bridging between a thermodynamical model for transcription and a mutation-selection-drift
model for monomorphic populations. I mainly address the typical evolutionary rates,
and how they de- pend on biophysical parameters (e.g. binding length and specificity)
and population genetic parameters (e.g. population size and selection strength).\r\nIn
the second part of the thesis, I analyse empirical data for a better evolutionary
and biophysical understanding of sequence-specific binding of bacterial RNA polymerase.
First, I infer selection on regulatory and non-regulatory binding sites of RNA
polymerase in the E. coli K12 genome. Second, I infer the chemical potential of
RNA polymerase, an important but unknown physical parameter defining the threshold
energy for strong binding. Furthermore, I try to understand the relation between
the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial
isolates by constructing a simple but biophysically motivated gene expression
model. Lastly, I lay out a statistical framework to predict adaptive point mutations
in de novo promoter evolution in a selection experiment."
acknowledgement: This PhD thesis may not have been completed without the help and
care I received from some peo- ple during my PhD life. I am especially grateful
to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices
but also for their patience and support. I thank Calin Guet and Jonathan Bollback
for allowing me to “play around” in their labs and get some experience on experimental
evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and
sharing their experimental data with me. I thank Johannes Jaeger for reviewing my
thesis. I thank all members of Barton group (aka bartonians) for their feedback,
and all workers of IST Austria for making the best working conditions. Lastly, I
thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous
support and encouragement. I truly had a great chance of having right people around
me.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Evolution of transcriptional regulatory sequences. 2016.
apa: Tugrul, M. (2016). Evolution of transcriptional regulatory sequences.
Institute of Science and Technology Austria.
chicago: Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute
of Science and Technology Austria, 2016.
ieee: M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute
of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute
of Science and Technology Austria.
mla: Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute
of Science and Technology Austria, 2016.
short: M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2024-02-21T13:50:34Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
- access_level: closed
checksum: 66cb61a59943e4fb7447c6a86be5ef51
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T08:53:52Z
date_updated: 2019-08-13T08:53:52Z
file_id: '6810'
file_name: Tugrul_thesis_w_signature_page.pdf
file_size: 3695257
relation: main_file
- access_level: open_access
checksum: 293e388d70563760f6b24c3e66283dda
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:45:20Z
date_updated: 2021-02-22T11:45:20Z
file_id: '9182'
file_name: 2016_Tugrul_Thesis.pdf
file_size: 3880811
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:45:20Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6229'
related_material:
record:
- id: '1666'
relation: part_of_dissertation
status: public
- id: '5554'
relation: research_data
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolution of transcriptional regulatory sequences
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1401'
abstract:
- lang: eng
text: 'The human ability to recognize objects in complex scenes has driven research
in the computer vision field over couple of decades. This thesis focuses on the
object recognition task in images. That is, given the image, we want the computer
system to be able to predict the class of the object that appears in the image.
A recent successful attempt to bridge semantic understanding of the image perceived
by humans and by computers uses attribute-based models. Attributes are semantic
properties of the objects shared across different categories, which humans and
computers can decide on. To explore the attribute-based models we take a statistical
machine learning approach, and address two key learning challenges in view of
object recognition task: learning augmented attributes as mid-level discriminative
feature representation, and learning with attributes as privileged information.
Our main contributions are parametric and non-parametric models and algorithms
to solve these frameworks. In the parametric approach, we explore an autoencoder
model combined with the large margin nearest neighbor principle for mid-level
feature learning, and linear support vector machines for learning with privileged
information. In the non-parametric approach, we propose a supervised Indian Buffet
Process for automatic augmentation of semantic attributes, and explore the Gaussian
Processes classification framework for learning with privileged information. A
thorough experimental analysis shows the effectiveness of the proposed models
in both parametric and non-parametric views.'
acknowledgement: "I would like to thank my supervisor, Christoph Lampert, for guidance
throughout my studies and for patience in transforming me into a scientist, and
my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice.
\r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative
needs and was always nice and friendly to me, and the campus team for making the
IST Austria campus my second home. \r\nI was honored to collaborate with brilliant
researchers and to learn from their experience. Undoubtedly, I learned most of all
from Novi Quadrianto: brainstorming our projects and getting exciting results was
the most enjoyable part of my work – thank you! I am also grateful to David Knowles,
Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina
for the fantastic projects we worked on together, and to Kristen Grauman and Adriana
Kovashka for the exceptional experience working with user studies. I would like
to thank my colleagues at IST Austria and my office mates who shared their happy
moods, scientific breakthroughs and thought-provoking conversations with me: Chao,
Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina,
Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael,
Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games
of table soccer we played together and the tournaments we teamed up for: we will
definitely win next time:) A very warm hug to Asya for always being so inspiring
and supportive to me, and for helping me to increase the proportion of female computer
scientists in our group. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
citation:
ama: 'Sharmanska V. Learning with attributes for object recognition: Parametric
and non-parametrics views. 2015. doi:10.15479/at:ista:1401'
apa: 'Sharmanska, V. (2015). Learning with attributes for object recognition:
Parametric and non-parametrics views. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:1401'
chicago: 'Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition:
Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria,
2015. https://doi.org/10.15479/at:ista:1401.'
ieee: 'V. Sharmanska, “Learning with attributes for object recognition: Parametric
and non-parametrics views,” Institute of Science and Technology Austria, 2015.'
ista: 'Sharmanska V. 2015. Learning with attributes for object recognition: Parametric
and non-parametrics views. Institute of Science and Technology Austria.'
mla: 'Sharmanska, Viktoriia. Learning with Attributes for Object Recognition:
Parametric and Non-Parametrics Views. Institute of Science and Technology
Austria, 2015, doi:10.15479/at:ista:1401.'
short: 'V. Sharmanska, Learning with Attributes for Object Recognition: Parametric
and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.'
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:11Z
day: '01'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ChLa
- _id: GradSch
doi: 10.15479/at:ista:1401
file:
- access_level: open_access
checksum: 3605b402bb6934e09ae4cf672c84baf7
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:33:17Z
date_updated: 2021-02-22T11:33:17Z
file_id: '9177'
file_name: 2015_Thesis_Sharmanska.pdf
file_size: 7964342
relation: main_file
success: 1
- access_level: closed
checksum: e37593b3ee75bf3180629df2d6ca8f4e
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:40:45Z
date_updated: 2021-11-17T13:47:24Z
file_id: '10297'
file_name: 2015_Thesis_Sharmanska_pdfa.pdf
file_size: 7372241
relation: main_file
file_date_updated: 2021-11-17T13:47:24Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- url: http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf
month: '04'
oa: 1
oa_version: Published Version
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5806'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: 'Learning with attributes for object recognition: Parametric and non-parametrics
views'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1400'
abstract:
- lang: eng
text: Cancer results from an uncontrolled growth of abnormal cells. Sequentially
accumulated genetic and epigenetic alterations decrease cell death and increase
cell replication. We used mathematical models to quantify the effect of driver
gene mutations. The recently developed targeted therapies can lead to dramatic
regressions. However, in solid cancers, clinical responses are often short-lived
because resistant cancer cells evolve. We estimated that approximately 50 different
mutations can confer resistance to a typical targeted therapeutic agent. We find
that resistant cells are likely to be present in expanded subclones before the
start of the treatment. The dominant strategy to prevent the evolution of resistance
is combination therapy. Our analytical results suggest that in most patients,
dual therapy, but not monotherapy, can result in long-term disease control. However,
long-term control can only occur if there are no possible mutations in the genome
that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous
therapy with two drugs is much more likely to result in long-term disease control
than sequential therapy with the same drugs. To improve our understanding of the
underlying subclonal evolution we reconstruct the evolutionary history of a patient's
cancer from next-generation sequencing data of spatially-distinct DNA samples.
Using a quantitative measure of genetic relatedness, we found that pancreatic
cancers and their metastases demonstrated a higher level of relatedness than that
expected for any two cells randomly taken from a normal tissue. This minimal amount
of genetic divergence among advanced lesions indicates that genetic heterogeneity,
when quantitatively defined, is not a fundamental feature of the natural history
of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics
finds evidence for seeding patterns of metastases and can directly be used to
discover rules governing the evolution of solid malignancies to transform cancer
into a more predictable disease.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
citation:
ama: Reiter J. The subclonal evolution of cancer. 2015.
apa: Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science
and Technology Austria.
chicago: Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science
and Technology Austria, 2015.
ieee: J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology
Austria, 2015.
ista: Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and
Technology Austria.
mla: Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science
and Technology Austria, 2015.
short: J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology
Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:44Z
day: '01'
degree_awarded: PhD
department:
- _id: KrCh
language:
- iso: eng
month: '04'
oa_version: None
page: '183'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5807'
related_material:
record:
- id: '1709'
relation: part_of_dissertation
status: public
- id: '2000'
relation: part_of_dissertation
status: public
- id: '2247'
relation: part_of_dissertation
status: public
- id: '2816'
relation: part_of_dissertation
status: public
- id: '2858'
relation: part_of_dissertation
status: public
- id: '3157'
relation: part_of_dissertation
status: public
- id: '3260'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: The subclonal evolution of cancer
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1399'
abstract:
- lang: eng
text: This thesis is concerned with the computation and approximation of intrinsic
volumes. Given a smooth body M and a certain digital approximation of it, we develop
algorithms to approximate various intrinsic volumes of M using only measurements
taken from its digital approximations. The crucial idea behind our novel algorithms
is to link the recent theory of persistent homology to the theory of intrinsic
volumes via the Crofton formula from integral geometry and, in particular, via
Euler characteristic computations. Our main contributions are a multigrid convergent
digital algorithm to compute the first intrinsic volume of a solid body in R^n
as well as an appropriate integration pipeline to approximate integral-geometric
integrals defined over the Grassmannian manifold.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. On the approximation of intrinsic volumes. 2015.
apa: Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute
of Science and Technology Austria.
chicago: Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute
of Science and Technology Austria, 2015.
ieee: F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science
and Technology Austria, 2015.
ista: Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of
Science and Technology Austria.
mla: Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute
of Science and Technology Austria, 2015.
short: F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science
and Technology Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
degree_awarded: PhD
department:
- _id: HeEd
language:
- iso: eng
month: '06'
oa_version: None
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5808'
related_material:
record:
- id: '1662'
relation: part_of_dissertation
status: public
- id: '1792'
relation: part_of_dissertation
status: public
- id: '2255'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: On the approximation of intrinsic volumes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1404'
abstract:
- lang: eng
text: "The co-evolution of hosts and pathogens is characterized by continuous adaptations
of both parties. Pathogens of social insects need to adapt towards disease defences
at two levels: 1) individual immunity of each colony member consisting of behavioural
defence strategies as well as humoral and cellular immune responses and 2) social
immunity that is collectively performed by all group members comprising behavioural,
physiological and organisational defence strategies.\r\n\r\nTo disentangle the
selection pressure on pathogens by the collective versus individual level of disease
defence in social insects, we performed an evolution experiment using the Argentine
Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic
fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution
over 10 serial host passages to two different evolution host treatments: (1) only
individual host immunity in a single host treatment, and (2) simultaneously acting
individual and social immunity in a social host treatment, in which an exposed
ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen
evolution experiment, the 6 Metarhizium spp. strains were characterised concerning
conidiospore size killing rates in singly and socially reared ants, their competitiveness
under coinfecting conditions and their influence on ant behaviour. We analysed
how the ancestral atrain mixture changed in conidiospere size, killing rate and
strain composition dependent on host treatment (single or social hosts) during
10 passages and found that killing rate and conidiospere size of the pathogen
increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting
the evolved strain mixtures that evolved under either the single or social host
treatment under both single and social current rearing conditions in a full factorial
design experiment revealed that the additional collective defences in insect societies
add new selection pressure for their coevolving pathogens that compromise their
ability to adapt to its host at the group level. To our knowledge, this is the
first study directly measuring the influence of social immunity on pathogen evolution."
acknowledgement: This work was funded by the DFG and the ERC.
alternative_title:
- IST Austria Thesis
author:
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
citation:
ama: Stock M. Evolution of a fungal pathogen towards individual versus social immunity
in ants. 2014.
apa: Stock, M. (2014). Evolution of a fungal pathogen towards individual versus
social immunity in ants. IST Austria.
chicago: Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus
Social Immunity in Ants.” IST Austria, 2014.
ieee: M. Stock, “Evolution of a fungal pathogen towards individual versus social
immunity in ants,” IST Austria, 2014.
ista: Stock M. 2014. Evolution of a fungal pathogen towards individual versus social
immunity in ants. IST Austria.
mla: Stock, Miriam. Evolution of a Fungal Pathogen towards Individual versus
Social Immunity in Ants. IST Austria, 2014.
short: M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social
Immunity in Ants, IST Austria, 2014.
date_created: 2018-12-11T11:51:49Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:50:30Z
day: '01'
department:
- _id: SyCr
language:
- iso: eng
month: '04'
oa_version: None
page: '101'
publication_status: published
publisher: IST Austria
publist_id: '5803'
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Evolution of a fungal pathogen towards individual versus social immunity in
ants
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1395'
abstract:
- lang: eng
text: In this thesis I studied various individual and social immune defences employed
by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The
first two chapters of this thesis address the phenomenon of 'social immunisation'.
Social immunisation, that is the immunological protection of group members due
to social contact to a pathogen-exposed nestmate, has been described in various
social insect species against different types of pathogens. However, in the case
of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation
exists at all. Its underlying mechanisms r any other properties were, however,
unknown. In the first chapter of this thesis I identified the mechanistic basis
of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium.
I could show that nestmates of a pathogen-exposed individual contract low-level
infections due to social interactions. These low-level infections are, however,
non-lethal and cause an active stimulation of the immune system, which protects
the nestmates upon subsequent pathogen encounters. In the second chapter of this
thesis I investigated the specificity and colony level effects of social immunisation.
I demonstrated that the protection conferred by social immunisation is highly
specific, protecting ants only against the same pathogen strain. In addition,
depending on the respective context, social immunisation may even cause fitness
costs. I further showed that social immunisation crucially affects sanitary behaviour
and disease dynamics within ant groups. In the third chapter of this thesis I
studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its
host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic
fungi, research concerning host fitness consequence is sparse. I showed that highly
Laboulbenia-infected ants sustain fitness costs under resource limitation, however,
gain fitness benefits when exposed to an entomopathogenus fungus. These effects
are probably cause by a prophylactic upregulation of behavioural as well as physiological
immune defences in highly infected ants.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
citation:
ama: 'Konrad M. Immune defences in ants: Effects of social immunisation and a fungal
ectosymbiont in the ant Lasius neglectus. 2014.'
apa: 'Konrad, M. (2014). Immune defences in ants: Effects of social immunisation
and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science
and Technology Austria.'
chicago: 'Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation
and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and
Technology Austria, 2014.'
ieee: 'M. Konrad, “Immune defences in ants: Effects of social immunisation and a
fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology
Austria, 2014.'
ista: 'Konrad M. 2014. Immune defences in ants: Effects of social immunisation and
a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology
Austria.'
mla: 'Konrad, Matthias. Immune Defences in Ants: Effects of Social Immunisation
and a Fungal Ectosymbiont in the Ant Lasius Neglectus. Institute of Science
and Technology Austria, 2014.'
short: 'M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a
Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology
Austria, 2014.'
date_created: 2018-12-11T11:51:46Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2023-09-07T11:38:56Z
day: '01'
degree_awarded: PhD
department:
- _id: SyCr
language:
- iso: eng
month: '02'
oa_version: None
page: '131'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5814'
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: 'Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont
in the ant Lasius neglectus'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '1402'
abstract:
- lang: eng
text: Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated
into various lipid signaling molecules, designated polyphosphoinositides (PPIs).
The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol
is performed by a set of organelle-specific kinases and phosphatases, and the
characteristic head groups make these molecules ideal for regulating biological
processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2
play crucial roles in trafficking toward the lytic compartments, whereas the role
in plants is not yet fully understood. Here we identified the role of a land plant-specific
subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during
vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize
to the tonoplast along with Ptdlns3P, the presumable product of their activity.
in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates
and bisphosphates were changed, with opposite effects on the morphology of storage
and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover,
multiple sac knockout mutants had an increased number of smaller storage and lytic
vacuoles, whereas extralarge vacuoles were observed in the overexpression lines,
correlating with various growth and developmental defects. The fragmented vacuolar
phenotype of sac mutants could be mimicked by treating wild-type seedlings with
Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology.
Taken together, these results provide evidence that PPIs, together with their
metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar
morphology and function in plants.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
citation:
ama: Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in
Arabidopsis thaliana. 2014.
apa: Marhavá, P. (2014). Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana. Institute of Science and Technology Austria.
chicago: Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.
ieee: P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.
ista: Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana. Institute of Science and Technology Austria.
mla: Marhavá, Petra. Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2014.
short: P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.
date_created: 2018-12-11T11:51:49Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2023-09-07T11:39:38Z
day: '01'
degree_awarded: PhD
department:
- _id: JiFr
language:
- iso: eng
month: '12'
oa_version: None
page: '90'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5805'
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis
thaliana
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '1403'
abstract:
- lang: eng
text: A variety of developmental and disease related processes depend on epithelial
cell sheet spreading. In order to gain insight into the biophysical mechanism(s)
underlying the tissue morphogenesis we studied the spreading of an epithelium
during the early development of the zebrafish embryo. In zebrafish epiboly the
enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk
cell to completely engulf it at the end of gastrulation. Previous studies have
proposed that an actomyosin ring forming within the yolk syncytial layer (YSL)
acts as purse string that through constriction along its circumference pulls on
the margin of the EVL. Direct biophysical evidence for this hypothesis has however
been missing. The aim of the thesis was to understand how the actomyosin ring
may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate
the spreading of the epithelium. Using laser ablation to measure cortical tension
within the actomyosin ring we found an anisotropic tension distribution, which
was highest along the circumference of the ring. However the low degree of anisotropy
was incompatible with the actomyosin ring functioning as a purse string only.
Additionally, we observed retrograde cortical flow from vegetal parts of the ring
into the EVL margin. Interpreting the experimental data using a theoretical distribution
that models the tissues as active viscous gels led us to proposen that the actomyosin
ring has a twofold contribution to EVL epiboly. It not only acts as a purse string
through constriction along its circumference, but in addition constriction along
the width of the ring generates pulling forces through friction-resisted cortical
flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly
proceeded normally indicating that the flow-friction mechanism is sufficient to
drive the process. Aiming to understand what cellular mechanism(s) may facilitate
the spreading of the epithelium we found that tension-oriented EVL cell divisions
limit tissue anisotropy by releasing tension along the division axis and promote
epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions
in which oriented-cell division is impaired or the epithelium is mechanically
challenged. Taken together our study of EVL epiboly suggests a novel mechanism
of force generation for actomyosin rings through friction-resisted cortical flow
and highlights the importance of tension-oriented cell divisions in epithelial
morphogenesis.
acknowledged_ssus:
- _id: SSU
alternative_title:
- IST Austria Thesis
author:
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
citation:
ama: Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014.
apa: Behrndt, M. (2014). Forces driving epithelial spreading in zebrafish epiboly.
IST Austria.
chicago: Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.”
IST Austria, 2014.
ieee: M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST
Austria, 2014.
ista: Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly.
IST Austria.
mla: Behrndt, Martin. Forces Driving Epithelial Spreading in Zebrafish Epiboly.
IST Austria, 2014.
short: M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST
Austria, 2014.
date_created: 2018-12-11T11:51:49Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T12:16:58Z
day: '01'
department:
- _id: CaHe
language:
- iso: eng
month: '08'
oa_version: None
page: '91'
publication_status: published
publisher: IST Austria
publist_id: '5804'
related_material:
record:
- id: '2282'
relation: part_of_dissertation
status: public
- id: '2950'
relation: part_of_dissertation
status: public
- id: '3373'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: Forces driving epithelial spreading in zebrafish epiboly
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1405'
abstract:
- lang: eng
text: "Motivated by the analysis of highly dynamic message-passing systems, i.e.
unbounded thread creation, mobility, etc. we present a framework for the analysis
of depth-bounded systems. Depth-bounded systems are one of the most expressive
known fragment of the π-calculus for which interesting verification problems are
still decidable. Even though they are infinite state systems depth-bounded systems
are well-structured, thus can be analyzed algorithmically. We give an interpretation
of depth-bounded systems as graph-rewriting systems. This gives more flexibility
and ease of use to apply depth-bounded systems to other type of systems like shared
memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for
depth-bounded systems, a prerequisite for the effective representation of downward-closed
sets. Downward-closed sets are needed by forward saturation-based algorithms to
represent potentially infinite sets of states. Then, we present an abstract interpretation
framework to compute the covering set of well-structured transition systems. Because,
in general, the covering set is not computable, our abstraction over-approximates
the actual covering set. Our abstraction captures the essence of acceleration
based-algorithms while giving up enough precision to ensure convergence. We have
implemented the analysis in the PICASSO tool and show that it is accurate in practice.
Finally, we build some further analyses like termination using the covering set
as starting point."
acknowledgement: "This work was supported in part by the Austrian Science Fund NFN
RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative
Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger
and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of
Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal
Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint
work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS
2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this
part is mostly related to the implementation. The theory required to understand
the method and its implementation is quickly recalled to make the thesis self-contained,
but should not be considered as a contribution. For the details of the methods,
we refer the reader to the orig- inal publication [13] and the corresponding technical
report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar,
and Thomas Wies. I also would like to thank the people who supported over the past
4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on
projects I was interested in. My collaborators, especially Thomas Wies with whom
I worked since the beginning. The members of my thesis committee, Viktor Kun- cak
and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny,
Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created
an enjoyable environment. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Zufferey D. Analysis of dynamic message passing programs. 2013. doi:10.15479/at:ista:1405
apa: Zufferey, D. (2013). Analysis of dynamic message passing programs. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:1405
chicago: Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute
of Science and Technology Austria, 2013. https://doi.org/10.15479/at:ista:1405.
ieee: D. Zufferey, “Analysis of dynamic message passing programs,” Institute of
Science and Technology Austria, 2013.
ista: Zufferey D. 2013. Analysis of dynamic message passing programs. Institute
of Science and Technology Austria.
mla: Zufferey, Damien. Analysis of Dynamic Message Passing Programs. Institute
of Science and Technology Austria, 2013, doi:10.15479/at:ista:1405.
short: D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science
and Technology Austria, 2013.
date_created: 2018-12-11T11:51:50Z
date_published: 2013-09-05T00:00:00Z
date_updated: 2023-09-07T11:36:37Z
day: '05'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
- _id: GradSch
doi: 10.15479/at:ista:1405
ec_funded: 1
file:
- access_level: open_access
checksum: ed2d7b52933d134e8dc69d569baa284e
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:28:36Z
date_updated: 2021-02-22T11:28:36Z
file_id: '9176'
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success: 1
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checksum: cecc4c4b14225bee973d32e3dba91a55
content_type: application/pdf
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file_size: 1378313
relation: main_file
file_date_updated: 2021-11-17T13:47:58Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- url: http://dzufferey.github.io/files/2013_thesis.pdf
month: '09'
oa: 1
oa_version: Published Version
page: '134'
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5802'
related_material:
record:
- id: '2847'
relation: part_of_dissertation
status: public
- id: '3251'
relation: part_of_dissertation
status: public
- id: '4361'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Analysis of dynamic message passing programs
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2013'
...
---
_id: '1406'
abstract:
- lang: eng
text: Epithelial spreading is a critical part of various developmental and wound
repair processes. Here we use zebrafish epiboly as a model system to study the
cellular and molecular mechanisms underlying the spreading of epithelial sheets.
During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium,
spreads over the embryo to eventually cover the entire yolk cell by the end of
gastrulation. The EVL leading edge is anchored through tight junctions to the
yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile
actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent
view in the field was that the contractile ring exerts a pulling force on the
EVL margin, which pulls the EVL towards the vegetal pole. However, how this force
is generated and how it affects EVL morphology still remains elusive. Moreover,
the cellular mechanisms mediating the increase in EVL surface area, while maintaining
tissue integrity and function are still unclear. Here we show that the YSL actomyosin
ring pulls on the EVL margin by two distinct force-generating mechanisms. One
mechanism is based on contraction of the ring around its circumference, as previously
proposed. The second mechanism is based on actomyosin retrogade flows, generating
force through resistance against the substrate. The latter can function at any
epiboly stage even in situations where the contraction-based mechanism is unproductive.
Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic
tension, which guides the orientation of EVL cell division along the main axis
(animal-vegetal) of tension. The influence of tension in cell division orientation
involves cell elongation and requires myosin-2 activity for proper spindle alignment.
Strikingly, we reveal that tension-oriented cell divisions release anisotropic
tension within the EVL and that in the absence of such divisions, EVL cells undergo
ectopic fusions. We conclude that forces applied to the EVL by the action of the
YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell
divisions, which in turn limit tissue tension increase thereby facilitating tissue
spreading.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
citation:
ama: 'Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions
limit anisotropic tissue tension in epithelial spreading. 2013.'
apa: 'Campinho, P. (2013). Mechanics of zebrafish epiboly: Tension-oriented cell
divisions limit anisotropic tissue tension in epithelial spreading. Institute
of Science and Technology Austria.'
chicago: 'Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell
Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute
of Science and Technology Austria, 2013.'
ieee: 'P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions
limit anisotropic tissue tension in epithelial spreading,” Institute of Science
and Technology Austria, 2013.'
ista: 'Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions
limit anisotropic tissue tension in epithelial spreading. Institute of Science
and Technology Austria.'
mla: 'Campinho, Pedro. Mechanics of Zebrafish Epiboly: Tension-Oriented Cell
Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading. Institute
of Science and Technology Austria, 2013.'
short: 'P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions
Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science
and Technology Austria, 2013.'
date_created: 2018-12-11T11:51:50Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2023-09-07T11:36:07Z
day: '01'
degree_awarded: PhD
department:
- _id: CaHe
language:
- iso: eng
month: '10'
oa_version: None
page: '123'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5801'
status: public
supervisor:
- 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
title: 'Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic
tissue tension in epithelial spreading'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2013'
...
---
_id: '2964'
abstract:
- lang: eng
text: 'CA3 pyramidal neurons are important for memory formation and pattern completion
in the hippocampal network. These neurons receive multiple excitatory inputs from
numerous sources. Therefore, the rules of spatiotemporal integration of multiple
synaptic inputs and propagation of action potentials are important to understand
how CA3 neurons contribute to higher brain functions at cellular level. By using
confocally targeted patch-clamp recording techniques, we investigated the biophysical
properties of rat CA3 pyramidal neuron dendrites. We found two distinct dendritic
domains critical for action potential initiation and propagation: In the proximal
domain, action potentials initiated in the axon backpropagate actively with large
amplitude and fast time course. In the distal domain, Na+-channel mediated dendritic
spikes are efficiently evoked by local dendritic depolarization or waveforms mimicking
synaptic events. These findings can be explained by a high Na+-to-K+ conductance
density ratio of CA3 pyramidal neuron dendrites. The results challenge the prevailing
view that proximal mossy fiber inputs activate CA3 pyramidal neurons more efficiently
than distal perforant inputs by showing that the distal synapses trigger a different
form of activity represented by dendritic spikes. The high probability of dendritic
spike initiation in the distal area may enhance the computational power of CA3
pyramidal neurons in the hippocampal network. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sooyun
full_name: Kim, Sooyun
id: 394AB1C8-F248-11E8-B48F-1D18A9856A87
last_name: Kim
citation:
ama: Kim S. Active properties of hippocampal CA3 pyramidal neuron dendrites. 2012.
apa: Kim, S. (2012). Active properties of hippocampal CA3 pyramidal neuron dendrites.
Institute of Science and Technology Austria.
chicago: Kim, Sooyun. “Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites.”
Institute of Science and Technology Austria, 2012.
ieee: S. Kim, “Active properties of hippocampal CA3 pyramidal neuron dendrites,”
Institute of Science and Technology Austria, 2012.
ista: Kim S. 2012. Active properties of hippocampal CA3 pyramidal neuron dendrites.
Institute of Science and Technology Austria.
mla: Kim, Sooyun. Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites.
Institute of Science and Technology Austria, 2012.
short: S. Kim, Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites,
Institute of Science and Technology Austria, 2012.
date_created: 2018-12-11T12:00:35Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2023-09-07T11:43:51Z
day: '01'
degree_awarded: PhD
department:
- _id: PeJo
- _id: GradSch
language:
- iso: eng
month: '06'
oa_version: None
page: '65'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '3755'
related_material:
record:
- id: '3258'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Active properties of hippocampal CA3 pyramidal neuron dendrites
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2012'
...
---
_id: '3275'
abstract:
- lang: eng
text: 'Chemokines organize immune cell trafficking by inducing either directed (tactic)
or random (kinetic) migration and by activating integrins in order to support
surface adhesion (haptic). Beyond that the same chemokines can establish clearly
defined functional areas in secondary lymphoid organs. Until now it is unclear
how chemokines can fulfill such diverse functions. One decisive prerequisite to
explain these capacities is to know how chemokines are presented in tissue. In
theory chemokines could occur either soluble or immobilized, and could be distributed
either homogenously or as a concentration gradient. To dissect if and how the
presenting mode of chemokines influences immune cells, I tested the response of
dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen
presenting cells that reside in the periphery and migrate into draining lymph
nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs
are guided to and within the LN by the chemokine receptor CCR7, which has two
ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic
reticular cells in the LN, but differ in their ability to bind to heparan sulfate
residues. CCL21 has a highly charged C-terminal extension, which mediates binding
to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes
as a soluble molecule. This study shows that surface-bound CCL21 causes random,
haptokinetic DC motility, which is confined to the chemokine coated area by insideout
activation of β2 integrins that mediate cell binding to the surface. CCL19 on
the other hand forms concentration gradients which trigger directional, chemotactic
movement, but no surface adhesion. In addition DCs can actively manipulate this
system by recruiting and activating serine proteases on their surfaces, which
create - by proteolytically removing the adhesive C-terminus - a solubilized variant
of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration
gradient DCs establish a positive feedback loop to recruit further DCs from the
periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients
as well as immobilized haptokinetic fields at the same time and integrate these
signals. The result is chemotactically biased haptokinesis - directional migration
confined to a chemokine coated track or area - which could explain the dynamic
but spatially tightly controlled swarming leukocyte locomotion patterns that have
been observed in lymphatic organs by intravital microscopists. The finding that
DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces
coated with immobilized cues raises the question how these cells transmit intracellular
forces to the environment, especially in the non-adherent migration mode. In order
to migrate, cells have to generate and transmit force to the extracellular substrate.
Force transmission is the prerequisite to procure an expansion of the leading
edge and a forward motion of the whole cell body. In the current conceptions actin
polymerization at the leading edge is coupled to extracellular ligands via the
integrin family of transmembrane receptors, which allows the transmission of intracellular
force. Against the paradigm of force transmission during migration, leukocytes,
like DCs, are able to migrate in threedimensional environments without using integrin
transmembrane receptors (Lämmermann et al., 2008). This reflects the biological
function of leukocytes, as they can invade almost all tissues, whereby their migration
has to be independent from the extracellular environment. How the cells can achieve
this is unclear. For this study I examined DC migration in a defined threedimensional
environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result
was that chemotactic DCs can switch between integrin-dependent and integrin- independent
locomotion and can thereby adapt to the adhesive properties of their environment.
If the cells are able to couple their actin cytoskeleton to the substrate, actin
polymerization is entirely converted into protrusion. Without coupling the actin
cortex undergoes slippage and retrograde actin flow can be observed. But retrograde
actin flow can be completely compensated by higher actin polymerization rate keeping
the migration velocity and the shape of the cells unaltered. Mesenchymal cells
like fibroblast cannot balance the loss of adhesive interaction, cannot protrude
into open space and, therefore, strictly depend on integrinmediated force coupling.
This leukocyte specific phenomenon of “adaptive force transmission” endows these
cells with the unique ability to transit and invade almost every type of tissue. '
acknowledgement: "I would like to express my sincere gratitude to the following people
who made with their continuous support and encouragement this thesis possible: First,
I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring,
especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and
the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant
support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf.
Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my
thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz,
the Recombinant Protein Production core facility and the animal care takers for
providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler,
Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy
labmates for their help, a lot of discussions and to make the Sixt lab to a convenient
place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele
Weber and Alexander Eichner All members of the Department of Molecular Medicine
for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael
Ruppert for their friendship, nice chats and their uncensored point of view. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Schumann, Kathrin
id: F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F
last_name: Schumann
citation:
ama: Schumann K. The role of chemotactic gradients in dendritic cell migration.
2011.
apa: Schumann, K. (2011). The role of chemotactic gradients in dendritic cell
migration. Institute of Science and Technology Austria.
chicago: Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell
Migration.” Institute of Science and Technology Austria, 2011.
ieee: K. Schumann, “The role of chemotactic gradients in dendritic cell migration,”
Institute of Science and Technology Austria, 2011.
ista: Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration.
Institute of Science and Technology Austria.
mla: Schumann, Kathrin. The Role of Chemotactic Gradients in Dendritic Cell Migration.
Institute of Science and Technology Austria, 2011.
short: K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration,
Institute of Science and Technology Austria, 2011.
date_created: 2018-12-11T12:02:24Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2023-09-07T11:31:48Z
day: '01'
ddc:
- '570'
- '579'
degree_awarded: PhD
department:
- _id: MiSi
file:
- access_level: closed
checksum: e69eee6252660f0b694a2ea8923ddc72
content_type: application/pdf
creator: dernst
date_created: 2019-03-26T08:12:21Z
date_updated: 2020-07-14T12:46:06Z
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title: The role of chemotactic gradients in dendritic cell migration
type: dissertation
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year: '2011'
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---
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ama: Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors.
2011.
apa: Maître, J.-L. (2011). Mechanics of adhesion and de‐adhesion in zebrafish
germ layer progenitors. Institute of Science and Technology Austria.
chicago: Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish
Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.
ieee: J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer
progenitors,” Institute of Science and Technology Austria, 2011.
ista: Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ
layer progenitors. Institute of Science and Technology Austria.
mla: Maître, Jean-Léon. Mechanics of Adhesion and De‐adhesion in Zebrafish Germ
Layer Progenitors. Institute of Science and Technology Austria, 2011.
short: J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer
Progenitors, Institute of Science and Technology Austria, 2011.
date_created: 2018-12-11T12:02:23Z
date_published: 2011-12-12T00:00:00Z
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title: Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2011'
...
---
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citation:
ama: Pflicke H. Dendritic cell migration across basement membranes in the skin.
2010.
apa: Pflicke, H. (2010). Dendritic cell migration across basement membranes
in the skin. Institute of Science and Technology Austria.
chicago: Pflicke, Holger. “ Dendritic Cell Migration across Basement Membranes
in the Skin.” Institute of Science and Technology Austria, 2010.
ieee: H. Pflicke, “ Dendritic cell migration across basement membranes in the skin,”
Institute of Science and Technology Austria, 2010.
ista: Pflicke H. 2010. Dendritic cell migration across basement membranes in the
skin. Institute of Science and Technology Austria.
mla: Pflicke, Holger. Dendritic Cell Migration across Basement Membranes in
the Skin. Institute of Science and Technology Austria, 2010.
short: H. Pflicke, Dendritic Cell Migration across Basement Membranes in the Skin,
Institute of Science and Technology Austria, 2010.
date_created: 2018-12-11T12:06:08Z
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full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: "\uFEFF\uFEFFDendritic cell migration across basement membranes in the skin"
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2010'
...